test_geo
Testing Bio.Geo on GSE16.txt


GEO Type: SAMPLE
GEO Id: GSM804
Sample_author: Antoine,M,Snijders

Sample_author: Norma,,Nowak

Sample_author: Richard,,Segraves

Sample_author: Stephanie,,Blackwood

Sample_author: Nils,,Brown

Sample_author: Jeffery,,Conroy

Sample_author: Greg,,Hamilton

Sample_author: Anna,K,Hindle

Sample_author: Bing,,Huey

Sample_author: Karen,,Kimura

Sample_author: Sindy,,Law

Sample_author: Ken,,Myambo

Sample_author: Joel,,Palmer

Sample_author: Bauke,,Ylstra

Sample_author: Jingzhu,P,Yue

Sample_author: Joe,W,Gray

Sample_author: Ajay,N,Jain

Sample_author: Daniel,,Pinkel

Sample_author: Donna,G,Albertson

Sample_description: Coriell Cell Repositories cell line <a h
ref="http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM05296">GM05296</a>.

Sample_description: Fibroblast cell line derived from a 1 mo
nth old female with multiple congenital malformations, dysmorphic features, intr
auterine growth retardation, heart murmur, cleft palate, equinovarus deformity, 
microcephaly, coloboma of right iris, clinodactyly, reduced RBC catalase activit
y, and 1 copy of catalase gene.

Sample_description: Chromosome abnormalities are present.

Sample_description: Karyotype is 46,XX,-11,+der(11)inv ins(1
1;10)(11pter> 11p13::10q21>10q24::11p13>11qter)mat

Sample_organism: Homo sapiens

Sample_platform_id: GPL28

Sample_pubmed_id: 11687795

Sample_series_id: GSE16

Sample_status: Public on Feb 12 2002

Sample_submission_date: Jan 17 2002

Sample_submitter_city: San Francisco,CA,94143,USA

Sample_submitter_department: Comprehensive Cancer Center

Sample_submitter_email: albertson@cc.ucsf.edu

Sample_submitter_institute: University of California San Francisco

Sample_submitter_name: Donna,G,Albertson

Sample_submitter_phone: 415 502-8463

Sample_target_source1: Cell line GM05296

Sample_target_source2: normal male reference genomic DNA

Sample_title: CGH_Albertson_GM05296-001218

Sample_type: dual channel genomic

Column Header Definitions
    ID_REF: Unique row identifier, genome position o
    rder

    LINEAR_RATIO: Mean of replicate Cy3/Cy5 ratios

    LOG2STDDEV: Standard deviation of VALUE

    NO_REPLICATES: Number of replicate spot measurements

    VALUE: aka LOG2RATIO, mean of log base 2 of LIN
    EAR_RATIO

0: ID_REF	VALUE	LINEAR_RATIO	LOG2STDDEV	NO_REPLICATES	
1: 1		1.047765	0.011853	3	
2: 2				0	
3: 3	0.008824	1.006135	0.00143	3	
4: 4	-0.000894	0.99938	0.001454	3	
5: 5	0.075875	1.054	0.003077	3	
6: 6	0.017303	1.012066	0.005876	2	
7: 7	-0.006766	0.995321	0.013881	3	
8: 8	0.020755	1.014491	0.005506	3	
9: 9	-0.094938	0.936313	0.012662	3	
10: 10	-0.054527	0.96291	0.01073	3	
11: 11	-0.025057	0.982782	0.003855	3	
12: 12				0	
13: 13	0.108454	1.078072	0.005196	3	
14: 14	0.078633	1.056017	0.009165	3	
15: 15	0.098571	1.070712	0.007834	3	
16: 16	0.044048	1.031003	0.013651	3	
17: 17	0.018039	1.012582	0.005471	3	
18: 18	-0.088807	0.9403	0.010571	3	
19: 19	0.016349	1.011397	0.007113	3	
20: 20	0.030977	1.021704	0.016798	3	



Testing Bio.Geo on GSM645.txt


GEO Type: SAMPLE
GEO Id: GSM645
Sample_author: Reinhard,,Hoffmann

Sample_author: Thomas,,Seidl

Sample_author: Ton,,Rolink

Sample_author: Fritz,,Melchers

Sample_description: B220+CD25+sIg- Large Pre BII cells sorte
d out of mouse bone marrow, sort no. 8

Sample_organism: Mus musculus

Sample_platform_id: GPL22

Sample_series_id: GSE13

Sample_status: Public on Dec 17 2001

Sample_submission_date: Nov 27 2001

Sample_submitter_address: Pettenkoferstr. 9a

Sample_submitter_city: Munich,80336,Germany

Sample_submitter_department: Bacteriology

Sample_submitter_email: r_hoffmann@m3401.mpk.med.uni-muenchen.de

Sample_submitter_institute: Max von Pettenkofer Institut

Sample_submitter_name: Reinhard,,Hoffmann

Sample_submitter_phone: +49-89-5160-5424

Sample_target_source: Large Pre-BII cells

Sample_title: Large Pre-BII cells 8b

Sample_type: single channel

Column Header Definitions
    ABS_CALL: Whether a probe set is present, marginal
    , or absent; see Affymetrix Literature

    Experiment Name: Experiment Name

    ID_REF: Affymetrix Probe Set Identifier

    Log Avg: 

    MM Excess: Number of probe peirs where MM/PM exceed
    s 1/ratio limit (10 by default)

    NEGATIVE: number of negative probe pairs

    PAIRS: number of probe set specific probe pairs
     on the array

    PAIRS_IN_AVG: Trimmed probe pair set

    PAIRS_USED: 

    PM Excess: number of probe pairs  where PM/MM excee
    ds the ratio limit (10 by default)

    POS/NEG: Positive/Negative

    POSITIVE: number of poisitive probe pairs

    POS_FRACTION: Positive/Pairs Used

    VALUE: Average Difference Intensity

0: ID_REF	Experiment Name	POSITIVE	NEGATIVE	PAIRS	PAIRS_USED	PAIRS_IN_AVG	POS_FRACTION	Log Avg	PM Excess	MM Excess	POS/NEG	VALUE	ABS_CALL	
1: IL2_at	RHMu8LarB	4	4	19	19	19	0.21	-0.58	0	0	1.0	-78	A	
2: IL10_at	RHMu8LarB	7	4	20	20	18	0.35	1.87	1	0	1.8	161	A	
3: GMCSF_at	RHMu8LarB	4	4	20	20	19	0.20	0.39	0	0	1.0	-11	A	
4: TNFRII_at	RHMu8LarB	2	2	20	20	18	0.10	0.48	0	0	1.0	52	A	
5: MIP1-B_at	RHMu8LarB	6	4	20	20	19	0.30	0.43	0	0	1.5	373	A	
6: IL4_at	RHMu8LarB	3	3	20	20	19	0.15	0.29	0	0	1.0	27	A	
7: IL12_P40_at	RHMu8LarB	3	5	20	20	19	0.15	-0.22	0	0	0.6	-163	A	
8: TNFa_at	RHMu8LarB	3	4	20	20	20	0.15	-0.57	1	0	0.8	-95	A	
9: TCRa_at	RHMu8LarB	1	4	20	20	19	0.05	-0.50	0	0	0.3	-186	A	
10: AFFX-BioB-5_at	RHMu8LarB	0	1	20	20	19	0.00	0.35	0	0	0.0	120	A	
11: AFFX-BioB-M_at	RHMu8LarB	0	1	20	20	19	0.00	0.02	0	0	0.0	-13	A	
12: AFFX-BioB-3_at	RHMu8LarB	2	0	20	20	19	0.10	0.38	0	0	Undef	136	A	
13: AFFX-BioC-5_at	RHMu8LarB	9	0	20	20	20	0.45	1.33	0	0	Undef	606	P	
14: AFFX-BioC-3_at	RHMu8LarB	2	0	20	20	19	0.10	0.64	0	0	Undef	257	A	
15: AFFX-BioDn-5_at	RHMu8LarB	8	0	20	20	20	0.40	1.23	0	0	Undef	380	P	
16: AFFX-BioDn-3_at	RHMu8LarB	16	0	20	20	19	0.80	2.79	0	0	Undef	2764	P	
17: AFFX-CreX-5_at	RHMu8LarB	19	0	20	20	19	0.95	5.65	0	0	Undef	4391	P	
18: AFFX-CreX-3_at	RHMu8LarB	19	0	20	20	20	0.95	6.42	2	0	Undef	10787	P	
19: AFFX-BioB-5_st	RHMu8LarB	5	3	20	20	19	0.25	0.48	0	0	1.7	80	A	
20: AFFX-BioB-M_st	RHMu8LarB	2	3	20	20	17	0.10	0.16	0	0	0.7	24	A	



Testing Bio.Geo on GSM691.txt


GEO Type: SAMPLE
GEO Id: GSM691
Sample_anchor: NlaIII

Sample_author: Jeffrey,,Marks

Sample_author: Gregory,J,Riggins

Sample_author: Robert,L,Strausberg

Sample_description: This library represents a Cancer Genome 
Anatomy Project library, which was either produced through CGAP funding, or dona
ted to CGAP.

Sample_description: The Cancer Genome Anatomy Project (CGAP:
 http://cgap.nci.nih.gov) is an interdisciplinary program established and admini
stered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generat
e the information and technological tools needed to decipher the molecular anato
my of the cancer cell.

Sample_description: Library constructed by Riggins laborator
y Tissue supplied by Jeffrey Marks, Ph.D.

Sample_description: Organ: Breast

Sample_description: Tissue_type: normal epithelial organoids

Sample_description: Library treatment: non-normalized

Sample_description: Tissue description: Breast, Isolated nor
mal epithelial organoids. Derived from a reduction mammoplasty.

Sample_description: Tissue supplier: Jeffrey Marks, Ph.D.

Sample_description: Sample type: Bulk

Sample_description: Producer: Riggins Laboratory

Sample_description: Clones generated to date: 768

Sample_description: Sequences generated to date: 572

Sample_organism: Homo sapiens

Sample_platform_id: GPL4

Sample_series_id: GSE14

Sample_status: Public on Nov 28 2001

Sample_submission_date: Nov 28 2001

Sample_submitter_city: Bethesda,MD,20892,USA

Sample_submitter_department: Cancer Genome Anatomy Project

Sample_submitter_email: cgapbs-r@mail.nih.gov

Sample_submitter_institute: National Cancer Institute

Sample_submitter_name: Robert,L,Strausberg

Sample_submitter_phone: 301-496-1550

Sample_submitter_web_link: http://cgap.nci.nih.gov/

Sample_tag_count: 7165

Sample_target_source: Breast, isolated normal epithelial organ
oids

Sample_title: SAGE_Duke_40N

Sample_type: sage

Sample_web_link: http://cgap.nci.nih.gov

Column Header Definitions
    COUNT: Absolute tag count

    TAG: Ten base SAGE tag, LINK_PRE:"http://www.
    ncbi.nlm.nih.gov/SAGE/SAGEtag.cgi?tag="

    TPM: Tags per million, or (1000000*COUNT)/(To
    tal tags)

0: TAG	COUNT	TPM	
1: TTGGGGTTTC	202	28192.6	
2: TAGGTTGTCT	129	18004.2	
3: GAGGGAGTTT	109	15212.8	
4: TGCACGTTTT	92	12840.2	
5: CTGGGTTAAT	83	11584.1	
6: GTTGTGGTTA	82	11444.5	
7: GATCCCAACT	63	8792.74	
8: TGCAGTCACT	59	8234.47	
9: GGATTTGGCC	58	8094.91	
10: GGGCTGGGGT	56	7815.77	
11: ATAATTCTTT	44	6140.96	
12: CTTCCTTGCC	42	5861.83	
13: TTGGTCCTCT	40	5582.69	
14: GGCAAGCCCC	36	5024.42	
15: AACTAAAAAA	34	4745.29	
16: AGGGCTTCCA	34	4745.29	
17: AGGCTACGGA	33	4605.72	
18: GTGAAACCCC	32	4466.15	
19: AACTAACAAA	31	4326.59	
20: GAAAAATGGT	30	4187.02	



Testing Bio.Geo on GSM700.txt


GEO Type: SAMPLE
GEO Id: GSM700
Sample_anchor: NlaIII

Sample_author: Gregory,J,Riggins

Sample_author: Robert,L,Strausberg

Sample_description: This library represents a Cancer Genome 
Anatomy Project library, which was either produced through CGAP funding, or dona
ted to CGAP.

Sample_description: The Cancer Genome Anatomy Project (CGAP:
 http://cgap.nci.nih.gov) is an interdisciplinary program established and admini
stered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generat
e the information and technological tools needed to decipher the molecular anato
my of the cancer cell.

Sample_description: Cell line grown under 1.5% oxygen condit
ions for 24 hours prior to harvesting in zinc option media with 10% RBS and harv
ested at passage 102. Library constructed in the laboratory of G. Riggins, M.D.,
 Ph.D. (Duke University).

Sample_description: Organ: brain

Sample_description: Tissue_type: glioblastoma multiforme

Sample_description: Cell_line: H247

Sample_description: Lab host: DH10B

Sample_description: Vector: pZErO-1

Sample_description: Vector type: plasmid

Sample_description: R. Site 1: Sph1

Sample_description: R. Site 2: Sph1

Sample_description: Library treatment: non-normalized

Sample_description: Tissue description: Brain, Duke glioblas
toma multiforme cell line, H247, grown under 1.5% oxygen conditions  for 24 hour
s prior to harvesting.

Sample_description: Tissue

Sample_organism: Homo sapiens

Sample_platform_id: GPL4

Sample_series_id: GSE14

Sample_status: Public on Nov 28 2001

Sample_submission_date: Nov 28 2001

Sample_submitter_city: Bethesda,MD,20892,USA

Sample_submitter_department: Cancer Genome Anatomy Project

Sample_submitter_email: cgapbs-r@mail.nih.gov

Sample_submitter_institute: National Cancer Institute

Sample_submitter_name: Robert,L,Strausberg

Sample_submitter_phone: 301-496-1550

Sample_submitter_web_link: http://cgap.nci.nih.gov/

Sample_tag_count: 72031

Sample_target_source: Brain, glioblastoma multiforme, cell-lin
e H247

Sample_title: SAGE_Duke_H247_Hypoxia

Sample_type: sage

Sample_web_link: http://cgap.nci.nih.gov

Column Header Definitions
    COUNT: Absolute tag count

    TAG: Ten base SAGE tag, LINK_PRE:"http://www.
    ncbi.nlm.nih.gov/SAGE/SAGEtag.cgi?tag="

    TPM: Tags per million, or (1000000*COUNT)/(To
    tal tags)

0: TAG	COUNT	TPM	
1: TCCAAATCGA	520	7219.11	
2: TACCATCAAT	434	6025.18	
3: TTGGGGTTTC	389	5400.45	
4: CCCATCGTCC	367	5095.03	
5: GTGAAACCCC	365	5067.26	
6: GGGGAAATCG	357	4956.2	
7: CCTGTAATCC	346	4803.49	
8: TGATTTCACT	334	4636.89	
9: TGTGTTGAGA	315	4373.12	
10: GCCCCCAATA	303	4206.52	
11: CTAAGACTTC	279	3873.33	
12: GCGACCGTCA	276	3831.68	
13: TTGGTCCTCT	276	3831.68	
14: CCTAGCTGGA	268	3720.62	
15: GATGAGGAGA	251	3484.61	
16: ACTTTTTCAA	244	3387.43	
17: CCACTGCACT	223	3095.89	
18: GTGTGTTTGT	223	3095.89	
19: GAAATACAGT	218	3026.47	
20: GCTTTATTTG	218	3026.47	



Testing Bio.Geo on GSM804.txt


GEO Type: SAMPLE
GEO Id: GSM804
Sample_author: Antoine,M,Snijders

Sample_author: Norma,,Nowak

Sample_author: Richard,,Segraves

Sample_author: Stephanie,,Blackwood

Sample_author: Nils,,Brown

Sample_author: Jeffery,,Conroy

Sample_author: Greg,,Hamilton

Sample_author: Anna,K,Hindle

Sample_author: Bing,,Huey

Sample_author: Karen,,Kimura

Sample_author: Sindy,,Law

Sample_author: Ken,,Myambo

Sample_author: Joel,,Palmer

Sample_author: Bauke,,Ylstra

Sample_author: Jingzhu,P,Yue

Sample_author: Joe,W,Gray

Sample_author: Ajay,N,Jain

Sample_author: Daniel,,Pinkel

Sample_author: Donna,G,Albertson

Sample_description: Coriell Cell Repositories cell line <a h
ref="http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM05296">GM05296</a>.

Sample_description: Fibroblast cell line derived from a 1 mo
nth old female with multiple congenital malformations, dysmorphic features, intr
auterine growth retardation, heart murmur, cleft palate, equinovarus deformity, 
microcephaly, coloboma of right iris, clinodactyly, reduced RBC catalase activit
y, and 1 copy of catalase gene.

Sample_description: Chromosome abnormalities are present.

Sample_description: Karyotype is 46,XX,-11,+der(11)inv ins(1
1;10)(11pter> 11p13::10q21>10q24::11p13>11qter)mat

Sample_organism: Homo sapiens

Sample_platform_id: GPL28

Sample_pubmed_id: 11687795

Sample_series_id: GSE16

Sample_status: Public on Feb 12 2002

Sample_submission_date: Jan 17 2002

Sample_submitter_city: San Francisco,CA,94143,USA

Sample_submitter_department: Comprehensive Cancer Center

Sample_submitter_email: albertson@cc.ucsf.edu

Sample_submitter_institute: University of California San Francisco

Sample_submitter_name: Donna,G,Albertson

Sample_submitter_phone: 415 502-8463

Sample_target_source1: Cell line GM05296

Sample_target_source2: normal male reference genomic DNA

Sample_title: CGH_Albertson_GM05296-001218

Sample_type: dual channel genomic

Column Header Definitions
    ID_REF: Unique row identifier, genome position o
    rder

    LINEAR_RATIO: Mean of replicate Cy3/Cy5 ratios

    LOG2STDDEV: Standard deviation of VALUE

    NO_REPLICATES: Number of replicate spot measurements

    VALUE: aka LOG2RATIO, mean of log base 2 of LIN
    EAR_RATIO

0: ID_REF	VALUE	LINEAR_RATIO	LOG2STDDEV	NO_REPLICATES	
1: 1		1.047765	0.011853	3	
2: 2				0	
3: 3	0.008824	1.006135	0.00143	3	
4: 4	-0.000894	0.99938	0.001454	3	
5: 5	0.075875	1.054	0.003077	3	
6: 6	0.017303	1.012066	0.005876	2	
7: 7	-0.006766	0.995321	0.013881	3	
8: 8	0.020755	1.014491	0.005506	3	
9: 9	-0.094938	0.936313	0.012662	3	
10: 10	-0.054527	0.96291	0.01073	3	
11: 11	-0.025057	0.982782	0.003855	3	
12: 12				0	
13: 13	0.108454	1.078072	0.005196	3	
14: 14	0.078633	1.056017	0.009165	3	
15: 15	0.098571	1.070712	0.007834	3	
16: 16	0.044048	1.031003	0.013651	3	
17: 17	0.018039	1.012582	0.005471	3	
18: 18	-0.088807	0.9403	0.010571	3	
19: 19	0.016349	1.011397	0.007113	3	
20: 20	0.030977	1.021704	0.016798	3	



Testing Bio.Geo on soft_ex_affy.txt


GEO Type: SAMPLE
GEO Id: Drosophila_T0-1
Sample_characteristics_ch1: Genotype: yellow white and Oregon R pare
nts

Sample_characteristics_ch1: Age: embryos younger than nuclear cycle 
9, i.e. before pole cells budding

Sample_data_processing: The data were analyzed with Microarray S
uite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global
 scaling as normalization method. The trimmed mean target intensity of each arra
y was arbitrarily set to 100.

Sample_description: Gene expression data from embryos younge
r than nuclear cycle 9, i.e. before zygotic genome activation.

Sample_extract_protocol_ch1: Trizol extraction of total RNA was perfo
rmed according to the manufacturer's instructions.

Sample_growth_protocol_ch1: 30 min egg collections of OreR and yw fl
ies at 25C were aged at room temperature (RT) according to the different tempora
l classes T0-T4.

Sample_hyb_protocol: Following fragmentation, 10 microg of cR
NA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChi
ps were washed and stained in the Affymetrix Fluidics Station 400.

Sample_label_ch1: biotin

Sample_label_protocol_ch1: Biotinylated cRNA were prepared accordin
g to the standard Affymetrix protocol from 6 microg total RNA (Expression Analys
is Technical Manual, 2001, Affymetrix).

Sample_molecule_ch1: total RNA

Sample_organism_ch1: Drosophila melanogaster

Sample_platform_id: GPL72

Sample_scan_protocol: GeneChips were scanned using the Hewlett
-Packard GeneArray Scanner G2500A.

Sample_source_name_ch1: Drosophila embryos before nuclear cycle 
9 (maternal transcripts)

Sample_supplementary_file: Drosophila_T0-1.CEL

Sample_table_begin: 

Sample_table_end: 

Sample_title: embryo at T0, biological rep1

Sample_treatment_protocol_ch1: Embryos were dechorionated with 50% blea
ch, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of t
he appropriate stage were manually selected under the dissecting scope. Selected
 embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% tri
ton-X100 and placed on ice in the Trizol solution (GibcoBRL).

Column Header Definitions
    ABS_CALL: the call in an absolute analysis that in
    dicates if the transcript was present (P), absent (A), marginal (M), or no call 
    (NC)

    DETECTION P-VALUE: 'detection p-value', p-value that indica
    tes the significance level of the detection call

    ID_REF: 

    VALUE: MAS5-calculated Signal intensity

0: ID_REF	VALUE	ABS_CALL	DETECTION P-VALUE	
1: 141200_at	36.6	A	0.818657	
2: 141201_at	41.5	A	0.703191	
3: 141202_at	607.3	P	0.000944	
4: 141203_at	1509.1	P	0.000762	
5: 141204_at	837.3	P	0.000613	
6: 141205_at	363.2	P	0.003815	
7: 141206_at	1193.6	P	0.000491	
8: 141207_at	346.6	P	0.001165	
9: 141208_at	257.8	P	0.006575	
10: 141209_at	337.1	P	0.002607	
11: 141210_at	48	A	0.150145	
12: 141211_at	130.7	P	0.005504	
13: 141212_at	1454.3	P	0.000491	
14: 141213_at	21.2	A	0.635055	
15: 142121_at	133.7	A	0.889551	
16: 142122_at	275.3	A	0.611218	
17: 142123_at	307.6	A	0.611218	
18: 142124_at	132.6	A	0.437646	
19: 142125_at	195.8	A	0.110449	
20: 142126_at	174.1	A	0.681117	
...
21: 142127_at	316.3	A	0.65838	

GEO Type: SAMPLE
GEO Id: Drosophila_T0-2
Sample_characteristics_ch1: Genotype: yellow white and Oregon R pare
nts

Sample_characteristics_ch1: Age: embryos younger than nuclear cycle 
9, i.e. before pole cells budding

Sample_data_processing: The data were analyzed with Microarray S
uite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global
 scaling as normalization method. The trimmed mean target intensity of each arra
y was arbitrarily set to 100.

Sample_description: Gene expression data from embryos younge
r than nuclear cycle 9, i.e. before zygotic genome activation.

Sample_extract_protocol_ch1: Trizol extraction of total RNA was perfo
rmed according to the manufacturer's instructions.

Sample_growth_protocol_ch1: 30 min egg collections of OreR and yw fl
ies at 25C were aged at room temperature (RT) according to the different tempora
l classes T0-T4.

Sample_hyb_protocol: Following fragmentation, 10 microg of cR
NA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChi
ps were washed and stained in the Affymetrix Fluidics Station 400.

Sample_label_ch1: biotin

Sample_label_protocol_ch1: Biotinylated cRNA were prepared accordin
g to the standard Affymetrix protocol from 6 microg total RNA (Expression Analys
is Technical Manual, 2001, Affymetrix).

Sample_molecule_ch1: total RNA

Sample_organism_ch1: Drosophila melanogaster

Sample_platform_id: GPL72

Sample_scan_protocol: GeneChips were scanned using the Hewlett
-Packard GeneArray Scanner G2500A.

Sample_source_name_ch1: Drosophila embryos before nuclear cycle 
9 (maternal transcripts)

Sample_supplementary_file: Drosophila_T0-2.CEL

Sample_table_begin: 

Sample_table_end: 

Sample_title: embryo at T0, biological rep2

Sample_treatment_protocol_ch1: Embryos were dechorionated with 50% blea
ch, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of t
he appropriate stage were manually selected under the dissecting scope. Selected
 embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% tri
ton-X100 and placed on ice in the Trizol solution (GibcoBRL).

Column Header Definitions
    ABS_CALL: the call in an absolute analysis that in
    dicates if the transcript was present (P), absent (A), marginal (M), or no call 
    (NC)

    DETECTION P-VALUE: 'detection p-value', p-value that indica
    tes the significance level of the detection call

    ID_REF: 

    VALUE: MAS5-calculated Signal intensity

0: ID_REF	VALUE	ABS_CALL	DETECTION P-VALUE	
1: 141200_at	70.3	A	0.216313	
2: 141201_at	38	A	0.635055	
3: 141202_at	831.8	P	0.000613	
4: 141203_at	2215.5	P	0.000944	
5: 141204_at	965.6	P	0.000491	
6: 141205_at	383.2	P	0.001432	
7: 141206_at	1195	P	0.000491	
8: 141207_at	413.7	P	0.000613	
9: 141208_at	447.3	P	0.000762	
10: 141209_at	294.4	P	0.004591	
11: 141210_at	81.7	M	0.054711	
12: 141211_at	84.9	P	0.005504	
13: 141212_at	1456.4	P	0.000491	
14: 141213_at	37	A	0.122747	
15: 142121_at	133.7	A	0.889551	
16: 142122_at	275.3	A	0.611218	
17: 142123_at	307.6	A	0.611218	
18: 142124_at	132.6	A	0.437646	
19: 142125_at	195.8	A	0.110449	
20: 142126_at	174.1	A	0.681117	
...
21: 142127_at	316.3	A	0.65838	

GEO Type: SAMPLE
GEO Id: Drosophila_T1-1
Sample_characteristics_ch1: Genotype: yellow white and Oregon R pare
nts

Sample_characteristics_ch1: Age: embryos in slow phase of cellularis
ation

Sample_data_processing: The data were analyzed with Microarray S
uite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global
 scaling as normalization method. The trimmed mean target intensity of each arra
y was arbitrarily set to 100.

Sample_description: Gene expression data from embryos in slo
w phase of cellularisation.

Sample_extract_protocol_ch1: Trizol extraction of total RNA was perfo
rmed according to the manufacturer's instructions.

Sample_growth_protocol_ch1: 30 min egg collections of OreR and yw fl
ies at 25C were aged at room temperature (RT) according to the different tempora
l classes T0-T4.

Sample_hyb_protocol: Following fragmentation, 10 microg of cR
NA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChi
ps were washed and stained in the Affymetrix Fluidics Station 400.

Sample_label_ch1: biotin

Sample_label_protocol_ch1: Biotinylated cRNA were prepared accordin
g to the standard Affymetrix protocol from 6 microg total RNA (Expression Analys
is Technical Manual, 2001, Affymetrix).

Sample_molecule_ch1: total RNA

Sample_organism_ch1: Drosophila melanogaster

Sample_platform_id: GPL72

Sample_scan_protocol: GeneChips were scanned using the Hewlett
-Packard GeneArray Scanner G2500A.

Sample_source_name_ch1: Drosophila embryos in slow phase of cell
ularisation

Sample_supplementary_file: Drosophila_T1-1.CEL

Sample_table_begin: 

Sample_table_end: 

Sample_title: embryo at T1, biological rep1

Sample_treatment_protocol_ch1: Embryos were dechorionated with 50% blea
ch, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of t
he appropriate stage were manually selected under the dissecting scope. Selected
 embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% tri
ton-X100 and placed on ice in the Trizol solution (GibcoBRL).

Column Header Definitions
    ABS_CALL: the call in an absolute analysis that in
    dicates if the transcript was present (P), absent (A), marginal (M), or no call 
    (NC)

    DETECTION P-VALUE: 'detection p-value', p-value that indica
    tes the significance level of the detection call

    ID_REF: 

    VALUE: MAS5-calculated Signal intensity

0: ID_REF	VALUE	ABS_CALL	DETECTION P-VALUE	
1: 141200_at	20.8	A	0.801637	
2: 141201_at	85.8	A	0.48748	
3: 141202_at	704.8	P	0.000613	
4: 141203_at	1036.6	P	0.000944	
5: 141204_at	700.3	P	0.000491	
6: 141205_at	462.4	P	0.003159	
7: 141206_at	1301.9	P	0.000491	
8: 141207_at	454.8	P	0.000944	
9: 141208_at	438.6	P	0.000944	
10: 141209_at	264.4	P	0.004591	
11: 141210_at	65.6	A	0.150145	
12: 141211_at	72.2	A	0.070073	
13: 141212_at	1200	P	0.000491	
14: 141213_at	13.7	A	0.635055	
15: 142121_at	133.7	A	0.889551	
16: 142122_at	275.3	A	0.611218	
17: 142123_at	307.6	A	0.611218	
18: 142124_at	132.6	A	0.437646	
19: 142125_at	195.8	A	0.110449	
20: 142126_at	174.1	A	0.681117	
...
21: 142127_at	316.3	A	0.65838	

GEO Type: SERIES
GEO Id: Dros_embryo_timecourse
Series_contributor: Jane,Doe

Series_contributor: John,A,Smith

Series_contributor: Hans,van Elton

Series_contributor: John,Smithers Jr

Series_contributor: Jie,D,Chen

Series_overall_design: Drosophila embryos were selected at succ
essive stages of early development for RNA extraction and hybridization on Affym
etrix microarrays. We sought to obtain homogeneous populations of embryos at eac
h developmental stage in order to increase the temporal resolution of expression
 profiles. To that end, we hand-selected embryos according to morphological crit
eria at five time-points: before pole cell formation, i.e. before zygotic transc
ription (T0), during the slow phase (T1) and the fast phase (T2) of cellularisat
ion and at the beginning (T3) and the end (T4) of gastrulation.

Series_sample_id: Drosophila_T0-1

Series_sample_id: Drosophila_T0-2

Series_sample_id: Drosophila_T1-1

Series_summary: Morphogenesis of epithelial tissues reli
es on the precise developmental control of cell polarity and architecture. In th
e early Drosophila embryo, the primary epithelium forms during cellularisation, 
following a tightly controlled genetic programme where specific sets of genes ar
e up-regulated. Some of them, for instance, control membrane invagination betwee
n the nuclei anchored at the apical surface of the syncytium.

Series_summary: We used microarrays to detail the global
 programme of gene expression underlying cellularisation and identified distinct
 classes of up-regulated genes during this process.

Series_title: Expression data from early Drosophila em
bryo

Series_type: time course

Column Header Definitions



Testing Bio.Geo on soft_ex_affy_chp.txt


GEO Type: SAMPLE
GEO Id: Drosophila_T0-1
Sample_characteristics_ch1: Genotype: yellow white and Oregon R pare
nts

Sample_characteristics_ch1: Age: embryos younger than nuclear cycle 
9, i.e. before pole cells budding

Sample_data_processing: The data were analyzed with Microarray S
uite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global
 scaling as normalization method. The trimmed mean target intensity of each arra
y was arbitrarily set to 100.

Sample_description: Gene expression data from embryos younge
r than nuclear cycle 9, i.e. before zygotic genome activation.

Sample_extract_protocol_ch1: Trizol extraction of total RNA was perfo
rmed according to the manufacturer's instructions.

Sample_growth_protocol_ch1: 30 min egg collections of OreR and yw fl
ies at 25C were aged at room temperature (RT) according to the different tempora
l classes T0-T4.

Sample_hyb_protocol: Following fragmentation, 10 microg of cR
NA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChi
ps were washed and stained in the Affymetrix Fluidics Station 400.

Sample_label_ch1: biotin

Sample_label_protocol_ch1: Biotinylated cRNA were prepared accordin
g to the standard Affymetrix protocol from 6 microg total RNA (Expression Analys
is Technical Manual, 2001, Affymetrix).

Sample_molecule_ch1: total RNA

Sample_organism_ch1: Drosophila melanogaster

Sample_scan_protocol: GeneChips were scanned using the Hewlett
-Packard GeneArray Scanner G2500A.

Sample_source_name_ch1: Drosophila embryos before nuclear cycle 
9 (maternal transcripts)

Sample_supplementary_file: Drosophila_T0-1.CEL

Sample_table: Drosophila_T0-1.CHP

Sample_title: embryo at T0, biological rep1

Sample_treatment_protocol_ch1: Embryos were dechorionated with 50% blea
ch, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of t
he appropriate stage were manually selected under the dissecting scope. Selected
 embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% tri
ton-X100 and placed on ice in the Trizol solution (GibcoBRL).

Column Header Definitions

GEO Type: SAMPLE
GEO Id: Drosophila_T0-2
Sample_characteristics_ch1: Genotype: yellow white and Oregon R pare
nts

Sample_characteristics_ch1: Age: embryos younger than nuclear cycle 
9, i.e. before pole cells budding

Sample_data_processing: The data were analyzed with Microarray S
uite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global
 scaling as normalization method. The trimmed mean target intensity of each arra
y was arbitrarily set to 100.

Sample_description: Gene expression data from embryos younge
r than nuclear cycle 9, i.e. before zygotic genome activation.

Sample_extract_protocol_ch1: Trizol extraction of total RNA was perfo
rmed according to the manufacturer's instructions.

Sample_growth_protocol_ch1: 30 min egg collections of OreR and yw fl
ies at 25C were aged at room temperature (RT) according to the different tempora
l classes T0-T4.

Sample_hyb_protocol: Following fragmentation, 10 microg of cR
NA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChi
ps were washed and stained in the Affymetrix Fluidics Station 400.

Sample_label_ch1: biotin

Sample_label_protocol_ch1: Biotinylated cRNA were prepared accordin
g to the standard Affymetrix protocol from 6 microg total RNA (Expression Analys
is Technical Manual, 2001, Affymetrix).

Sample_molecule_ch1: total RNA

Sample_organism_ch1: Drosophila melanogaster

Sample_scan_protocol: GeneChips were scanned using the Hewlett
-Packard GeneArray Scanner G2500A.

Sample_source_name_ch1: Drosophila embryos before nuclear cycle 
9 (maternal transcripts)

Sample_supplementary_file: Drosophila_T0-2.CEL

Sample_table: Drosophila_T0-2.CHP

Sample_title: embryo at T0, biological rep2

Sample_treatment_protocol_ch1: Embryos were dechorionated with 50% blea
ch, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of t
he appropriate stage were manually selected under the dissecting scope. Selected
 embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% tri
ton-X100 and placed on ice in the Trizol solution (GibcoBRL).

Column Header Definitions

GEO Type: SAMPLE
GEO Id: Drosophila_T1-1
Sample_characteristics_ch1: Genotype: yellow white and Oregon R pare
nts

Sample_characteristics_ch1: Age: embryos in slow phase of cellularis
ation

Sample_data_processing: The data were analyzed with Microarray S
uite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global
 scaling as normalization method. The trimmed mean target intensity of each arra
y was arbitrarily set to 100.

Sample_description: Gene expression data from embryos in slo
w phase of cellularisation.

Sample_extract_protocol_ch1: Trizol extraction of total RNA was perfo
rmed according to the manufacturer's instructions.

Sample_growth_protocol_ch1: 30 min egg collections of OreR and yw fl
ies at 25C were aged at room temperature (RT) according to the different tempora
l classes T0-T4.

Sample_hyb_protocol: Following fragmentation, 10 microg of cR
NA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChi
ps were washed and stained in the Affymetrix Fluidics Station 400.

Sample_label_ch1: biotin

Sample_label_protocol_ch1: Biotinylated cRNA were prepared accordin
g to the standard Affymetrix protocol from 6 microg total RNA (Expression Analys
is Technical Manual, 2001, Affymetrix).

Sample_molecule_ch1: total RNA

Sample_organism_ch1: Drosophila melanogaster

Sample_scan_protocol: GeneChips were scanned using the Hewlett
-Packard GeneArray Scanner G2500A.

Sample_source_name_ch1: Drosophila embryos in slow phase of cell
ularisation

Sample_supplementary_file: Drosophila_T1-1.CEL

Sample_table: Drosophila_T1-1.CHP

Sample_title: embryo at T1, biological rep1

Sample_treatment_protocol_ch1: Embryos were dechorionated with 50% blea
ch, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of t
he appropriate stage were manually selected under the dissecting scope. Selected
 embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% tri
ton-X100 and placed on ice in the Trizol solution (GibcoBRL).

Column Header Definitions

GEO Type: SERIES
GEO Id: Dros_embryo_timecourse
Series_contributor: Jane,Doe

Series_contributor: John,A,Smith

Series_contributor: Hans,van Elton

Series_contributor: John,Smithers Jr

Series_contributor: Jie,D,Chen

Series_overall_design: Drosophila embryos were selected at succ
essive stages of early development for RNA extraction and hybridization on Affym
etrix microarrays. We sought to obtain homogeneous populations of embryos at eac
h developmental stage in order to increase the temporal resolution of expression
 profiles. To that end, we hand-selected embryos according to morphological crit
eria at five time-points: before pole cell formation, i.e. before zygotic transc
ription (T0), during the slow phase (T1) and the fast phase (T2) of cellularisat
ion and at the beginning (T3) and the end (T4) of gastrulation.

Series_sample_id: Drosophila_T0-1

Series_sample_id: Drosophila_T0-2

Series_sample_id: Drosophila_T1-1

Series_summary: Morphogenesis of epithelial tissues reli
es on the precise developmental control of cell polarity and architecture. In th
e early Drosophila embryo, the primary epithelium forms during cellularisation, 
following a tightly controlled genetic programme where specific sets of genes ar
e up-regulated. Some of them, for instance, control membrane invagination betwee
n the nuclei anchored at the apical surface of the syncytium.

Series_summary: We used microarrays to detail the global
 programme of gene expression underlying cellularisation and identified distinct
 classes of up-regulated genes during this process.

Series_title: Expression data from early Drosophila em
bryo

Series_type: time course

Column Header Definitions



Testing Bio.Geo on soft_ex_dual.txt


GEO Type: SAMPLE
GEO Id: Control Embyronic Stem Cell Replicate 1
Sample_characteristics_ch1: ES-D3 cell line (CRL-1934)

Sample_characteristics_ch1: Age: day 4

Sample_characteristics_ch1: Tissue: blastocytes

Sample_characteristics_ch1: Strain: 129/Sv mice

Sample_characteristics_ch2: Strain: C57BL/6

Sample_characteristics_ch2: Age: e17.5 d

Sample_characteristics_ch2: Tissue: whole embryo

Sample_data_processing: LOWESS normalized, background subtracted
 VALUE data obtained from log of processed Red signal/processed Green signal.

Sample_description: Biological replicate 1 of 4. Control emb
ryonic stem cells, untreated, harvested after several passages.

Sample_extract_protocol_ch1: TriZol procedure

Sample_extract_protocol_ch2: TriZol procedure

Sample_growth_protocol_ch1: ES cells were kept in an undifferentiate
d, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemic
on, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder lay
er inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cult
ured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modi
fied Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoet
hanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

Sample_hyb_protocol: Oligoarray control targets and hybridiza
tion buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples wer
e applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chamb
ers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Tri
ton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridiz
ed for 17 h at 60°C in a rotating oven, and washed.

Sample_label_ch1: Cy5

Sample_label_ch2: Cy3

Sample_label_protocol_ch1: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_label_protocol_ch2: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_molecule_ch1: total RNA

Sample_molecule_ch2: total RNA

Sample_organism_ch1: Mus musculus

Sample_organism_ch2: Mus musculus

Sample_platform_id: GPL3759

Sample_scan_protocol: Scanned on an Agilent G2565AA scanner.

Sample_scan_protocol: Images were quantified using Agilent Fea
ture Extraction Software (version A.7.5).

Sample_source_name_ch1: Total RNA from murine ES-D3 embryonic st
em cells labeled with Cyanine-5 (red).

Sample_source_name_ch2: Total RNA from pooled whole mouse embryo
s e17.5, labeled with Cyanine-3 (green).

Sample_supplementary_file: file1.gpr

Sample_title: Control Embyronic Stem Cell Replicate 1

sample_table_begin: 

sample_table_end: 

Column Header Definitions
    ID_REF: 

    LogRatioError: error of the log ratio calculated accord
    ing to the error model chosen.

    PValueLogRatio: Significance level of the Log Ratio comp
    uted for a feature.

    VALUE: log(REDsignal/GREENsignal) per feature (
    processed signals used).

    gProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," green "channel," used for computation of log ratio.

    rProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," red "channel," used for computation of log ratio.

0: ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal	
1: 1	-1.6274758	1.36E-01	6.41E-33	9.13E+03	2.15E+02	
2: 2	0.1412248	1.34E+00	1.00E+00	4.14E+01	5.72E+01	
3: 3	0.1827684	5.19E-02	4.33E-04	5.13E+03	7.81E+03	
4: 4	-0.3932267	6.08E-02	1.02E-10	4.65E+03	1.88E+03	
5: 5	-0.9865994	1.05E-01	6.32E-21	2.91E+03	3.01E+02	
6: 6	0.0238812	1.02E-01	8.15E-01	7.08E+02	7.48E+02	
7: 7	-1.4841822	1.25E-01	1.42E-32	1.02E+04	3.36E+02	
8: 8	-1.8261356	4.15E-01	1.10E-05	7.19E+02	1.07E+01	
9: 9	-1.0344779	1.78E+00	1.00E+00	9.62E+01	8.89E+00	
10: 10	0.2405891	3.09E-01	4.36E-01	1.61E+02	2.80E+02	
11: 11	0.3209366	3.59E-01	3.71E-01	1.25E+02	2.61E+02	
12: 12	0.358304	2.06E+00	1.00E+00	2.04E+01	4.66E+01	
13: 13	-0.0122072	3.64E-01	9.73E-01	1.84E+02	1.79E+02	
14: 14	-1.5480396	1.30E-01	7.21E-33	1.02E+04	2.90E+02	
15: 15	0.0073419	2.98E-01	9.80E-01	2.21E+02	2.25E+02	
16: 16	-0.2267015	9.44E-01	8.10E-01	8.90E+01	5.28E+01	
17: 17	-0.1484023	8.01E-01	8.53E-01	9.65E+01	6.86E+01	
18: 18	-0.6122195	1.28E-01	1.69E-06	1.12E+03	2.73E+02	
19: 19	0.0796905	8.78E-02	3.64E-01	8.21E+02	9.87E+02	
20: 20	-0.084895	9.38E-01	9.28E-01	7.68E+01	6.32E+01	

GEO Type: SAMPLE
GEO Id: Control Embyronic Stem Cell Replicate 2
Sample_characteristics_ch1: ES-D3 cell line (CRL-1934)

Sample_characteristics_ch1: Age: day 4

Sample_characteristics_ch1: Tissue: blastocytes

Sample_characteristics_ch1: Strain: 129/Sv mice

Sample_characteristics_ch2: Strain: C57BL/6

Sample_characteristics_ch2: Age: e17.5 d

Sample_characteristics_ch2: Tissue: whole embryo

Sample_data_processing: LOWESS normalized, background subtracted
 VALUE data obtained from log of processed Red signal/processed Green signal.

Sample_description: Biological replicate 2 of 4. Control emb
ryonic stem cells, untreated, harvested after several passages.

Sample_extract_protocol_ch1: TriZol procedure

Sample_extract_protocol_ch2: TriZol procedure

Sample_growth_protocol_ch1: ES cells were kept in an undifferentiate
d, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemic
on, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder lay
er inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cult
ured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modi
fied Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoet
hanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

Sample_hyb_protocol: Oligoarray control targets and hybridiza
tion buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples wer
e applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chamb
ers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Tri
ton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridiz
ed for 17 h at 60°C in a rotating oven, and washed.

Sample_label_ch1: Cy5

Sample_label_ch2: Cy3

Sample_label_protocol_ch1: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_label_protocol_ch2: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_molecule_ch1: total RNA

Sample_molecule_ch2: total RNA

Sample_organism_ch1: Mus musculus

Sample_organism_ch2: Mus musculus

Sample_platform_id: GPL3759

Sample_scan_protocol: Scanned on an Agilent G2565AA scanner.

Sample_scan_protocol: Images were quantified using Agilent Fea
ture Extraction Software (version A.7.5).

Sample_source_name_ch1: Total RNA from murine ES-D3 embryonic st
em cells labeled with Cyanine-5 (red).

Sample_source_name_ch2: Total RNA from pooled whole mouse embryo
s e17.5, labeled with Cyanine-3 (green).

Sample_supplementary_file: file2.gpr

Sample_title: Control Embyronic Stem Cell Replicate 2

sample_table_begin: 

sample_table_end: 

Column Header Definitions
    ID_REF: 

    LogRatioError: error of the log ratio calculated accord
    ing to the error model chosen.

    PValueLogRatio: Significance level of the Log Ratio comp
    uted for a feature.

    VALUE: log(REDsignal/GREENsignal) per feature (
    processed signals used).

    gProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," green "channel," used for computation of log ratio.

    rProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," red "channel," used for computation of log ratio.

0: ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal	
1: 1	-1.1697263	1.23E-01	2.14E-21	3.17E+03	2.14E+02	
2: 2	-0.1111353	1.63E+00	9.46E-01	5.43E+01	4.20E+01	
3: 3	0.1400597	5.11E-02	6.17E-03	6.72E+03	9.28E+03	
4: 4	-0.4820633	6.38E-02	4.06E-14	6.46E+03	2.13E+03	
5: 5	-1.2116196	1.22E-01	2.31E-23	3.62E+03	2.22E+02	
6: 6	-0.0230528	1.04E-01	8.24E-01	8.76E+02	8.31E+02	
7: 7	-1.1380152	1.13E-01	9.23E-24	3.94E+03	2.86E+02	
8: 8	-1.834596	5.40E-01	6.74E-04	6.44E+02	9.43E+00	
9: 9	-0.9747637	2.14E+00	1.00E+00	9.17E+01	9.72E+00	
10: 10	0.3874005	2.92E-01	1.85E-01	1.69E+02	4.11E+02	
11: 11	0.5340442	3.29E-01	1.04E-01	1.23E+02	4.20E+02	
12: 12	0.3260696	1.92E+00	8.65E-01	2.73E+01	5.77E+01	
13: 13	0.3010618	2.84E-01	2.90E-01	1.93E+02	3.87E+02	
14: 14	-1.0760413	1.08E-01	1.63E-23	4.06E+03	3.41E+02	
15: 15	-0.1167371	3.87E-01	7.63E-01	2.32E+02	1.77E+02	
16: 16	-0.1936322	9.44E-01	8.38E-01	1.02E+02	6.56E+01	
17: 17	-0.3275898	7.87E-01	6.77E-01	1.41E+02	6.65E+01	
18: 18	-0.4805853	1.14E-01	2.41E-05	1.34E+03	4.42E+02	
19: 19	0.1109524	9.56E-02	2.46E-01	8.38E+02	1.08E+03	
20: 20	0.1677912	6.51E-01	7.97E-01	9.84E+01	1.45E+02	

GEO Type: SAMPLE
GEO Id: Triple-Fusion Transfected Embryonic Stem Cells Replicate 1
Sample_characteristics_ch1: ES-D3 cell line (CRL-1934)

Sample_characteristics_ch1: Transfected with pUb-fluc-mrfp-ttk tripl
e fusion reporter gene.

Sample_characteristics_ch1: Age: day 4

Sample_characteristics_ch1: Tissue: blastocytes

Sample_characteristics_ch1: Strain: 129/Sv mice

Sample_characteristics_ch2: Strain: C57BL/6

Sample_characteristics_ch2: Age: e17.5 d

Sample_characteristics_ch2: Tissue: whole embryo

Sample_data_processing: LOWESS normalized, background subtracted
 VALUE data obtained from log of processed Red signal/processed Green signal.

Sample_description: Biological replicate 1 of 3. Stable trip
le-fusion-reporter-gene transfected embryonic stem cells, harvested after severa
l passages.

Sample_extract_protocol_ch1: TriZol procedure

Sample_extract_protocol_ch2: TriZol procedure

Sample_growth_protocol_ch1: ES cells were kept in an undifferentiate
d, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemic
on, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder lay
er inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cult
ured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modi
fied Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoet
hanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

Sample_hyb_protocol: Oligoarray control targets and hybridiza
tion buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples wer
e applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chamb
ers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Tri
ton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridiz
ed for 17 h at 60°C in a rotating oven, and washed.

Sample_label_ch1: Cy5

Sample_label_ch2: Cy3

Sample_label_protocol_ch1: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Science
, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNas
e A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_label_protocol_ch2: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_molecule_ch1: total RNA

Sample_molecule_ch2: total RNA

Sample_organism_ch1: Mus musculus

Sample_organism_ch2: Mus musculus

Sample_platform_id: GPL3759

Sample_scan_protocol: Scanned on an Agilent G2565AA scanner.

Sample_source_name_ch1: Total RNA from murine ES-D3 triple-trans
fected embryonic stem cells labeled with Cyanine-5 (red).

Sample_source_name_ch2: Total RNA from pooled whole mouse embryo
s e17.5, labeled with Cyanine-3 (green).

Sample_supplementary_file: file3.gpr

Sample_title: Triple-Fusion Transfected Embryonic Stem
 Cells Replicate 1

Sample_treatment_protocol_ch1: PCR amplification and standard cloning t
echniques were used to insert fluc and mrfp genes from plasmids pCDNA 3.1-CMV-fl
uc (Promega, Madison, WI) and pCDNA3.1-CMV-mrfp in frame with the ttk gene into 
the pCDNA3.1-truncated	sr39tk. This triple fusion (TF) reporter gene fragment (3
.3 kbp) was released from the plasmid with Not1 and BamH1 restriction enzymes be
fore blunt-end ligation into the multiple cloning site of lentiviral transfer ve
ctor, FUG, driven by the human ubiquitin-C promoter. Self-inactivating (SIN) len
tivirus was prepared by transient transfection of 293T cells. Briefly, pFUG-TF c
ontaining the triple fusion reporter gene was co-transfected into 293T cells wit
h HIV-1 packaging vector (?8.9) and vesicular stomatitis virus G glycoprotein-ps
eudotyped envelop vector (pVSVG). Lentivirus supernatant was concentrated by sed
iment centrifugation using a SW29 rotor at 50,000 x g for two hours. Concentrate
d virus was titered on 293T cells. Murine ES cells were transfected with LV-pUb-
fluc-mrfp-ttk at a multiplicity of infection (MOI) of 10.

sample_table_begin: 

sample_table_end: 

Column Header Definitions
    ID_REF: 

    LogRatioError: error of the log ratio calculated accord
    ing to the error model chosen.

    PValueLogRatio: Significance level of the Log Ratio comp
    uted for a feature.

    VALUE: log(REDsignal/GREENsignal) per feature (
    processed signals used).

    gProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," green "channel," used for computation of log ratio.

    rProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," red "channel," used for computation of log ratio.

0: ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal	
1: 1	-0.7837546	1.30E-01	1.70E-09	2.10E+03	3.46E+02	
2: 2	0.3797837	1.15E+00	7.41E-01	5.59E+01	1.34E+02	
3: 3	0.2079269	5.38E-02	1.12E-04	5.04E+03	8.14E+03	
4: 4	-0.4730291	6.71E-02	1.86E-12	5.66E+03	1.91E+03	
5: 5	-0.9481128	1.19E-01	1.30E-15	3.10E+03	3.49E+02	
6: 6	-0.0159867	1.33E-01	9.05E-01	8.45E+02	8.14E+02	
7: 7	-0.819922	1.14E-01	7.01E-13	2.75E+03	4.16E+02	
8: 8	-0.1559774	9.16E-01	8.65E-01	1.34E+02	9.34E+01	
9: 9	0.145267	3.90E+00	1.00E+00	2.22E+01	3.10E+01	
10: 10	0.3611211	3.40E-01	2.88E-01	1.97E+02	4.52E+02	
11: 11	0.5092089	4.39E-01	2.46E-01	1.24E+02	4.01E+02	
12: 12	0.3715387	1.69E+00	8.26E-01	3.84E+01	9.04E+01	
13: 13	0.1734934	3.57E-01	6.27E-01	2.37E+02	3.53E+02	
14: 14	-0.9340707	1.20E-01	6.90E-15	2.96E+03	3.45E+02	
15: 15	-0.2956317	5.78E-01	6.09E-01	2.46E+02	1.25E+02	
16: 16	-0.2321102	1.22E+00	8.49E-01	1.09E+02	6.37E+01	
17: 17	-0.1603561	1.16E+00	8.90E-01	1.06E+02	7.34E+01	
18: 18	-0.5063897	1.63E-01	1.95E-03	1.15E+03	3.58E+02	
19: 19	0.1990761	1.32E-01	1.32E-01	6.65E+02	1.05E+03	
20: 20	0.2985912	8.89E-01	7.37E-01	8.06E+01	1.60E+02	



Testing Bio.Geo on soft_ex_family.txt


GEO Type: PLATFORM
GEO Id: Murine 15K long oligo array version 2.0
Platform_coating: polysine

Platform_contributor: Jane,Doe

Platform_contributor: John,A,Smith

Platform_contributor: Hans,van Elton

Platform_contributor: John,Smithers Jr

Platform_contributor: Jie,D,Chen

Platform_distribution: non-commercial

Platform_manufacture_protocol: 1.  Oligos are arrayed in Greiner 384-we
ll flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.

Platform_manufacture_protocol: 2. Resuspend oligos in water to 20 uM an
d rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).

Platform_manufacture_protocol: 3. Allow Genetix plates to dry through p
assive water evaporation in a protected environment (e.g., chemical hood).

Platform_manufacture_protocol: 4. Before printing, add 5 µL of 1X Print
ing Buffer to each well. This can be done the night before a print run is starte
d.

Platform_manufacture_protocol: 5. Seal plates with Corning seals.

Platform_manufacture_protocol: 6. Incubate at 37°C for 30 minutes to ai
d resuspension of DNA.

Platform_manufacture_protocol: 7. Shake plates near maximum rotational 
speed on flat-bed shaker for 1 minute.

Platform_manufacture_protocol: 8. Centrifuge plates at 2000 rpm for 3 m
inutes.

Platform_manufacture_protocol: 9. Remove seals and cover with plate lid
s. Place in appropriate location of plate cassette. This should be done with fir
st plates just before print run is started to minimize evaporation time before p
rinting. For second and third cassettes, wait until 30 minutes before next casse
tte is needed to begin centrifugation.

Platform_manufacture_protocol: 10. Make sure plates rest behind both ho
lding clips in the cassettes. Push plates back into the cassettes as far as they
 will go, putting them in the proper position for the server arm.

Platform_manufacture_protocol: 11. After the print run is completed, al
low plates to dry through passive evaporation in a protected environment.

Platform_manufacture_protocol: 12. For each subsequent preparation of t
hese plates for a print run, add water to the wells instead of sodium phosphate 
buffer. The amount of water should be decreased by 0.25 µL per print run, as thi
s is the amount drawn up by the pin capillary during each dip.

Platform_manufacturer: Un. London microarray facility

Platform_organism: Mus musculus

Platform_support: glass

Platform_technology: spotted oligonucleotide

Platform_title: Murine 15K long oligo array version 2.0

Platform_web_link: http://www.microarray.protocols.html

platform_table_begin: 

platform_table_end: 

Column Header Definitions
    GB_ACC: GenBank accession number of sequence use
    d to design oligonucleotide probe   LINK_PRE:"http://www.ncbi.nlm.nih.gov/entrez
    /query.fcgi?cmd=Search&db=Nucleotide&term="

    Gene_Desc: Gene description

    Gene_Sym: Gene symbols

    ID: 

    SEQUENCE: Probe sequence information

    SPOT_ID: alternative identifier

0: ID	GB_ACC	Gene_Desc	Gene_Sym	SPOT_ID	SEQUENCE	
1: 1	U02079	nuclear factor of activated T-cells, cytoplasmic 2	Nfatc2		ACCTGGATGACGCAGCCACTTCAGAAAGCTGGGTTGGGACAGAAAGGTATATAGAGAGAAAATTTTGGAA	
2: 2	NM_008154	G-protein coupled receptor 3	Gpr3		CTGTACAATGCTCTCACTTACTACTCAGAGACAACGGTAACTCGGACTTATGTGATGCTGGCCTTGGTGT	
3: 3	AK015719	tropomodulin 2	Tmod2		CACCAGGCTCAGTGCCTAGTATCGGCTTCACCTAGTGTGGTTACTCAGGGCACGCAGAGCTACAGAACAC	
4: 4	AK003367	mitochondrial ribosomal protein L15	Mrpl15		CAAGAAGTCTAGAAATTCTGTGCAAGCCTATTCCATTCTTTCTGCGGGGACAACCAATTCCGAAAAGAAT	
5: 5	BC003333	RIKEN cDNA 0610033I05 gene	0610033I05Rik		AGAACTGGGTGGCAGATATCCTAGAGTTTTGACCAACGTTCACAGCACACATATTGATCTTATAGGACCT	
6: 6	NM_008462	killer cell lectin-like receptor, subfamily A, member 2	Klra2		TGAATTGAAGTTCCTTAAATCCCAACTTCAAAGAAACACATACTGGATTTCACTGACACATCATAAAAGC	
7: 7	NM_008029	FMS-like tyrosine kinase 4	Flt4		GAGGTGCTGTGGGATGACCGCCGGGGCATGCGGGTGCCCACTCAACTGTTGCGCGATGCCCTGTACCTGC	
8: 8	NM_054088	adiponutrin	Adpn		GTCTGAGTTCCATTCCAAAGACGAAGTCGTGGATGCCCTGGTGTGTTCCTGCTTCATTCCCCTCTTCTCT	
9: 9	NM_009750	nerve growth factor receptor (TNFRSF16) associated protein 1	Ngfrap1		TACAGCTGAGAAATTGTCTACGCATCCTTATGGGGGAGCTGTCTAACCACCACGATCACCATGATGAATT	
10: 10	AB045323	DNA segment, Chr 8, ERATO Doi 594, expressed	D8Ertd594e		GATTCAGACTCGGGAGGAGCATCCCAACCTCTCCTTGAGGATAAAGGCCTGAGCGATTGCCCTGGGGAGC	
11: 11	AK005789	dynein, cytoplasmic, light chain 2B	Dncl2b		TGCAGAAGGCATTCCAATCCGAACAACCCTGGACAACTCCACAACGGTTCAGTATGCGGGTCTTCTCCAC	
12: 12	NM_010517	insulin-like growth factor binding protein 4	Igfbp4		GGAGAAGCTGGCGCGCTGCCGCCCCCCCGTGGGTTGCGAGGAGTTGGTGCGGGAGCCAGGCTGCGGTTGT	
13: 13	AK010722	RIKEN cDNA 2410075D05 gene	2410075D05Rik		GGAGCATCTGGAGTTCCGCTTACCGGAAATAAAGTCTTTACTATCGGTGATTGGAGGGCAGTTCACTAAC	
14: 14	AK003755	DNA segment, Chr 4, ERATO Doi 421, expressed	D4Ertd421e		AGCAAAGAGATCTCCCTCAGTGTGCCCATAGGTGGCGGTGCGAGCTTGCGGTTATTGGCCAGTGACTTGC	
15: 15	BC003241	cleavage stimulation factor, 3' pre-RNA, subunit 3	Cstf3		AAATTAGAAGAAAATCCATATGACCTTGATGCTTGGAGCATTCTCATTCGAGAGGCACAGAATCAACCTA	
16: 16	AK004937	RIKEN cDNA 1300007O09 gene	1300007O09Rik		CAGACACAAACCCTAGGTTGTATTGTAGACCGGAGTTTAAGCAGGCACTACCTGTCTGTCTTTTCTTCAT	
17: 17	AK004524	unnamed protein product; hypothetical SOCS domain			CGGAGCCCTGCGCGCCCAGAGCCCCCTCCCACCCGCTTCCACCAAGTGCATGGAGCCAACATCCGCATGG	
18: 18	NM_025999	RIKEN cDNA 2610110L04 gene	2610110L04Rik		TGCATTGATAAATGGAGTGATCGACACAGGAACTGCCCCATTTGTCGCCTACAGATGACTGGAGCAAATG	
19: 19				-- CONTROL		
20: 20	NM_023120	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	Gnb1l		ACCGCCTGGTCCCAGATTTGTCCTCCGAGGCACACAGTCGGCTGTGAACACGCTCCATTTCTGCCCACCA	

GEO Type: SAMPLE
GEO Id: Control Embyronic Stem Cell Replicate 1
Sample_characteristics_ch1: ES-D3 cell line (CRL-1934)

Sample_characteristics_ch1: Age: day 4

Sample_characteristics_ch1: Tissue: blastocytes

Sample_characteristics_ch1: Strain: 129/Sv mice

Sample_characteristics_ch2: Strain: C57BL/6

Sample_characteristics_ch2: Age: e17.5 d

Sample_characteristics_ch2: Tissue: whole embryo

Sample_data_processing: LOWESS normalized, background subtracted
 VALUE data obtained from log of processed Red signal/processed Green signal.

Sample_description: Biological replicate 1 of 4. Control emb
ryonic stem cells, untreated, harvested after several passages.

Sample_extract_protocol_ch1: TriZol procedure

Sample_extract_protocol_ch2: TriZol procedure

Sample_growth_protocol_ch1: ES cells were kept in an undifferentiate
d, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemic
on, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder lay
er inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cult
ured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modi
fied Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoet
hanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

Sample_hyb_protocol: Oligoarray control targets and hybridiza
tion buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples wer
e applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chamb
ers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Tri
ton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridiz
ed for 17 h at 60°C in a rotating oven, and washed.

Sample_label_ch1: Cy5

Sample_label_ch2: Cy3

Sample_label_protocol_ch1: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_label_protocol_ch2: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_molecule_ch1: total RNA

Sample_molecule_ch2: total RNA

Sample_organism_ch1: Mus musculus

Sample_organism_ch2: Mus musculus

Sample_platform_id: Murine 15K long oligo array version 2.0

Sample_scan_protocol: Scanned on an Agilent G2565AA scanner.

Sample_scan_protocol: Images were quantified using Agilent Fea
ture Extraction Software (version A.7.5).

Sample_source_name_ch1: Total RNA from murine ES-D3 embryonic st
em cells labeled with Cyanine-5 (red).

Sample_source_name_ch2: Total RNA from pooled whole mouse embryo
s e17.5, labeled with Cyanine-3 (green).

Sample_supplementary_file: file1.gpr

Sample_title: Control Embyronic Stem Cell Replicate 1

sample_table_begin: 

sample_table_end: 

Column Header Definitions
    ID_REF: 

    LogRatioError: error of the log ratio calculated accord
    ing to the error model chosen.

    PValueLogRatio: Significance level of the Log Ratio comp
    uted for a feature.

    VALUE: log(REDsignal/GREENsignal) per feature (
    processed signals used).

    gProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," green "channel," used for computation of log ratio.

    rProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," red "channel," used for computation of log ratio.

0: ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal	
1: 1	-1.6274758	1.36E-01	6.41E-33	9.13E+03	2.15E+02	
2: 2	0.1412248	1.34E+00	1.00E+00	4.14E+01	5.72E+01	
3: 3	0.1827684	5.19E-02	4.33E-04	5.13E+03	7.81E+03	
4: 4	-0.3932267	6.08E-02	1.02E-10	4.65E+03	1.88E+03	
5: 5	-0.9865994	1.05E-01	6.32E-21	2.91E+03	3.01E+02	
6: 6	0.0238812	1.02E-01	8.15E-01	7.08E+02	7.48E+02	
7: 7	-1.4841822	1.25E-01	1.42E-32	1.02E+04	3.36E+02	
8: 8	-1.8261356	4.15E-01	1.10E-05	7.19E+02	1.07E+01	
9: 9	-1.0344779	1.78E+00	1.00E+00	9.62E+01	8.89E+00	
10: 10	0.2405891	3.09E-01	4.36E-01	1.61E+02	2.80E+02	
11: 11	0.3209366	3.59E-01	3.71E-01	1.25E+02	2.61E+02	
12: 12	0.358304	2.06E+00	1.00E+00	2.04E+01	4.66E+01	
13: 13	-0.0122072	3.64E-01	9.73E-01	1.84E+02	1.79E+02	
14: 14	-1.5480396	1.30E-01	7.21E-33	1.02E+04	2.90E+02	
15: 15	0.0073419	2.98E-01	9.80E-01	2.21E+02	2.25E+02	
16: 16	-0.2267015	9.44E-01	8.10E-01	8.90E+01	5.28E+01	
17: 17	-0.1484023	8.01E-01	8.53E-01	9.65E+01	6.86E+01	
18: 18	-0.6122195	1.28E-01	1.69E-06	1.12E+03	2.73E+02	
19: 19	0.0796905	8.78E-02	3.64E-01	8.21E+02	9.87E+02	
20: 20	-0.084895	9.38E-01	9.28E-01	7.68E+01	6.32E+01	

GEO Type: SAMPLE
GEO Id: Control Embyronic Stem Cell Replicate 2
Sample_characteristics_ch1: ES-D3 cell line (CRL-1934)

Sample_characteristics_ch1: Age: day 4

Sample_characteristics_ch1: Tissue: blastocytes

Sample_characteristics_ch1: Strain: 129/Sv mice

Sample_characteristics_ch2: Strain: C57BL/6

Sample_characteristics_ch2: Age: e17.5 d

Sample_characteristics_ch2: Tissue: whole embryo

Sample_data_processing: LOWESS normalized, background subtracted
 VALUE data obtained from log of processed Red signal/processed Green signal.

Sample_description: Biological replicate 2 of 4. Control emb
ryonic stem cells, untreated, harvested after several passages.

Sample_extract_protocol_ch1: TriZol procedure

Sample_extract_protocol_ch2: TriZol procedure

Sample_growth_protocol_ch1: ES cells were kept in an undifferentiate
d, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemic
on, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder lay
er inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cult
ured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modi
fied Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoet
hanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

Sample_hyb_protocol: Oligoarray control targets and hybridiza
tion buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples wer
e applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chamb
ers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Tri
ton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridiz
ed for 17 h at 60°C in a rotating oven, and washed.

Sample_label_ch1: Cy5

Sample_label_ch2: Cy3

Sample_label_protocol_ch1: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_label_protocol_ch2: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_molecule_ch1: total RNA

Sample_molecule_ch2: total RNA

Sample_organism_ch1: Mus musculus

Sample_organism_ch2: Mus musculus

Sample_platform_id: Murine 15K long oligo array version 2.0

Sample_scan_protocol: Scanned on an Agilent G2565AA scanner.

Sample_scan_protocol: Images were quantified using Agilent Fea
ture Extraction Software (version A.7.5).

Sample_source_name_ch1: Total RNA from murine ES-D3 embryonic st
em cells labeled with Cyanine-5 (red).

Sample_source_name_ch2: Total RNA from pooled whole mouse embryo
s e17.5, labeled with Cyanine-3 (green).

Sample_supplementary_file: file2.gpr

Sample_title: Control Embyronic Stem Cell Replicate 2

sample_table_begin: 

sample_table_end: 

Column Header Definitions
    ID_REF: 

    LogRatioError: error of the log ratio calculated accord
    ing to the error model chosen.

    PValueLogRatio: Significance level of the Log Ratio comp
    uted for a feature.

    VALUE: log(REDsignal/GREENsignal) per feature (
    processed signals used).

    gProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," green "channel," used for computation of log ratio.

    rProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," red "channel," used for computation of log ratio.

0: ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal	
1: 1	-1.1697263	1.23E-01	2.14E-21	3.17E+03	2.14E+02	
2: 2	-0.1111353	1.63E+00	9.46E-01	5.43E+01	4.20E+01	
3: 3	0.1400597	5.11E-02	6.17E-03	6.72E+03	9.28E+03	
4: 4	-0.4820633	6.38E-02	4.06E-14	6.46E+03	2.13E+03	
5: 5	-1.2116196	1.22E-01	2.31E-23	3.62E+03	2.22E+02	
6: 6	-0.0230528	1.04E-01	8.24E-01	8.76E+02	8.31E+02	
7: 7	-1.1380152	1.13E-01	9.23E-24	3.94E+03	2.86E+02	
8: 8	-1.834596	5.40E-01	6.74E-04	6.44E+02	9.43E+00	
9: 9	-0.9747637	2.14E+00	1.00E+00	9.17E+01	9.72E+00	
10: 10	0.3874005	2.92E-01	1.85E-01	1.69E+02	4.11E+02	
11: 11	0.5340442	3.29E-01	1.04E-01	1.23E+02	4.20E+02	
12: 12	0.3260696	1.92E+00	8.65E-01	2.73E+01	5.77E+01	
13: 13	0.3010618	2.84E-01	2.90E-01	1.93E+02	3.87E+02	
14: 14	-1.0760413	1.08E-01	1.63E-23	4.06E+03	3.41E+02	
15: 15	-0.1167371	3.87E-01	7.63E-01	2.32E+02	1.77E+02	
16: 16	-0.1936322	9.44E-01	8.38E-01	1.02E+02	6.56E+01	
17: 17	-0.3275898	7.87E-01	6.77E-01	1.41E+02	6.65E+01	
18: 18	-0.4805853	1.14E-01	2.41E-05	1.34E+03	4.42E+02	
19: 19	0.1109524	9.56E-02	2.46E-01	8.38E+02	1.08E+03	
20: 20	0.1677912	6.51E-01	7.97E-01	9.84E+01	1.45E+02	

GEO Type: SAMPLE
GEO Id: Triple-Fusion Transfected Embryonic Stem Cells Replicate 1
Sample_characteristics_ch1: ES-D3 cell line (CRL-1934)

Sample_characteristics_ch1: Transfected with pUb-fluc-mrfp-ttk tripl
e fusion reporter gene.

Sample_characteristics_ch1: Age: day 4

Sample_characteristics_ch1: Tissue: blastocytes

Sample_characteristics_ch1: Strain: 129/Sv mice

Sample_characteristics_ch2: Strain: C57BL/6

Sample_characteristics_ch2: Age: e17.5 d

Sample_characteristics_ch2: Tissue: whole embryo

Sample_data_processing: LOWESS normalized, background subtracted
 VALUE data obtained from log of processed Red signal/processed Green signal.

Sample_description: Biological replicate 1 of 3. Stable trip
le-fusion-reporter-gene transfected embryonic stem cells, harvested after severa
l passages.

Sample_extract_protocol_ch1: TriZol procedure

Sample_extract_protocol_ch2: TriZol procedure

Sample_growth_protocol_ch1: ES cells were kept in an undifferentiate
d, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemic
on, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder lay
er inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cult
ured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modi
fied Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoet
hanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

Sample_hyb_protocol: Oligoarray control targets and hybridiza
tion buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples wer
e applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chamb
ers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Tri
ton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridiz
ed for 17 h at 60°C in a rotating oven, and washed.

Sample_label_ch1: Cy5

Sample_label_ch2: Cy3

Sample_label_protocol_ch1: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Science
, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNas
e A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_label_protocol_ch2: 10 µg of total RNA were primed with 2 µl
 of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°
C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM
 each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Scienc
e, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNa
se A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

Sample_molecule_ch1: total RNA

Sample_molecule_ch2: total RNA

Sample_organism_ch1: Mus musculus

Sample_organism_ch2: Mus musculus

Sample_platform_id: Murine 15K long oligo array version 2.0

Sample_scan_protocol: Scanned on an Agilent G2565AA scanner.

Sample_source_name_ch1: Total RNA from murine ES-D3 triple-trans
fected embryonic stem cells labeled with Cyanine-5 (red).

Sample_source_name_ch2: Total RNA from pooled whole mouse embryo
s e17.5, labeled with Cyanine-3 (green).

Sample_supplementary_file: file3.gpr

Sample_title: Triple-Fusion Transfected Embryonic Stem
 Cells Replicate 1

Sample_treatment_protocol_ch1: PCR amplification and standard cloning t
echniques were used to insert fluc and mrfp genes from plasmids pCDNA 3.1-CMV-fl
uc (Promega, Madison, WI) and pCDNA3.1-CMV-mrfp in frame with the ttk gene into 
the pCDNA3.1-truncated	sr39tk. This triple fusion (TF) reporter gene fragment (3
.3 kbp) was released from the plasmid with Not1 and BamH1 restriction enzymes be
fore blunt-end ligation into the multiple cloning site of lentiviral transfer ve
ctor, FUG, driven by the human ubiquitin-C promoter. Self-inactivating (SIN) len
tivirus was prepared by transient transfection of 293T cells. Briefly, pFUG-TF c
ontaining the triple fusion reporter gene was co-transfected into 293T cells wit
h HIV-1 packaging vector (?8.9) and vesicular stomatitis virus G glycoprotein-ps
eudotyped envelop vector (pVSVG). Lentivirus supernatant was concentrated by sed
iment centrifugation using a SW29 rotor at 50,000 x g for two hours. Concentrate
d virus was titered on 293T cells. Murine ES cells were transfected with LV-pUb-
fluc-mrfp-ttk at a multiplicity of infection (MOI) of 10.

sample_table_begin: 

sample_table_end: 

Column Header Definitions
    ID_REF: 

    LogRatioError: error of the log ratio calculated accord
    ing to the error model chosen.

    PValueLogRatio: Significance level of the Log Ratio comp
    uted for a feature.

    VALUE: log(REDsignal/GREENsignal) per feature (
    processed signals used).

    gProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," green "channel," used for computation of log ratio.

    rProcessedSignal: Dye-normalized signal after surrogate "a
    lgorithm," red "channel," used for computation of log ratio.

0: ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal	
1: 1	-0.7837546	1.30E-01	1.70E-09	2.10E+03	3.46E+02	
2: 2	0.3797837	1.15E+00	7.41E-01	5.59E+01	1.34E+02	
3: 3	0.2079269	5.38E-02	1.12E-04	5.04E+03	8.14E+03	
4: 4	-0.4730291	6.71E-02	1.86E-12	5.66E+03	1.91E+03	
5: 5	-0.9481128	1.19E-01	1.30E-15	3.10E+03	3.49E+02	
6: 6	-0.0159867	1.33E-01	9.05E-01	8.45E+02	8.14E+02	
7: 7	-0.819922	1.14E-01	7.01E-13	2.75E+03	4.16E+02	
8: 8	-0.1559774	9.16E-01	8.65E-01	1.34E+02	9.34E+01	
9: 9	0.145267	3.90E+00	1.00E+00	2.22E+01	3.10E+01	
10: 10	0.3611211	3.40E-01	2.88E-01	1.97E+02	4.52E+02	
11: 11	0.5092089	4.39E-01	2.46E-01	1.24E+02	4.01E+02	
12: 12	0.3715387	1.69E+00	8.26E-01	3.84E+01	9.04E+01	
13: 13	0.1734934	3.57E-01	6.27E-01	2.37E+02	3.53E+02	
14: 14	-0.9340707	1.20E-01	6.90E-15	2.96E+03	3.45E+02	
15: 15	-0.2956317	5.78E-01	6.09E-01	2.46E+02	1.25E+02	
16: 16	-0.2321102	1.22E+00	8.49E-01	1.09E+02	6.37E+01	
17: 17	-0.1603561	1.16E+00	8.90E-01	1.06E+02	7.34E+01	
18: 18	-0.5063897	1.63E-01	1.95E-03	1.15E+03	3.58E+02	
19: 19	0.1990761	1.32E-01	1.32E-01	6.65E+02	1.05E+03	
20: 20	0.2985912	8.89E-01	7.37E-01	8.06E+01	1.60E+02	

GEO Type: SERIES
GEO Id: Murine ES Cells
Series_contributor: Joseph,C,Wu

Series_contributor: Joshua,M,Spin

Series_contributor: Feng,,Cao

Series_contributor: Shaun,,Lin

Series_contributor: Olivier,,Gheysens

Series_contributor: Ian,Y,Chen

Series_contributor: Anya,,Tsalenko

Series_contributor: Sanjiv,S,Ghambhir

Series_contributor: Thomas,,Quertermous

Series_overall_design: Two-condition experiment, ES vs. TF-ES c
ells. Biological replicates: 4 control, 3 transfected, independently grown and h
arvested. One replicate per array.

Series_pubmed_id: 16390873

Series_sample_id: Control Embyronic Stem Cell Replicate 1

Series_sample_id: Control Embyronic Stem Cell Replicate 2

Series_sample_id: Triple-Fusion Transfected Embryonic Stem
 Cells Replicate 1

Series_summary: Transcriptional profiling of mouse embry
onic stem cells comparing control untreated ES cells with ES cells transfected w
ith a pUb-fluc-mrfp-ttk triple fusion reporter gene. The latter makes ES visuali
zation possible by FACS and single ce

Series_title: Murine ES Cells: Control vs. Triple-Fusi
on Transfected

Series_type: Genetic modification

Column Header Definitions



Testing Bio.Geo on soft_ex_platform.txt


GEO Type: PLATFORM
GEO Id: Murine 15K long oligo array version 2.0
Platform_coating: polysine

Platform_contributor: Jane,Doe

Platform_contributor: John,A,Smith

Platform_contributor: Hans,van Elton

Platform_contributor: John,Smithers Jr

Platform_contributor: Jie,D,Chen

Platform_distribution: non-commercial

Platform_manufacture_protocol: 1.  Oligos are arrayed in Greiner 384-we
ll flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.

Platform_manufacture_protocol: 2. Resuspend oligos in water to 20 uM an
d rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).

Platform_manufacture_protocol: 3. Allow Genetix plates to dry through p
assive water evaporation in a protected environment (e.g., chemical hood).

Platform_manufacture_protocol: 4. Before printing, add 5 µL of 1X Print
ing Buffer to each well. This can be done the night before a print run is starte
d.

Platform_manufacture_protocol: 5. Seal plates with Corning seals.

Platform_manufacture_protocol: 6. Incubate at 37°C for 30 minutes to ai
d resuspension of DNA.

Platform_manufacture_protocol: 7. Shake plates near maximum rotational 
speed on flat-bed shaker for 1 minute.

Platform_manufacture_protocol: 8. Centrifuge plates at 2000 rpm for 3 m
inutes.

Platform_manufacture_protocol: 9. Remove seals and cover with plate lid
s. Place in appropriate location of plate cassette. This should be done with fir
st plates just before print run is started to minimize evaporation time before p
rinting. For second and third cassettes, wait until 30 minutes before next casse
tte is needed to begin centrifugation.

Platform_manufacture_protocol: 10. Make sure plates rest behind both ho
lding clips in the cassettes. Push plates back into the cassettes as far as they
 will go, putting them in the proper position for the server arm.

Platform_manufacture_protocol: 11. After the print run is completed, al
low plates to dry through passive evaporation in a protected environment.

Platform_manufacture_protocol: 12. For each subsequent preparation of t
hese plates for a print run, add water to the wells instead of sodium phosphate 
buffer. The amount of water should be decreased by 0.25 µL per print run, as thi
s is the amount drawn up by the pin capillary during each dip.

Platform_manufacturer: Un. London microarray facility

Platform_organism: Mus musculus

Platform_support: glass

Platform_technology: spotted oligonucleotide

Platform_title: Murine 15K long oligo array version 2.0

Platform_web_link: http://www.microarray.protocols.html

platform_table_begin: 

platform_table_end: 

Column Header Definitions
    GB_ACC: GenBank accession number of sequence use
    d to design oligonucleotide probe   LINK_PRE:"http://www.ncbi.nlm.nih.gov/entrez
    /query.fcgi?cmd=Search&db=Nucleotide&term="

    Gene_Desc: Gene description

    Gene_Sym: Gene symbols

    ID: 

    SEQUENCE: Probe sequence information

    SPOT_ID: alternative identifier

0: ID	GB_ACC	Gene_Desc	Gene_Sym	SPOT_ID	SEQUENCE	
1: 1	U02079	nuclear factor of activated T-cells, cytoplasmic 2	Nfatc2		ACCTGGATGACGCAGCCACTTCAGAAAGCTGGGTTGGGACAGAAAGGTATATAGAGAGAAAATTTTGGAA	
2: 2	NM_008154	G-protein coupled receptor 3	Gpr3		CTGTACAATGCTCTCACTTACTACTCAGAGACAACGGTAACTCGGACTTATGTGATGCTGGCCTTGGTGT	
3: 3	AK015719	tropomodulin 2	Tmod2		CACCAGGCTCAGTGCCTAGTATCGGCTTCACCTAGTGTGGTTACTCAGGGCACGCAGAGCTACAGAACAC	
4: 4	AK003367	mitochondrial ribosomal protein L15	Mrpl15		CAAGAAGTCTAGAAATTCTGTGCAAGCCTATTCCATTCTTTCTGCGGGGACAACCAATTCCGAAAAGAAT	
5: 5	BC003333	RIKEN cDNA 0610033I05 gene	0610033I05Rik		AGAACTGGGTGGCAGATATCCTAGAGTTTTGACCAACGTTCACAGCACACATATTGATCTTATAGGACCT	
6: 6	NM_008462	killer cell lectin-like receptor, subfamily A, member 2	Klra2		TGAATTGAAGTTCCTTAAATCCCAACTTCAAAGAAACACATACTGGATTTCACTGACACATCATAAAAGC	
7: 7	NM_008029	FMS-like tyrosine kinase 4	Flt4		GAGGTGCTGTGGGATGACCGCCGGGGCATGCGGGTGCCCACTCAACTGTTGCGCGATGCCCTGTACCTGC	
8: 8	NM_054088	adiponutrin	Adpn		GTCTGAGTTCCATTCCAAAGACGAAGTCGTGGATGCCCTGGTGTGTTCCTGCTTCATTCCCCTCTTCTCT	
9: 9	NM_009750	nerve growth factor receptor (TNFRSF16) associated protein 1	Ngfrap1		TACAGCTGAGAAATTGTCTACGCATCCTTATGGGGGAGCTGTCTAACCACCACGATCACCATGATGAATT	
10: 10	AB045323	DNA segment, Chr 8, ERATO Doi 594, expressed	D8Ertd594e		GATTCAGACTCGGGAGGAGCATCCCAACCTCTCCTTGAGGATAAAGGCCTGAGCGATTGCCCTGGGGAGC	
11: 11	AK005789	dynein, cytoplasmic, light chain 2B	Dncl2b		TGCAGAAGGCATTCCAATCCGAACAACCCTGGACAACTCCACAACGGTTCAGTATGCGGGTCTTCTCCAC	
12: 12	NM_010517	insulin-like growth factor binding protein 4	Igfbp4		GGAGAAGCTGGCGCGCTGCCGCCCCCCCGTGGGTTGCGAGGAGTTGGTGCGGGAGCCAGGCTGCGGTTGT	
13: 13	AK010722	RIKEN cDNA 2410075D05 gene	2410075D05Rik		GGAGCATCTGGAGTTCCGCTTACCGGAAATAAAGTCTTTACTATCGGTGATTGGAGGGCAGTTCACTAAC	
14: 14	AK003755	DNA segment, Chr 4, ERATO Doi 421, expressed	D4Ertd421e		AGCAAAGAGATCTCCCTCAGTGTGCCCATAGGTGGCGGTGCGAGCTTGCGGTTATTGGCCAGTGACTTGC	
15: 15	BC003241	cleavage stimulation factor, 3' pre-RNA, subunit 3	Cstf3		AAATTAGAAGAAAATCCATATGACCTTGATGCTTGGAGCATTCTCATTCGAGAGGCACAGAATCAACCTA	
16: 16	AK004937	RIKEN cDNA 1300007O09 gene	1300007O09Rik		CAGACACAAACCCTAGGTTGTATTGTAGACCGGAGTTTAAGCAGGCACTACCTGTCTGTCTTTTCTTCAT	
17: 17	AK004524	unnamed protein product; hypothetical SOCS domain			CGGAGCCCTGCGCGCCCAGAGCCCCCTCCCACCCGCTTCCACCAAGTGCATGGAGCCAACATCCGCATGG	
18: 18	NM_025999	RIKEN cDNA 2610110L04 gene	2610110L04Rik		TGCATTGATAAATGGAGTGATCGACACAGGAACTGCCCCATTTGTCGCCTACAGATGACTGGAGCAAATG	
19: 19				-- CONTROL		
20: 20	NM_023120	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	Gnb1l		ACCGCCTGGTCCCAGATTTGTCCTCCGAGGCACACAGTCGGCTGTGAACACGCTCCATTTCTGCCCACCA	



Testing Bio.Geo on soft_ex_series.txt


GEO Type: SERIES
GEO Id: Bone_marrow_stromal_cells
Series_contributor: Jane,Doe

Series_contributor: John,A,Smith

Series_contributor: Hans,van Elton

Series_contributor: John,Smithers Jr

Series_contributor: Jie,D,Chen

Series_overall_design: We analyzed 2 arrays for HS-5 cell line 
and 2 arrays for HS-27a cell line

Series_pubmed_id: 123456789

Series_sample_id: GSM10001

Series_sample_id: GSM10002

Series_sample_id: GSM10003

Series_sample_id: GSM10004

Series_summary: Two human stromal cell lines, HS-5 and H
S-27a, represent functionally distinct components of the bone marrow microenviro
nment.1,2 HS-27a supports cobblestone area formation by early hematopoietic prog
enitors, whereas HS-5 secretes multiple cytokines that support the proliferation
 of committed progenitors. These cell lines have been distributed to research gr
oups worldwide for use as a tool to understand interactions between hematopoieti
c cells and their microenvironment. We have used DNA microarray technology to ch
aracterize and compare the expression of over 17 000 genes in these cell lines. 
Gene expression differences in cytokines/chemokines, G-protein signaling molecul
es, and multiple extracellular matrix proteins add to the known protein and func
tional characterization of the lines, leading to new insight into the difference
s in their support function for hematopoietic progenitors.

Series_title: Profiling of the functionally distinct h
uman bone marrow stromal cell lines HS-5 and HS-27a.

Series_type: Cell Line Comparison

Series_variable_1: cell line

Series_variable_2: cell line

Series_variable_description_1: HS-5

Series_variable_description_2: HS-27a

Series_variable_sample_list_1: GSM10001, GSM10002

Series_variable_sample_list_2: GSM10003, GSM10004

Column Header Definitions



