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	



