Gene Expression Omnibus (GEO) Overview

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DataSet	:	Series(GSE) x Platform(GPL). A set of related gene expression data.
Sample	:	Biological materials.
platform	:	Methods or instruments used for the gene expression profilings.

Human
(4,712)

Bacteria
(313)

Viruses
(0)

Phages
(18)

Unclassified
(320)

All
(8,522)

SAGE NlaIII
(0)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

GeneChip
(174)

Tiling Array
(0)

cDNA Array
(132)

Oligo Array
(5)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(0)

HT-Seq
(0)

Other
(2)

All
(313)

brain
(0)

blood
(0)

connective
(0)

reproductive
(0)

muscular
(0)

digestive
(0)

liver
(0)

lung
(0)

urinary
(0)

endo/exo-crine
(0)

embryo
(0)

adult aerial structure
(0)

young aerial structure
(0)

root
(0)

meristem/growing tissue
(0)

flower/sexual organ
(0)

seed/fruit/grain
(0)

pooled
(0)

unclassified
(313)

all
(313)

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	Sample ID	Title	Number of Data	Institute	Submission date	Platform	Sample type	Species	Organ class	Reasoning of the classification Keywords used for the classification are shown with bold font.
1	GSM48951	WTCy3/Rv2869c Cy5 no Tween #1	10,080	Sloan Kettering Institute for Cancer Research	2005-04-23	[Oligo Array] M. tuberculosis oligo (GPL1983)	RNA	Mycobacterium tuberculosis	unclassified	source_name:Rv2869c mutant Wild Type M. tuberculosis title:WTCy3/Rv2869c Cy5 no Tween #1 description:o All RNA was from the indicated strain of M. tuberculosis (either wild type M. tuberculosis Erdman or the Mtb Rv2869c null mutant Ã¢â‚¬Â¢RNA was isolated from logarithmic phase cultures at OD600 .3. For (+Tween) conditions, the media was Middlebrook 7H9 with 10% OADC supplement, .5% glycerol, and .05% Tween 80. For (-Tween) conditions, bacilli were transferred to identical media without Tween 80 and harvested for RNA preparation 18hours later. Protocol for preparing the hybridization extract: 15ml of liquid culture described above were collected by centrifugation at 3000g, and cell pellets frozen on dry ice. Frozen pellets were resuspended in 1ml of Trizol reagent (Invitrogen) and lysed by mechanical disruption using .7mm Zirconia beads for 3 x 1min in a Mini bead beater 8 (Biospec products) at maximum speed. The remainder of the procedure was according to the Trizol manufacturers instructions with the addition of the optional high salt precipitation step. RNA was subsequently cleaned using Qiagen RNAeasy columns according ot the manufacturers RNA cleanup protocol. Labeling protocol(s). 5-7.5micrograms of total RNA was labeled using the Fairplay microrray labeling kit (Stratagene) with substitution of Random Hexamer primers. Aminoallyl labeled CDNA was coupled to Cy3/Cy5 using Post labeling reactive dye packs (Amersham). Excess dye was removed using Qiaquick nucleotide removal columns according to the manufacturerÃ¢â‚¬â„¢s instructions.
2	GSM49626	1_GLC_FRU	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, glucose L. acidophilus, fructose title:1_GLC_FRU description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
3	GSM49627	2_SUC_GLC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, sucrose L. acidophilus, glucose title:2_SUC_GLC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
4	GSM49628	3_GLC_FOS	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, glucose L. acidophilus, fructooligosaccharide title:3_GLC_FOS description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
5	GSM49629	4_RAF_GLC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, raffinose L. acidophilus, glucose title:4_RAF_GLC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
6	GSM49630	5_GLC_LAC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, glucose L. acidophilus, lactose title:5_GLC_LAC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
7	GSM49631	6_GAL_GLC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, galactose L. acidophilus, glucose title:6_GAL_GLC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
8	GSM49632	7_GLC_TRE	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, glucose L. acidophilus, trehalose title:7_GLC_TRE description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
9	GSM49633	8_FRU_SUC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, fructose L. acidophilus, sucrose title:8_FRU_SUC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
10	GSM49634	9_FOS_FRU	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, fructooligosaccharides L. acidophilus, fructose title:9_FOS_FRU description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
11	GSM49635	10_FRU_RAF	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, fructose L. acidophilus, raffinose title:10_FRU_RAF description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
12	GSM49636	11_LAC_FRU	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, lactose L. acidophilus, fructose title:11_LAC_FRU description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
13	GSM49637	12_FRU_GAL	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, fructose L. acidophilus, galactose title:12_FRU_GAL description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
14	GSM49638	13_TRE_FRU	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, trehalose L. acidophilus, fructose title:13_TRE_FRU description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
15	GSM49639	14_SUC_FOS	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, sucrose L. acidophilus, fructooligosaccharides title:14_SUC_FOS description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
16	GSM49640	15_RAF_SUC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, raffinose L. acidophilus, sucrose title:15_RAF_SUC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
17	GSM49641	16_SUC_LAC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, sucrose L. acidophilus, lactose title:16_SUC_LAC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
18	GSM49642	17_GAL_SUC	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, galactose L. acidophilus, sucrose title:17_GAL_SUC description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
19	GSM49643	18_SUC_TRE	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, sucrose L. acidophilus, trehalose title:18_SUC_TRE description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
20	GSM49644	19_FOS_RAF	5,736	North Carolina State University	2005-04-26	[cDNA Array] Whole Genome Array L. acidophilus NCFM (GPL1401)	RNA	Lactobacillus acidophilus	unclassified	source_name:L. acidophilus, fructooligosaccharides L. acidophilus, raffinose title:19_FOS_RAF description:L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).

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