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
(2,851)

Viruses
(0)

Phages
(0)

All
(6,302)

SAGE RsaI
(0)

Oligo Array
(1,212)

Bead Array
(0)

Protein Array
(0)

HT-Seq
(0)

urinary
(13)

adult aerial structure
(0)

young aerial structure
(0)

root
(0)

meristem/growing tissue
(0)

flower/sexual organ
(0)

seed/fruit/grain
(0)

pooled
(190)

unclassified
(153)

all
(1,212)

	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	GSM33957	Bladder	39,309	University of Toronto	2004-10-28	[Oligo Array] Mouse XM microarray set (GPL1537)	RNA	Mus musculus	bladder	Bladder
2	GSM33977	Kidney	39,309	University of Toronto	2004-10-28	[Oligo Array] Mouse XM microarray set (GPL1537)	RNA	Mus musculus	kidney	Kidney
3	GSM37569	Sprague Dawley Control 1	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Reference kidney total RNA Sprague Dawley control kidney total RNA
4	GSM37570	Sprague Dawley Diabetic 2	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Sprague Dawley diabetic kidney total RNA Reference kidney total RNA
5	GSM37571	Sprague Dawley Diabetic 1	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Reference kidney total RNA Sprague Dawley diabetic kidney total RNA
6	GSM37572	Sprague Dawley Control 2	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Sprague Dawley control kidney total RNA Reference kidney total RNA
7	GSM37573	Ren-2 Control 1	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Reference kidney total RNA Ren-2 control kidney total RNA
8	GSM37574	Ren-2 Control 2	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Ren-2 control kidney total RNA Reference kidney total RNA
9	GSM37575	Ren-2 Diabetic 1	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Reference kidney total RNA Ren-2 diabetic kidney total RNA
10	GSM37576	Ren-2 Diabetic 2	23,040	St Vincents Institute	2004-12-14	[Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747)	RNA	Rattus norvegicus	kidney	Ren-2 diabetic kidney total RNA Reference kidney total RNA
11	GSM37454	CD1 strain kidney	21,882	University of Toronto	2004-12-09	[Oligo Array] Agilent Custom Mouse Alternative Splicing Oligo Microarray (GPL1738)	RNA	Mus musculus	kidney	Pooled mouse CD1 strain kidney
12	GSM36124	Six1 target genes in mk4 cells	21,500	Jichi Medical School	2004-11-24	[Oligo Array] Agilent-011472 Mouse Development Oligo Microarray G4120A (Feature Number version) (GPL922)	RNA	Mus musculus	kidney	To identify Six1 target genes, we chose the mK4 cell line that represents later metanephric mesenchyme of the embryonic kidney. The cells were infected with adenovirus vectors (AxCAwt) overexpressing VP16-Six1wt or VP16-Six1W171R and cultured for 24h. Total RNA was extracted using Isogen reagent (Nippon Gene), treated with RNase-free DNase (Roche Diagnostics) and purified with RNeasy Midi Kit (QIAGEN). Poly A+ RNA was selected using Oligotex-dT30 <super> latex beads (TaKaRa). Poly A+ RNA (20 Ã‚Âµg) was reverse transcribed using an oligo(dT) primer in the presence of aminoallyl dUTP without the addition of spike-in controls. Then, single-stranded cDNAs were coupled with Cy3 (AxCAwt VP16-Six1wt infected sample) or Cy5 (AxCAwt VP16-Six1W171R infected sample) dyes, and the labeled probes were purified with QIAquick PCR Purification kit (QIAGEN). Hybridization to the microarray was carried out at 65Ã‚Â°C for 17h according to the manufacturer's instruction. The arrays were washed, dried and scanned using ScanArray 5000 (GSI Lumonics) at two different PMT voltage settings (high and low) to avoid signal saturation. Cy3 and Cy5 intensities for each spot on the array were determined by QuantArray software (Version 3.0.0.0, GSI Lumonics). The raw data thus obtained was processed and the Cy3 to Cy5 ratios were calculated as follows: 1) subtraction of the fluorescence intensity of negative control spots as background from the intensity of each of the Cy3 and Cy5 spots, 2) normalization of the entire data set using the global normalization method, 3) elimination of spots with high background intensity for either dye, and 4) determination of the Cy3 to Cy5 ratios.
13	GSM36125	Six4 target genes in mk4 cells	21,500	Jichi Medical School	2004-11-24	[Oligo Array] Agilent-011472 Mouse Development Oligo Microarray G4120A (Feature Number version) (GPL922)	RNA	Mus musculus	kidney	To identify Six4 target genes, we chose the mK4 cell line that represents later metanephric mesenchyme of the embryonic kidney. The cells were infected with adenovirus vectors (AxCAwt) overexpressing VP16-Six4wt or VP16-Six4W263R and cultured for 24h. Total RNA was extracted using Isogen reagent (Nippon Gene), treated with RNase-free DNase (Roche Diagnostics) and purified with RNeasy Midi Kit (QIAGEN). Poly A+ RNA was selected using Oligotex-dT30 <super> latex beads (TaKaRa). Poly A+ RNA (20 Ã‚Âµg) was reverse transcribed using an oligo(dT) primer in the presence of aminoallyl dUTP without the addition of spike-in controls. Then, single-stranded cDNAs were coupled with Cy3 (AxCAwt VP16-Six4wt infected sample) or Cy5 (AxCAwt VP16-Six4W263R infected sample) dyes, and the labeled probes were purified with QIAquick PCR Purification kit (QIAGEN). Hybridization to the microarray was carried out at 65Ã‚Â°C for 17h according to the manufacturer's instruction. The arrays were washed, dried and scanned using ScanArray 5000 (GSI Lumonics) at two different PMT voltage settings (high and low) to avoid signal saturation. Cy3 and Cy5 intensities for each spot on the array were determined by QuantArray software (Version 3.0.0.0, GSI Lumonics). The raw data thus obtained was processed and the Cy3 to Cy5 ratios were calculated as follows: 1) subtraction of the fluorescence intensity of negative control spots as background from the intensity of each of the Cy3 and Cy5 spots, 2) normalization of the entire data set using the global normalization method, 3) elimination of spots with high background intensity for either dye, and 4) determination of the Cy3 to Cy5 ratios.