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)

Plants
(464)

Viruses
(0)

Phages
(0)

Unclassified
(120)

All
(6,302)

SAGE NlaIII
(5)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(0)

HT-Seq
(0)

Other
(0)

All
(464)

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
(23)

young aerial structure
(0)

root
(0)

meristem/growing tissue
(12)

flower/sexual organ
(6)

seed/fruit/grain
(0)

pooled
(76)

unclassified
(347)

all
(464)

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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.
81	GSM34786	Ifh1+(2)	6,814	University of Geneva	2004-11-08	[Oligo Array] yeast intergenic array (GPL1695)	RNA	Saccharomyces cerevisiae	unclassified	source_name:W303+IFH1-13myc-TRP1MX6 W303 title:Ifh1+(2) description:Experiment design -Type of experiment: genome wide binding analysis -Experimental factor: genotype (Wild-Type, Fhl1-myc, Ifh1-myc); drug (rapamycin) -Number of hybridization performed in the experiment: 15 (four conditions with three to five biological replicates each) -Reference used for each condition: ChIP from the wild-type strain -Quality control: one dye-swap per condition Samples used, extract preparation and labeling -The origin of the biological sample: o Species: S. cerevisiae o Cell type: (1) W303; (2) W303+IFH1-13myc-TRP1MX6;(3) W303+FHL1-13myc-HIS3MX6. -Growth conditions: log phase (2x107/mL) at 30Ã‚ÂºC in YPD medium; when indicated rapamycin was added at the final concentration of 200 ng/mL. -Cross-linking for 30 min at 30Ã‚ÂºC -Chromatin immunoprecipitation: Dynabeads M280 coupled to sheep anti-mouse IgG or sheep anti-rabbit IgG and mouse monoclonal antibodies against the myc epitope (culture supernatant of 9E10) were used for immunoprecipitation according to standard techniques. -Labeling protocol(s): each IP was blunt-ended, ligated to linker DNA, then subjected to Ligation Mediated (LM)-PCR in the presence of amino-allyl dUTP. Labeling was performed for 1 hour at room temperature in the presence of NHS-ester Cy3 or Cy5 in 0.1 M Sodium Carbonate. The labeling reaction was stopped with 2 M Hydroxylamine and the labeled DNA purified. Hybridization procedures and parameters -Standard protocols were used Measurement data and specifications -Software for scanning: GenePix Pro 4.0 (Axon Instruments, Inc.) -Scanner: GenePix 4000A (Axon Instruments, Inc.) Keywords = Genome-wide binding of Fhl1 and Ifh1
82	GSM34787	Ifh1+(3)	6,814	University of Geneva	2004-11-08	[Oligo Array] yeast intergenic array (GPL1695)	RNA	Saccharomyces cerevisiae	unclassified	source_name:W303+IFH1-13myc-TRP1MX6 W303 title:Ifh1+(3) description:Experiment design -Type of experiment: genome wide binding analysis -Experimental factor: genotype (Wild-Type, Fhl1-myc, Ifh1-myc); drug (rapamycin) -Number of hybridization performed in the experiment: 15 (four conditions with three to five biological replicates each) -Reference used for each condition: ChIP from the wild-type strain -Quality control: one dye-swap per condition Samples used, extract preparation and labeling -The origin of the biological sample: o Species: S. cerevisiae o Cell type: (1) W303; (2) W303+IFH1-13myc-TRP1MX6;(3) W303+FHL1-13myc-HIS3MX6. -Growth conditions: log phase (2x107/mL) at 30Ã‚ÂºC in YPD medium; when indicated rapamycin was added at the final concentration of 200 ng/mL. -Cross-linking for 30 min at 30Ã‚ÂºC -Chromatin immunoprecipitation: Dynabeads M280 coupled to sheep anti-mouse IgG or sheep anti-rabbit IgG and mouse monoclonal antibodies against the myc epitope (culture supernatant of 9E10) were used for immunoprecipitation according to standard techniques. -Labeling protocol(s): each IP was blunt-ended, ligated to linker DNA, then subjected to Ligation Mediated (LM)-PCR in the presence of amino-allyl dUTP. Labeling was performed for 1 hour at room temperature in the presence of NHS-ester Cy3 or Cy5 in 0.1 M Sodium Carbonate. The labeling reaction was stopped with 2 M Hydroxylamine and the labeled DNA purified. Hybridization procedures and parameters -Standard protocols were used Measurement data and specifications -Software for scanning: GenePix Pro 4.0 (Axon Instruments, Inc.) -Scanner: GenePix 4000A (Axon Instruments, Inc.) Keywords = Genome-wide binding of Fhl1 and Ifh1
83	GSM37909	Diamide treated 0.25 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 15 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37718.
84	GSM37910	Diamide treated 0.25 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 15 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37718.
85	GSM37927	Diamide treated 0.50 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 30 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37720.
86	GSM37928	Diamide treated 0.50 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 30 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37720.
87	GSM37942	Diamide treated 1.00 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37721.
88	GSM37948	Diamide treated 1.00 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37721.
89	GSM37949	Diamide treated 3.00 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 3 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37722.
90	GSM37950	Diamide treated 3.00 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 3 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37722.
91	GSM37951	Diamide treated 6.00 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 6 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37723.
92	GSM37952	Diamide treated 6.00 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 6 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37723.
93	GSM37953	H2O2 treated 0.25 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 15 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37724.
94	GSM37954	H2O2 treated 0.25 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 15 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37724.
95	GSM37955	H2O2 treated 0.50 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 30 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37725.
96	GSM37956	H2O2 treated 0.50 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 30 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37725.
97	GSM37957	H2O2 treated 1.00 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37726.
98	GSM37958	H2O2 treated 1.00 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-21	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37726.
99	GSM37959	H2O2 treated 3.00 h sample- 1st print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-22	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 3 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37728.
100	GSM37960	H2O2 treated 3.00 h sample- 2nd print of spots - primary experimental data.	4,352	University of Debrecen	2004-12-22	[cDNA Array] Emericella nidulans EST-based chip primary data (GPL1756)	RNA	Emericella nidulans	pooled	Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 3 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37728.

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