title: Tup12-GFP ChIP-CHIP ORF/IGR E120D Sl7

description:
Chromatin Immunoprecipitations.
Chromatin immunoprecipitations were essentially performed as described previously (Robyr et al, 2003, Wiren et al, 2005). Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking. The lysate was subjected to sonication 3x60 sec for generation of chromatin fragments with appropriate length. The lysate from the two sonications was pooled, aliquoted and subjected to immunoprecipiation with a polyclonal a-GFP antibody 1:100 (Applied Biosciences 8372-2) and protein A sepharose beads (Amersham 17-5280-01). Chromatin bound beads were washed and eluated fromm beads. DNA was purified with phenol-chloroform extraction and ethanol-sodium acetate precipitation. Precipitated chromatin and input DNA fragments from three individually separated experiments were subjected to a two step linear amplification. Round A was performed with Sequenase (USB 70775Y) and TPCRA priming. Round B was performed with Amplitaq (Roche) with TPCRB priming. Amplified material (500-1000ng) was subjected to Klenow labelling (Invitrogen 18094-011) with Cy3 and Cy5 (Amersham 53021 and 55021). Generally the input fragments was labelled with Cy3 and precipitated material was labelled with Cy5. Reportedly minimal dye swap bias has previously been observed (Robyr et al, 2003) and labelling was therefore not carried out in dye swap. Labelled fragments were hybridized to IGR+ORF microarrays from Eurogentech SA, Seraing, Belgium. Microarray signals were visualized with ScanExpress laser scanner and quantified with the TIGR spotfinder quantification software. Data was analysed and median normalized to the 50th percentile with the GeneSpring software (Silicon Genetics) to generate six data points for each binding map. Flag values were subtracted from the data set and ratios were subjected to median percentile ranking analysis described (Buck et al, 2004). Cutoff values for the generation of binding lists were set to the 85th percentile.

data_processing: Genespring Silicon Genetics

source_name: Tup12-GFP Chromatin Input

tag: Tup12-GFP Input. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and subjected to crosslinking, sonication, extraction, amplification,labelling,hybridization,washing. scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)

source_name: Tup12-GFP Chromatin Immunoprecipitation

tag: Tup12-GFP Chromatin Immunoprecipitation. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking, sonication, precipitation, extraction, amplification, labelling,hybridization,washing scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)


title: L4_vs_L1

status: Public on Nov 23 2006

type: RNA

city: Minamidai, Kawagoe

first: Toshiro

last: Saito

state: Saitama

department: Life Science Group

country: Japan

institute: Hitachi, Ltd.

description: Sample Tissue: peripheral blood

data_processing: Global Normalization and Lowess

molecule: total RNA

organism: Homo sapiens

tag: 1.5 h after watching comic video

tag: before watching comic video


title: L5_vs_L1

description: Sample Tissue: peripheral blood

tag: 4 h after watching comic video


title: C4_vs_C1

description: Sample Tissue: peripheral blood

tag: 1.5 h after spending tedious time

tag: before spending tedious time


title: Ssn6-GFP ChIP ORF/IGR E120D Sl2

status: Public on Nov 15 2006

type: genomic

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: Chromatin immunoprecipitations were essentially performed as described previously (Robyr et al, 2003, Wiren et al, 2005). Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking. The lysate was subjected to sonication 3x60 sec for generation of chromatin fragments with appropriate length. The lysate from the two sonications was pooled, aliquoted and subjected to immunoprecipiation with a polyclonal a-GFP antibody 1:100 (Applied Biosciences 8372-2) and protein A sepharose beads (Amersham 17-5280-01). Chromatin bound beads were washed and eluated fromm beads. DNA was purified with phenol-chloroform extraction and ethanol-sodium acetate precipitation. Precipitated chromatin and input DNA fragments from three individually separated experiments were subjected to a two step linear amplification. Round A was performed with Sequenase (USB 70775Y) and TPCRA priming. Round B was performed with Amplitaq (Roche) with TPCRB priming. Amplified material (500-1000ng) was subjected to Klenow labelling (Invitrogen 18094-011) with Cy3 and Cy5 (Amersham 53021 and 55021). Generally the input fragments was labelled with Cy3 and precipitated material was labelled with Cy5. Reportedly minimal dye swap bias has previously been observed (Robyr et al, 2003) and labelling was therefore not carried out in dye swap. Labelled fragments were hybridized to IGR+ORF microarrays from Eurogentech SA, Seraing, Belgium. Microarray signals were visualized with ScanExpress laser scanner and quantified with the TIGR spotfinder quantification software. Data was analysed and median normalized to the 50th percentile with the GeneSpring software (Silicon Genetics) to generate six data points for each binding map. Flag values were subtracted from the data set and ratios were subjected to median percentile ranking analysis described (Buck et al, 2004). Cutoff values for the generation of binding lists were set to the 85th percentile.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Ssn6-GFP Chromatin input

tag: Ssn6-GFP Input. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and subjected to crosslinking, sonication, extraction, amplification,labelling,hybridization,washing. scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)

source_name: Ssn6-GFP Chromatin Immunoprecipitation

tag: Ssn6-GFP Chromatin Immunoprecipitation. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking, sonication, precipitation, extraction, amplification, labelling,hybridization,washing scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)


title: Tup11-GFP ChIP-CHIP ORF/IGR E120D Sl6

source_name: Tup11-GFP Chromatin Input

tag: Tup11-GFP Input. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and subjected to crosslinking, sonication, extraction, amplification,labelling,hybridization,washing. scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)

source_name: Tup11-GFP Chromatin Immunoprecipitation

tag: Tup11-GFP Chromatin Immunoprecipitation. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking, sonication, precipitation, extraction, amplification, labelling,hybridization,washing scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)


title: C5_vs_C1

description: Sample Tissue: peripheral blood

tag: 4 h after spending tedious time


title: Tup11-GFP ChIP-CHIP ORF/IGR F060D Sl1


title: C-3

status: Public on Dec 31 2006

city: Chapel Hill

first: Monte

middle: S

last: Willis

state: NC

address: 103 Mason Farm Road

department: Pathology & Laboratory Medicine

country: USA

institute: UNC

description: MEC cell line

data_processing: quantile normalization of raw intensities, and log2 transformed ratios

organism: Mus musculus

source_name: MEC cell line (control)

extract_protocol: Agilent

tag: MEC cell line

source_name: Universal mouse reference RNA

tag: Universal mouse reference RNA


title: Ssn6 Overexpression L040B sl7

description: We have performed a genome wide expression profile study of the essential transcriptional co-repressor protein Ssn6 in Schizosaccharomyces pombe. Ssn6 affected targets were identified by over expression of Ssn6 protein in a WT strain. A WT strain holding a plasmid expressing Ssn6 (pDUAL-Ssn6) was compared against the expression in a WT with the empty plasmid (pDUAL-EMPTY) strain under selection for the plasmids MM-URA media at 30 degrees (Xue et al, 2004).

hyb_protocol: Xue et al, 2004

scan_protocol: Scanexpress Laser scanner TIGR spotfinder Quantification

data_processing: Genespring Silicon Genetics Software

label_protocol: Xue et al, 2004

growth_protocol: Xue et al, 2004

extract_protocol: Xue et al, 2004

treatment_protocol: Xue et al, 2004

tag: WT(FY367)-pDUAL-Ssn6 MM -URA 30 Deg

source_name: WT-pDUAL-empty

tag: WT(FY367)-pDUAL-Empty MM-URA 30 Deg


title: Tup12-GFP ChIP-CHIP ORF/IGR E120D Sl8


title: Tup11,12D/WT J290Dsl19

description: Gene expression profiling experiment with Tup11,12D/WT J290D sl19

scan_protocol: Scanexpress Laser scanner

data_processing: Genespring software Silicon Genetics

source_name: WT J290Dsl19

tag: WT YES 30 Deg

tag: Tup11,12D YES 30 Deg


title: FRT/TSHR-basal-rep1

status: Public on Oct 01 2006

city: Cusano Milanino

first: Davide

last: Calebiro

address: via Zucchi 18

country: Italy

institute: Istituto Auxologico Italiano

description: de-differentiated rat thyrocytes

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: data were quantile normalized and processed using the Robust Microarray Analysis (RMA) algorithm, available at http://www.bioconductor.org, under R statistical environment (Irizarry et al, 2003).

label: biotin

organism: Rattus norvegicus

source_name: FRT/TSHR cells, basal

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets, using the BioArray high yield RNA transcript labeling kit (Enzo Diagnostic).

growth_protocol: Cells were grown in Coon’s modified Ham’s F12 medium. Twelve hours before bTSH stimulation, cells were starved in serum-free medium

extract_protocol: total RNA samples were isolated using Trizol reagent (Invitrogen) and purified on RNeasy spin columns (Quiagen). Double-stranded cDNA was synthesized from 10 mcg RNA using Superscript Double Stranded cDNA synthesis kit (Invitrogen), phenol/chloroform extracted and ethanol precipitated.

treatment_protocol: No treatment

tag: Fisher Rat Thyroid Cell line (FRT/TSHR), early passage


title: Tup12-GFP ChIP-CHIP ORF/IGR E120D Sl9

tag: Tup12-GFP Input. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and subjected to crosslinking, sonication, extraction, amplification,labelling,hybridization,washing. scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)

tag: Tup12-GFP Chromatin Immunoprecipitation. Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking, sonication, precipitation, extraction, amplification, labelling,hybridization,washing scanning,quantification,normalisation and analysis as described previously (Robyr et al, 2003 and Wiren et al, 2005)


title: Tup11-GFP ChIP-CHIP ORF/IGR E120D Sl5


title: Ssn6-GFP ChIP ORF/IGR E120D Sl10

source_name: Ssn6 Chromatin Input


title: FRT/TSHR-basal-rep2

description: de-differentiated rat thyrocytes


title: FRT/TSHR-30min-rep3

description: de-differentiated rat thyrocytes stimulated with TSH

source_name: FRT/TSHR cells, 30 min TSH-stimulated

treatment_protocol: Cells were stimulated with 1 U/L bovine TSH


title: FRTL5-17hrs-rep2

description: differentiated rat thyrocytes stimulated with TSH

source_name: FRTL5 cells, 17 hrs TSH-stimulated

growth_protocol: Cells were grown in TSH-free medium (5H) for 5 days. Twelve hours before bTSH stimulation, cells were starved in serum-free medium

treatment_protocol: Cells were stimulated with 0.1 U/L bovine TSH


title: Tup11,12D/WT J290Dsl18

description: Gene expression profiling experiment with Tup11,12D/WT J290D sl18

source_name: Tup11,12D YES 30 Deg

source_name: WT


title: FRT/TSHR-17hrs-rep1

source_name: FRT/TSHR cells, 17 hrs TSH-stimulated


title: FRT/TSHR-30min-rep2


title: Tiling ChIP-CHIP Tup12-GFP

description: For the GeneChip® S. pombe Tiling Array from Affymetrix the DNA was amplified to obtain 5 micrograms of DNA then fragmented around 100 base pairs using DNAse I, labelled with biotin and hybridized according to Affymetrix recommendations (Lengronne et al., 2004). Antibodies specific for GFP (Applied Biosciences 8372-2) for each IP.

data_processing: ChIP-chip Affymetrix signals per chip normalized to the 50th percentile

label: Biotin

tag: CHIP IP using Anti GFP antibody


title: FRT/TSHR-17hrs-rep3


title: Tiling ChIP-CHIP Ssn6-GFP


title: FRTL5-30min-rep1

source_name: FRTL5 cells, 30 min TSH-stimulated

tag: Fisher Rat Thyroid Cell line (FRTL5), early passage


title: FRT/TSHR-30min-rep1


title: Ssn6-GFP ChIP ORF/IGR E120D Sl1

source_name: Ssn6-GFP Chromatin Input


title: FRTL5-basal-rep2

description: differentiated rat thyrocytes

source_name: FRTL5 cells, basal


title: FRTL5-30min-rep2


title: FRT/TSHR-17hrs-rep2


title: AKR/J Olfactory Bulb D1

status: Public on Sep 12 2006

first: Jessica

last: Nadler

address: 103 Mason Farm Rd.

department: Genetics

institute: University of North Carolina

description: 3x3 Pooling Strategy.  See Nadler et al., 2006

hyb_protocol: Agilent Hybridization Solution 3 Protocol

scan_protocol: Agilent Scanner

data_processing: Lowess normalization (SMA) followed by scale normalization

source_name: AKR/J Olfactory Bulb Pool D1

label_protocol: Agilent Direct Label

extract_protocol: Trizol Reagent

tag: AKR/J (3 animals)

tag: Male

tag: 4-5 weeks

tag: Olfactory Bulb

tag: Pool D

source_name: Stratagene UMRR

tag: Stratagene UMRR


title: FRT/TSHR-basal-rep3

description: de-differentiated rat thyrocytes


title: FRTL5-17hrs-rep3


title: FVB/NJ Olfactory Bulb C

description: 3x3 pooling strategy.  See Nadler et al, 2006

source_name: FVB/NJ Olfactory Bulb Pool C

tag: FVB/NJ (3 animals)

tag: Pool C


title: Tiling ChIP-CHIP Tup11-GFP


title: BTBR T+ tf/tf Cingulate Cortex C

source_name: BTBR T+ tf/tf Cingulate Cortex Pool C

tag: BTBR T+ tf/tf J (3 animals)

tag: Cingulate Cortex


title: DBA/2J Amygdala D

source_name: DBA/2J Amygdala Pool D

tag: DBA/2J (3 animals)

tag: Amygdala


title: BTBR T+ tf/tf Olfactory Bulb C

source_name: BTBR T+ tf/tf Olfactory Bulb Pool C


title: FRTL5-basal-rep3

description: differentiated rat thyrocytes


title: FVB/NJ Amygdala D

source_name: FVB/NJ Amygdala Pool D


title: BTBR T+ tf/tf Basal Ganglia B

source_name: BTBR T+ tf/tf Basal Ganglia Pool B

tag: Basal Ganglia

tag: Pool B


title: C57BL/6J Basal Ganglia E

source_name: C57BL/6J Basal Ganglia Pool E

tag: C57BL/6J (3 animals)

tag: Pool E


title: BTBR T+ tf/tf Basal Ganglia C

source_name: BTBR T+ tf/tf Basal Ganglia Pool C


title: C3H/HeJ Amygdala D

source_name: C3H/HeJ Amygdala Pool D

tag: C3H/HeJ (3 animals)


title: BTBR T+ tf/tf Hippocampus C

source_name: BTBR T+ tf/tf Hippocampus Pool C

tag: Hippocampus


title: FRTL5-17hrs-rep1

source_name: FRTL5 cells, 17 hrs TSH-stimulated

tag: Fisher Rat Thyroid Cell line (FRT/TSHR), early passage


title: BTBR T+ tf/tf Frontal Cortex B

source_name: BTBR T+ tf/tf Frontal Cortex Pool B

tag: Male

tag: 4-5 weeks

tag: Frontal Cortex


title: BTBR T+ tf/tf Frontal Cortex C

source_name: BTBR T+ tf/tf Frontal Cortex Pool C

tag: Stratagene UMRR


title: C57BL/6J Amygdala E

source_name: C57BL/6J Amygdala Pool E


title: C57L/J Amygdala D

source_name: C57L/J Amygdala Pool D

tag: C57L/J (3 animals)

tag: Pool D


title: BTBR T+ tf/tf Cerebellum C

source_name: BTBR T+ tf/tf Cerebellum Pool C

tag: BTBR T+ tf/tf J (3 animals)

tag: Cerebellum

tag: Pool C


title: FVB/NJ Cingulate Cortex B

description: 3x3 pooling strategy, see Nadler et al., 2006

source_name: FVB/NJ Cingulate Cortex Pool B

tag: FVB/NJ (3 animals)

tag: Cingulate Cortex

source_name: Stratagene UMRR


title: BTBR T+ tf/tf Amygdala C

source_name: BTBR T+ tf/tf Amygdala Pool C

tag: Amygdala


title: BALB/cByJ Cerebellum B

source_name: BALB/cByJ Cerebellum Pool B

tag: BALB/cByJ (3 animals)

tag: Pool B


title: BALB/cByJ Cingulate Cortex B

source_name: BALB/cByJ Cingulate Cortex Pool B

extract_protocol:
Trizol Reagent
RNeasy Cleanup


title: FRTL5-basal-rep1

description: differentiated rat thyrocytes

source_name: FRTL5 cells, basal

tag: Fisher Rat Thyroid Cell line (FRTL5), early passage


title: BTBR T+ tf/tf Cingulate Cortex B

source_name: BTBR T+ tf/tf Cingulate Cortex Pool B


title: BTBR T+ tf/tf Olfactory Bulb A

source_name: BTBR T+ tf/tf Olfactory Bulb Pool A

tag: Olfactory Bulb

tag: Pool A


title: BALB/cByJ Olfactory Bulb C

source_name: BALB/cByJ Olfactory Bulb Pool C

tag: Male


title: BTBR T+ tf/tf Amygdala B

source_name: BTBR T+ tf/tf Amygdala Pool B

tag: 4-5 weeks


title: BTBR T+ tf/tf Hippocampus B

source_name: BTBR T+ tf/tf Hippocampus Pool B

tag: Hippocampus


title: BALB/cByJ Amygdala B

source_name: BALB/cByJ Amygdala Pool B

tag: Stratagene UMRR


title: BALB/cByJ Olfactory Bulb B

source_name: BALB/cByJ Olfactory Bulb Pool B


title: BALB/cByJ Hippocampus B

source_name: BALB/cByJ Hippocampus Pool B


title: BTBR T+ tf/tf Amygdala A

source_name: BTBR T+ tf/tf Amygdala Pool A


title: BALB/cByJ Olfactory Bulb A

source_name: BALB/cByJ Olfactory Bulb Pool A


title: BALB/cByJ Frontal Cortex B

source_name: BALB/cByJ Frontal Cortex Pool B

tag: Frontal Cortex


title: BTBR T+ tf/tf Olfactory Bulb B

source_name: BTBR T+ tf/tf Olfactory Bulb Pool B


title: BTBR T+ tf/tf Hippocampus A

source_name: BTBR T+ tf/tf Hippocampus Pool A

source_name: Stratagene UMRR


title: C57L/J Cerebellum C

source_name: C57L/J Cerebellum Pool C

tag: C57L/J (3 animals)


title: BALB/cByJ Basal Ganglia B

source_name: BALB/cByJ Basal Ganglia Pool B

tag: Basal Ganglia


title: BTBR T+ tf/tf Frontal Cortex A

source_name: BTBR T+ tf/tf Frontal Cortex Pool A

tag: BTBR T+ tf/tf J (3 animals)


title: BALB/cByJ Cerebellum A

source_name: BALB/cByJ Cerebellum Pool A

tag: Cerebellum


title: BTBR T+ tf/tf Basal Ganglia A

source_name: BTBR T+ tf/tf Basal Ganglia Pool A


title: BTBR T+ tf/tf Cerebellum A

source_name: BTBR T+ tf/tf Cerebellum Pool A


title: C57L/J Hippocampus C

source_name: C57L/J Hippocampus Pool C

tag: Pool C


title: BTBR T+ tf/tf Cingulate Cortex A

source_name: BTBR T+ tf/tf Cingulate Cortex Pool A

tag: Cingulate Cortex


title: C57L/J Frontal Cortex C

source_name: C57L/J Frontal Cortex Pool C


title: C57L/J Basal Ganglia C

source_name: C57L/J Basal Ganglia Pool C


title: C57L/J Amygdala C

source_name: C57L/J Amygdala Pool C

tag: Amygdala


title: BALB/cByJ Hippocampus C

source_name: BALB/cByJ Hippocampus Pool C

tag: BALB/cByJ (3 animals)


title: BALB/cByJ Cingulate Cortex A

source_name: BALB/cByJ Cingulate Cortex Pool A


title: BALB/cByJ Basal Ganglia A

source_name: BALB/cByJ Basal Ganglia Pool A


title: BALB/cByJ Amygdala A

source_name: BALB/cByJ Amygdala Pool A


title: BALB/cByJ Frontal Cortex C

source_name: BALB/cByJ Frontal Cortex Pool C


title: BTBR T+ tf/tf Cerebellum B

source_name: BTBR T+ tf/tf Cerebellum Pool B

tag: Pool B

source_name: Stratagene UMRR


title: C57BL/6J Frontal Cortex D

source_name: C57BL/6J Frontal Cortex Pool D

tag: C57BL/6J (3 animals)

tag: Pool D


title: BALB/cByJ Cerebellum C

source_name: BALB/cByJ Cerebellum Pool C


title: BALB/cByJ Amygdala C

source_name: BALB/cByJ Amygdala Pool C


title: DBA/2J Amygdala B

source_name: DBA/2J Amygdala Pool B

tag: DBA/2J (3 animals)


title: BALB/cByJ Cingulate Cortex C

source_name: BALB/cByJ Cingulate Cortex Pool C

tag: Male


title: C57L/J Cerebellum B

source_name: C57L/J Cerebellum Pool B

tag: 4-5 weeks


title: BALB/cByJ Basal Ganglia C

source_name: BALB/cByJ Basal Ganglia Pool C


title: BALB/cByJ Hippocampus A

source_name: BALB/cByJ Hippocampus Pool A

tag: Hippocampus

tag: Pool A


title: C57L/J Cingulate Cortex B

source_name: C57L/J Cingulate Cortex Pool B

tag: Stratagene UMRR


title: AKR/J Amygdala D

source_name: AKR/J Amygdala Pool D

tag: AKR/J (3 animals)


title: 129/SvImJ Amygdala A

source_name: 129/ SvImJ Amygdala Pool A

tag: 129/SvImJ (3 animals)


title: C57BL/6J Hippocampus D

source_name: C57BL/6J Hippocampus Pool D


title: C3H/HeJ Amygdala E

source_name: C3H/HeJ Amygdala Pool E

tag: C3H/HeJ (3 animals)

tag: Pool E


title: BALB/cByJ Frontal Cortex A

source_name: BALB/cByJ Frontal Cortex Pool A

tag: Frontal Cortex


title: FVB/NJ Cingulate Cortex A

source_name: FVB/NJ Cingulate Cortex Pool A

tag: FVB/NJ (3 animals)

tag: Cingulate Cortex


title: C57BL/6J Amygdala D

source_name: C57BL/6J Amygdala Pool D

tag: Amygdala


title: C57L/J Hippocampus B

source_name: C57L/J Hippocampus Pool B

tag: C57L/J (3 animals)

tag: Pool B

source_name: Stratagene UMRR


title: C3H/HeJ Basal Ganglia B

source_name: C3H/HeJ Basal Ganglia Pool B

tag: Basal Ganglia


title: C57L/J Basal Ganglia B

source_name: C57L/J Basal Ganglia Pool B


title: C57L/J Olfactory Bulb C

source_name: C57L/J Olfactory Bulb Pool C

tag: Olfactory Bulb

tag: Pool C


title: A/J Amygdala E

source_name: A/J Amygdala Pool E

tag: A/J (3 animals)

tag: Male

tag: 4-5 weeks


title: C57BL/6J Cerebellum D

source_name: C57BL/6J Cerebellum Pool D

tag: C57BL/6J (3 animals)

tag: Cerebellum

tag: Pool D

tag: Stratagene UMRR


title: C57L/J Frontal Cortex B

source_name: C57L/J Frontal Cortex Pool B


title: C57L/J Cingulate Cortex C

source_name: C57L/J Cingulate Cortex Pool C


title: C57BL/6J Cingulate Cortex D

source_name: C57BL/6J Cingulate Cortex Pool D


title: C57BL/6J Basal Ganglia D

source_name: C57BL/6J Basal Ganglia Pool D


title: C57L/J Olfactory Bulb B

source_name: C57L/J Olfactory Bulb Pool B


title: DBA/2J Cingulate Cortex A

source_name: DBA/2J Cingulate Cortex Pool A

tag: DBA/2J (3 animals)

tag: Pool A


title: C3H/HeJ Basal Ganglia C

source_name: C3H/HeJ Basal Ganglia Pool C

tag: C3H/HeJ (3 animals)


title: AKR/J Cingulate Cortex E

source_name: AKR/J Cingulate Cortex Pool E

tag: AKR/J (3 animals)

tag: Cingulate Cortex

tag: Pool E


title: C57BL/6J Amygdala C

source_name: C57BL/6J Amygdala Pool C

tag: Amygdala


title: FVB/NJ Olfactory Bulb A

source_name: FVB/NJ Olfactory Bulb Pool A

tag: FVB/NJ (3 animals)


title: FVB/NJ Hippocampus C

source_name: FVB/NJ Hippocampus Pool C

tag: Hippocampus


title: FVB/NJ Cingulate Cortex C

source_name: FVB/NJ Cingulate Cortex Pool C

tag: Pool C

source_name: Stratagene UMRR


title: 129/SvImJ Olfactory Bulb B

source_name: 129/SvImJ Olfactory Bulb Pool B

tag: 129/SvImJ (3 animals)

tag: Olfactory Bulb

tag: Pool B


title: AKR/J Basal Ganglia A

source_name: AKR/J Basal Ganglia Pool A

tag: Male

tag: 4-5 weeks

tag: Basal Ganglia


title: FVB/NJ Frontal Cortex C

source_name: FVB/NJ Frontal Cortex Pool C

tag: Frontal Cortex

tag: Stratagene UMRR


title: C57BL/6J Olfactory Bulb C

source_name: C57BL/6J Olfactory Bulb Pool C

tag: C57BL/6J (3 animals)


title: C57L/J Cingulate Cortex A

source_name: C57L/J Cingulate Cortex Pool A

tag: C57L/J (3 animals)

tag: Pool A


title: C57L/J Amygdala A

source_name: C57L/J Amygdala Pool A


title: FVB/NJ Basal Ganglia C

source_name: FVB/NJ Basal Ganglia Pool C


title: C57L/J Hippocampus A

source_name: C57L/J Hippocampus Pool A


title: C57L/J Cerebellum A

source_name: C57L/J Cerebellum Pool A

tag: Cerebellum


title: FVB/NJ Cerebellum C

source_name: FVB/NJ Cerebellum Pool C


title: C57L/J Frontal Cortex A

source_name: C57L/J Frontal Cortex Pool A


title: FVB/NJ Hippocampus A

source_name: FVB/NJ Hippocampus Pool A


title: FVB/NJ Amygdala A

source_name: FVB/NJ Amygdala Pool A


title: C3H/HeJ Olfactory Bulb E

source_name: C3H/HeJ Olfactory Bulb Pool E

tag: C3H/HeJ (3 animals)

tag: Pool E


title: C3H/HeJ Cingulate Cortex E

source_name: C3H/HeJ Cingulate Cortex Pool E

tag: Cingulate Cortex


title: C57L/J Basal Ganglia A

source_name: C57L/J Basal Ganglia A


title: C57BL/6J Frontal Cortex C2

source_name: C57BL/6J Frontal Cortex Pool C2

tag: Pool C2

source_name: Stratagene UMRR


title: C57L/J Olfactory Bulb A

source_name: C57L/J Olfactory Bulb Pool A


title: AKR/J Amygdala E

source_name: AKR/J Amygdala Pool E

tag: AKR/J (3 animals)

tag: Amygdala


title: FVB/NJ Amygdala C

source_name: FVB/NJ Amygdala Pool C

tag: FVB/NJ (3 animals)

tag: Pool C


title: A/J Amygdala D

source_name: A/J Amygdala Pool D

tag: A/J (3 animals)

tag: Male

tag: Pool D


title: C3H/HeJ Frontal Cortex E

source_name: C3H/HeJ Frontal Cortex Pool E

tag: 4-5 weeks

tag: Frontal Cortex


title: DBA/2J Amygdala A

source_name: DBA/2J Amygdala Pool A

tag: DBA/2J (3 animals)

tag: Stratagene UMRR


title: C3H/HeJ Hippocampus E

source_name: C3H/HeJ Hippocampus Pool E

tag: Hippocampus


title: 129/SvImJ Basal Ganglia C

source_name: 129/ SvImJ Basal Ganglia Pool C

tag: 129/SvImJ (3 animals)

tag: Basal Ganglia


title: 129/SvImJ Cingulate Cortex B

source_name: 129/SvImJ Cingulate Cortex Pool B

tag: Pool B


title: 129/SvImJ Amygdala C

source_name: 129/ SvImJ Amygdala Pool C


title: 129/SvImJ Cerebellum C

source_name: 129/ SvImJ Cerebellum Pool C

tag: Cerebellum


title: 129/SvImJ Frontal Cortex B

source_name: 129/ SvImJ Frontal Cortex Pool B


title: 129/SvImJ Hippocampus B

source_name: 129/ SvImJ Hippocampus Pool B


title: C3H/HeJ Amygdala F

source_name: C3H/HeJ Amygdala Pool F

tag: C3H/HeJ (3 animals)

tag: Pool F


title: FVB/NJ Frontal Cortex A

source_name: FVB/NJ Frontal Cortex Pool A

tag: Pool A


title: 129/SvImJ Olfactory Bulb A

source_name: 129/ SvImJ Olfactory Bulb Pool A

tag: Olfactory Bulb


title: 129/SvImJ Cerebellum B

source_name: 129/ SvImJ Cerebellum Pool B

source_name: Stratagene UMRR


title: 129/SvImJ Amygdala B

source_name: 129/ SvImJ Amygdala Pool B

tag: Amygdala


title: AKR/J Olfactory Bulb F

source_name: AKR/J Olfactory Bulb Pool F

tag: AKR/J (3 animals)


title: 129/SvImJ Basal Ganglia B

source_name: 129/ SvImJ Basal Ganglia Pool B

tag: Male


title: AKR/J Cingulate Cortex F

source_name: AKR/J Cingulate Cortex Pool F

tag: Cingulate Cortex


title: 129/SvImJ Hippocampus C

source_name: 129/ SvImJ Hippocampus Pool C

tag: 4-5 weeks

tag: Pool C


title: AKR/J Basal Ganglia F

source_name: AKR/J Basal Ganglia Pool F


title: 129/SvImJ Cingulate Cortex A

source_name: 129/ SvImJ Cingulate Cortex Pool A


title: 129/SvImJ Hippocampus A

source_name: 129/ SvImJ Hippocampus Pool A


title: AKR/J Cingulate Cortex D

source_name: AKR/J Cingulate Cortex Pool D

tag: Pool D


title: AKR/J Frontal Cortex F

source_name: AKR/J Frontal Cortex Pool F

tag: Frontal Cortex

tag: Stratagene UMRR


title: 129/SvImJ Cerebellum A

source_name: 129/ SvImJ Cerebellum Pool A

tag: 129/SvImJ (3 animals)


title: 129/SvImJ Basal Ganglia A

source_name: 129/ SvImJ Basal Ganglia Pool A

tag: Basal Ganglia


title: 129/SvImJ Frontal Cortex A

source_name: 129/ SvImJ Frontal Cortex Pool A


title: 129/SvImJ Cingulate Cortex C

source_name: 129/ SvImJ Cingulate Cortex Pool C


title: FVB/NJ Cerebellum A

source_name: FVB/NJ Cerebellum Pool A

tag: FVB/NJ (3 animals)


title: FVB/NJ Basal Ganglia A

source_name: FVB/NJ Basal Ganglia Pool A

tag: Pool B


title: A/J Frontal Cortex F

source_name: A/J Frontal Cortex Pool F

tag: A/J (3 animals)

source_name: Stratagene UMRR


title: AKR/J Amygdala F

source_name: AKR/J Amygdala Pool F

tag: Pool F


title: C57BL/6J Frontal Cortex B

source_name: C57BL/6J Frontal Cortex Pool B

tag: C57BL/6J (3 animals)


title: C57BL/6J Olfactory Bulb B

source_name: C57BL/6J Olfactory Bulb Pool B

tag: Olfactory Bulb


title: A/J Cingulate Cortex F

source_name: A/J Cingulate Cortex Pool F


title: A/J Basal Ganglia E

hyb_protocol: Agilen Hybridization Solution 3 Protocol

source_name: A/J Basal Ganglia Pool E

tag: Pool E


title: C3H/HeJ Olfactory Bulb F

source_name: C3H/HeJ Olfactory Bulb Pool F

tag: C3H/HeJ (3 animals)


title: A/J Cerebellum E

source_name: A/J Cerebellum Pool E

tag: Male

tag: Cerebellum


title: C57BL/6J Cingulate Cortex B

source_name: C57BL/6J Cingulate Cortex Pool B

tag: 4-5 weeks

tag: Cingulate Cortex


title: AKR/J Basal Ganglia E

hyb_protocol: Agilent Hybridization Solution 3

source_name: AKR/J Basal Ganglia Pool E

tag: AKR/J (3 animals)


title: C3H/HeJ Cingulate Cortex F

source_name: C3H/HeJ Cingulate Cortex Pool F

tag: Stratageme UMRR


title: AKR/J Olfactory Bulb E

source_name: AKR/J Olfactory Bulb Pool E

tag: Stratagene UMRR


title: AKR/J Olfactory Bulb D

source_name: AKR/J Olfactory Bulb Pool D

tag: Pool D


title: AKR/J Frontal Cortex E

source_name: AKR/J Frontal Cortex Pool E

tag: Frontal Cortex


title: A/J Frontal Cortex E

source_name: A/J Frontal Cortex Pool E


title: C3H/HeJ Cerebellum D

source_name: C3H/HeJ Cerebellum Pool D


title: A/J Olfactory Bulb F

source_name: A/J Olfactory Bulb Pool F


title: A/J Hippocampus E

source_name: A/J Hippocampus Pool E

tag: Hippocampus

source_name: Stratagene UMRR


title: A/J Olfactory Bulb E

source_name: A/J Olfactory Bulb Pool E


title: C3H/HeJ Basal Ganglia F

source_name: C3H/HeJ Basal Ganglia Pool F

tag: Basal Ganglia


title: A/J Olfactory Bulb D

source_name: A/J Olfactory Bulb Pool D

tag: A/J (3 animals)


title: A/J Hippocampus D

source_name: A/J Hippocampus Pool D


title: C3H/HeJ Cerebellum F

source_name: C3H/HeJ Cerebellum Pool F

tag: Pool F


title: A/J Cingulate Cortex D

source_name: A/J Cingulate Cortex Pool D


title: C3H/HeJ Frontal Cortex F

source_name: C3H/HeJ Frontal Cortex Pool F


title: 129/SvImJ Olfactory Bulb C

source_name: 129/ SvImJ Olfactory Bulb Pool C

tag: 129/SvImJ (3 animals)

tag: Pool C


title: A/J Frontal Cortex D

source_name: A/J Frontal Cortex Pool D


title: A/J Cerebellum D

source_name: A/J Cerebellum Pool D


title: male MhmBN chip 26

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

description: pooled RNA of the kidney of 36 day old rats

data_processing: SAS Microarray Solution 1.0

source_name: male MhmBN

label_protocol: Approximately 15 µg of pooled total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: total RNA were isolated from the left kidney of 54 rats at the age of 36 days, using the Trizol-reganet from Invitrogen.

tag: kidney


title: FVB/NJ Hippocampus B

source_name: FVB/NJ Hippocampus Pool B

tag: FVB/NJ (3 animals)

tag: Pool B


title: C57BL/6J Hippocampus B

source_name: C57BL/6J Hippocampus Pool B

tag: C57BL/6J (3 animals)

tag: Male


title: FVB/NJ Frontal Cortex B

source_name: FVB/NJ Frontal Cortex Pool B

tag: 4-5 weeks


title: FVB/NJ Olfactory Bulb B

source_name: FVB/NJ Olfactory Bulb Pool B

tag: Olfactory Bulb


title: FVB/NJ Cerebellum B

source_name: FVB/NJ Cerebellum Pool B

tag: Cerebellum


title: A/J Cingulate Cortex E

source_name: A/J Cingulate Cortex Pool E

tag: Cingulate Cortex

tag: Pool E

source_name: Stratagene UMRR

tag: Stratagene UMRR


title: A/J Hippocampus F

source_name: A/J Hippocampus Pool F

tag: Hippocampus


title: A/J Amygdala F

source_name: A/J Amygdala Pool F

extract_protocol:
Trizol reagent
RNeasy Cleanup

tag: Amygdala


title: A/J Basal Ganglia D

source_name: A/J Basal Ganglia Pool D

tag: A/J (3 animals)

tag: Pool D


title: 129/SvImJ Frontal Cortex C

source_name: 129/ SvImJ Frontal Cortex Pool C

tag: 129/SvImJ (3 animals)

tag: Frontal Cortex


title: C57BL/6J Cingulate Cortex C

source_name: C57BL/6J Cingulate Cortex Pool C

tag: Pool C


title: A/J Basal Ganglia F

source_name: A/J Basal Ganglia Pool F

tag: Basal Ganglia

tag: Pool F


title: C3H/HeJ Olfactory Bulb D

source_name: C3H/HeJ Olfactory Bulb Pool D

label_protocol: Agilent Direct Labe

tag: C3H/HeJ (3 animals)


title: AKR/J Cerebellum C

source_name: AKR/J Cerebellum Pool C

tag: AKR/J (3 animals)

tag: Male


title: C57BL/6J Frontal Cortex C

source_name: C57BL/6J Frontal Cortex Pool C

tag: C57BL/6J (3 animals)

tag: 4-5 weeks


title: DBA/2J Hippocampus B

source_name: DBA/2J Hippocampus Pool B

tag: DBA/2J (3 animals)

tag: Pool B


title: C57BL/6J Hippocampus C

source_name: C57BL/6J Hippocampus Pool C

tag: Stratagene UMRR


title: C57BL/6J Cerebellum B

source_name: C57BL/6J Cerebellum Pool B

tag: Cerebellum


title: FVB/NJ Basal Ganglia B

source_name: FVB/NJ Basal Ganglia Pool B

tag: FVB/NJ (3 animals)


title: FRTL5-30min-rep3

source_name: FRTL5 cells, 30 min TSH-stimulated

tag: Fisher Rat Thyroid Cell line (FRTL5), early passage


title: A/J Cerebellum F

source_name: A/J Cerebellum Pool F

tag: A/J (3 animals)


title: DBA/2J Basal Ganglia B

source_name: DBA/2J Basal Ganglia Pool B


title: C3H/HeJ Cerebellum B

source_name: C3H/HeJ Cerebellum Pool B

source_name: Stratagene UMRR


title: C57BL/6J Cerebellum C

source_name: C57BL/6J Cerebellum Pool C


title: DBA/2J Cingulate Cortex C

source_name: DBA/2J Cingulate Cortex Pool C

tag: Cingulate Cortex


title: DBA/2J Frontal Cortex B

source_name: DBA/2J Frontal Cortex Pool B

tag: Frontal Cortex


title: C57BL/6J Basal Ganglia C

source_name: C57BL/6J Basal Ganglia Pool C

tag: Pool C


title: DBA/2J Olfactory Bulb C

source_name: DBA/2J Olfactory Bulb Pool C

tag: Olfactory Bulb


title: C3H/HeJ Cingulate Cortex D

source_name: C3H/HeJ Cingulate Cortex Pool D

tag: Pool D


title: DBA/2J Hippocampus C

source_name: DBA/2J Hippocampus Pool C

tag: Hippocampus


title: DBA/2J Cerebellum B

source_name: DBA/2J Cerebellum Pool B


title: DBA/2J Cingulate Cortex B

source_name: DBA/2J Cingulate Cortex Pool B


title: C3H/HeJ Frontal Cortex D

source_name: C3H/HeJ Frontal Cortex Pool D

tag: C3H/HeJ (3 animals)


title: DBA/2J Olfactory Bulb B

source_name: DBA/2J Olfactory Bulb Pool B

tag: Male


title: DBA/2J Hippocampus A

source_name: DBA/2J Hippocampus Pool A

tag: Pool A


title: DBA/2J Frontal Cortex A

source_name: DBA/2J Frontal Cortex Pool A

tag: 4-5 weeks


title: DBA/2J Olfactory Bulb A

source_name: DBA/2J Olfactory Bulb Pool A

tag: DBA/2J (3 animals)


title: DBA/2J Basal Ganglia A

source_name: DBA/2J Basal Ganglia Pool A

tag: Basal Ganglia


title: DBA/2J Frontal Cortex C

source_name: DBA/2J Frontal Cortex Pool C

tag: Stratagene UMRR


title: DBA/2J Cerebellum A

source_name: DBA/2J Cerebellum Pool A

tag: Cerebellum

source_name: Stratagene UMRR


title: AKR/J Cerebellum A

source_name: AKR/J Cerebellum Pool A

tag: AKR/J (3 animals)


title: C57BL/6J Olfactory Bulb A

source_name: C57BL/6J Olfactory Bulb Pool A

tag: C57BL/6J (3 animals)


title: AKR/J Hippocampus C

source_name: AKR/Hippocampus Pool C


title: DBA/2J Basal Ganglia C

source_name: DBA/2J Basal Ganglia Pool C


title: C3H/HeJ Hippocampus B

source_name: C3H/HeJ Hippocampus Pool B

tag: Pool B


title: DBA/2J Cerebellum C

source_name: DBA/2J Cerebellum Pool C


title: AKR/J Hippocampus B

source_name: AKR/J Cerebellum Pool B


title: AKR/J Hippocampus A

source_name: AKR/Hippocampus Pool A


title: C3H/HeJ Cerebellum A

source_name: C3H/HeJ Cerebellum Pool A


title: C3H/HeJ Hippocampus A

source_name: C3H/HeJ Basal Ganglia

extract_protocol:
Trizol
RNEasy Cleanup


title: C3H/HeJ Hippocampus C

source_name: C3H/HeJ Hippocampus Pool C


title: Aerobic NO exposed Chemostat Comparison of Wt & hmp mutant, Run 2 dye swap

status: Public on Sep 01 2006

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

description: Escherichia coli strains MG1655 and an isogenic hmp::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions.. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 was added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each unless stated otherwise. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

data_processing: background correction, log2 transformation and Loess normalisation were performed using Genesight 4.1 software, copyright BioDiscovery

organism: Escherichia coli

source_name: Aerobic hmp::Tn5 mutant experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes

tag: Strain MG1655, hmp::Tn5

source_name: Aerobic wild type experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes

tag: Wild Type Strain MG1655


title: Aerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 1 dye swap

description: Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions.. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 was added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each unless stated otherwise. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

source_name: aerobic norR::Tn5 mutant experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes

tag: Strain MG1655, norR::Tn5

source_name: aerobic wild type experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes


title: Aerobic NO exposed Chemostat Comparison of Wt & hmp mutant, Run 2


title: Aerobic NO exposed Chemostat Comparison of Wt & hmp mutant, Run 1 dye swap


title: Aerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 2 dye swap


title: Aerobic NO exposed Chemostat Comparison of Wt & hmp mutant, Run 1


title: CGR8.8 wild-type cells WT_4

city: Edinburgh

first: Joshua

middle: M

last: Brickman

address: King's Buildings, West Mains Rd.

department: Institute for Stem Cell Research

institute: University of  Edinburgh

description: CGR8 cell line is the cgr8.8 clone

data_processing: RMA normalised expression values generated using Genespring 7.2 (WinXP)

source_name: CGR8.8 wild-type cells

tag: CGR8.8 wild-type cells


title: Aerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 2


title: HexERTVP2 targetted to Rosa26, clone2, recombined, 4-OHT RRHETVPcl2+4-OHT_2

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone2, recombined, 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone2, recombined, 4-OHT RRHETVPcl2+4-OHT_3

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone2, recombined, 4-OHT"


title: CGR8.8 wild-type cells WT_3

description: CGR8 cell line is the cgr8.8 clone


title: Aerobic NO Chemostat Run 1, dye-swap

description: Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 was added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each unless stated otherwise. Samples were taken immediately prior to the addition of NOCs and after a period of 5 min exposure to NOCs for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

data_processing: background correction, log2 transformation and Loess normalisation performed using GeneSight 4.1 software, Copyright Biodiscovery.

source_name: Steady-state continuous cultured aerobic experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes

source_name: Steady-state continuous cultured control aerobic samples in absence of NOC compounds


title: Aerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 1

source_name: Aerobic norR::Tn5 mutant experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes


title: Anaerobic NO Chemostat Run 2

description: Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added to anaerobic medium at a final concentration of 50 mM to act as a terminal electron acceptor. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 were added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each, unless otherwise stated. Samples were taken immediately prior to the addition of NOCs and after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

source_name: Steady-state continuous cultured control anaerobic samples in absence of NOC compounds

source_name: Steady-state continuous cultured anaerobic experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes


title: Anaerobic NO Chemostat Run 1, dye swap


title: Anaerobic NO Chemostat Run 1


title: HexERTVP2 targetted to Rosa26, clone2, recombined, 4-OHT RRHETVPcl2+-4-OHT_4

description: CGR8 cell line is the cgr8.8 clone


title: Aerobic NO Chemostat Run 2, dye swap


title: HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT RRHETVPcl2+4-OHT_1

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT"


title: CGR8.8 wild-type cells WT_2

description: CGR8 cell line is the cgr8.8 clone


title: CGR8.8 wild-type cells WT_1

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone2, recombined, no 4-OHT RRHETVPcl2_4

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone2, recombined, no 4-OHT"


title: Aerobic NO Chemostat Run 2


title: Aerobic NO Chemostat Run 1

source_name: Steady-state continuous cultured control aerobic samples in absence of NOC compounds.

growth_protocol: stirring rate.


title: Anaerobic NO Chemostat Run 2, dye swap


title: HexERTVP2 targetted to Rosa26, clone2, recombined, no 4-OHT RRHETVPcl2_3

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone2, recombined, no 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone2, recombined, no 4-OHT RRHETVPcl2_2

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT RRHETVPcl2_1

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT RRHETVPcl1+4-OHT_3

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT RRHETVPcl1+4-OHT_1

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, recombined, no 4-OHT RRHETVPcl1_2

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone1, recombined, no 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT RRHETVPcl1+4-OHT_4

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, recombined, 4-OHT RRHETVPcl1+4-OHT_2

description: CGR8 cell line is the cgr8.8 clone


title: AKR/J Cerebellum B

source_name: AKR/J Cerebellum Pool B

tag: Male

source_name: Stratagene UMRR


title: HexERTVP2 targetted to Rosa26, clone1, recombined, no 4-OHT RRHETVPcl1_1

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone1, recombined, no 4-OHT"


title: FAIRE performed in human foreskin fibroblast cells crosslinked for 7 minutes

first: Jason

middle: D

last: Lieb

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description: Samples were amplified using ligation mediated (LM) PCR.

data_processing: log2 ratios of Cy5/Cy3 normalized so that the mean ratio

source_name: FAIRE sample from human foreskin fibroblast cells, crosslinked 7 minutes

tag: Human foreskin fibroblast (ATCC CRL 2091) grown to 90% confluent, then crosslinked with a 1% formaldehyde solution for 7 minutes.

source_name: Genomic DNA from human foreskin fibroblast cells

tag: Human foreskin fibroblast (ATCC CRL 2091) grown to 90% confluent, genomic DNA was extract using a phenol/chloroform extraction.


title: Hex targetted to Rosa26, recombined RRH_1

description: CGR8 cell line is the cgr8.8 clone

source_name: "Hex targetted to Rosa26, recombined"

tag: "Hex targetted to Rosa26, recombined"


title: Hex targetted to Rosa26, recombined RRH_4

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, recombined, no 4-OHT RRHETVPcl1_3

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, 4-OHT RHETVPcl2+4-OHT_4

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone2, unrecombined, 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, 4-OHT RHETVPcl2+4-OHT_3

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone2, unrecombined, 4-OHT"


title: Hex targetted to Rosa26, recombined RRH_3

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, no 4-OHT RHETVPcl2_3

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone2, unrecombined, no 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, 4-OHT RHETVPcl2+4-OHT_2

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, no 4-OHT RHETVPcl2_1

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone2, unrecombined, no 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, 4-OHT RHETVPcl1+4-OHT_4

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone1, unrecombined, 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone1, recombined, no 4-OHT RRHETVPcl1_4

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, no 4-OHT RHETVPcl2+4-OHT_1

description: CGR8 cell line is the cgr8.8 clone


title: Hex targetted to Rosa26, recombined RRH_2

description: CGR8 cell line is the cgr8.8 clone


title: FAIRE performed in human foreskin fibroblast cells crosslinked for 2 minute

data_processing: log2 ratios of Cy5/Cy3 normalized so that the mean ratio is 0

source_name: FAIRE sample from human foreskin fibroblast cells, crosslinked 2 minute

tag: Human foreskin fibroblast (ATCC CRL 2091) grown to 90% confluent, then crosslinked with a 1% formaldehyde solution for 2 minute.


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, 4-OHT RHETVPcl1+4-OHT_2

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone1, unrecombined, 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, no 4-OHT RHETVPcl2_2

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone2, unrecombined, 4-OHT RHETVPcl1+4-OHT_3

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, no 4-OHT RHETVPcl1_5

description: CGR8 cell line is the cgr8.8 clone

source_name: "HexERTVP2 targetted to Rosa26, clone1, unrecombined, no 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, 4-OHT RHETVPcl1+4-OHT_1

description: CGR8 cell line is the cgr8.8 clone


title: FAIRE performed in human foreskin fibroblast cells crosslinked for 4 minutes

source_name: FAIRE sample from human foreskin fibroblast cells, crosslinked 4 minutes

tag: Human foreskin fibroblast (ATCC CRL 2091) grown to 90% confluent, then crosslinked with a 1% formaldehyde solution for 4 minutes.


title: FAIRE performed in human foreskin fibroblast cells crosslinked for 1 minute

source_name: FAIRE sample from human foreskin fibroblast cells, crosslinked 1 minute

tag: Human foreskin fibroblast (ATCC CRL 2091) grown to 90% confluent, then crosslinked with a 1% formaldehyde solution for 1 minute.


title: Hex targetted to Rosa26, unrecombined RH_3

description: CGR8 cell line is the cgr8.8 clone

source_name: "Hex targetted to Rosa26, unrecombined"

tag: "Hex targetted to Rosa26, unrecombined"


title: Hex targetted to Rosa26, unrecombined RH_4

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, no 4-OHT RHETVPcl1_4

description: CGR8 cell line is the cgr8.8 clone

tag: "HexERTVP2 targetted to Rosa26, clone1, unrecombined, no 4-OHT"


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, no 4-OHT RHETVPcl1_1

description: CGR8 cell line is the cgr8.8 clone


title: Hex targetted to Rosa26, unrecombined RH_1

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, no 4-OHT RHETVPcl1_2

description: CGR8 cell line is the cgr8.8 clone


title: HexERTVP2 targetted to Rosa26, clone1, unrecombined, no 4-OHT RHETVPcl1_3

description: CGR8 cell line is the cgr8.8 clone


title: Hex targetted to Rosa26, unrecombined RH_2

description: CGR8 cell line is the cgr8.8 clone


title: 3rdRndAmpEPool1 Sample EC_AS_Spikein_AY_IP_B3_new.cel

status: Public on Aug 08 2006

city: Houston

first: Wei

state: TX

address: one baylor plaza, MS BCM305

institute: Baylor College of Medicine

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 1 = 96 putative novel promoter plasmids (20ng/uL). Amplification Conditions: E Biggin lab standard with low concentration of input DNA

data_processing: Raw data

source_name: genomic DNA + Pool 1 (1ug/uL).

tag: ChIP


title: 3rdRndAmpBPool1 Sample EC_AS_Spikein_AY_IP_B1_old.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 1 = 96 putative novel promoter plasmids (20ng/uL). Amplification Conditions: B Struhl lab standard.


title: 3rdRndAmpEPool1 Sample EC_AS_Spikein_AY_IP_B2_new.cel


title: Human MCF7 cells Replicate 3

status: Public on Aug 14 2006

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

description: Human MCF7

data_processing: log base 2 ratios

source_name: MCF7 cells - E2F1 antibody

tag: E2F1 antibody

source_name: MCF7 cells - control

tag: control total input


title: 1stRndAmpCPool1 Sample EC_AS_AY_C_C_B1_T2.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 1 = 96 putative novel promoter plasmids (20ng/uL). Amplification Conditions: C Re amplification of a small sample of B to increase yield.


title: 3rdRndAmpEGenomicInput Sample EC_AS_Spikein_AY_Input_low_B3_new.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Amplification Conditions: E Biggin lab standard with low concentration of input DNA

source_name: genomic DNA

tag: Input


title: 3rdRndAmpBPool1 Sample EC_AS_Spikein_AY_IP_B3_old.cel


title: Human MCF7 cells AP-2alpha Replicate 3

description: Human MCF7

source_name: MCF7 cells - AP-2alpha antibody

tag: AP-2alpha antibody


title: 3rdRndAmpDGenomicInput Sample EC_AS_Spikein_AY_Input_high_B3_new.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Amplification Conditions: D Biggin lab standard with high concentration of input DNA


title: 3rdRndAmpDGenomicInput Sample EC_AS_Spikein_AY_Input_high_B1_new.cel


title: 3rdRndAmpBGenomicInput Sample EC_AS_Spikein_AY_Input_B3_old.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)).Amplification Conditions: B Struhl lab standard


title: 1stRndAmpBPool2 Sample EC_AS_AY_B_D_B1_T2.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 2 = 96 promoters and random fragments (20ng/uL). Amplification Conditions: B Struhl lab standard.

source_name: genomic DNA + Pool 2 (1ug/uL).


title: 1stRndAmpBPool2 Sample EC_AS_AY_B_D_B1_T1.cel


title: 3rdRndAmpBGenomicInput Sample EC_AS_Spikein_AY_Input_B2_old.cel


title: 3rdRndAmpDGenomicInput Sample EC_AS_Spikein_AY_Input_high_B2_new.cel


title: 3rdRndAmpBGenomicInput Sample EC_AS_Spikein_AY_Input_B1_old.cel


title: 1stRndAmpBPool1 Sample EC_AS_AY_B_C_B1_T2.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 1 = 96 putative novel promoter plasmids (20ng/uL). Amplification Conditions: B Struhl lab standard


title: 1stRndAmpCGenomicInput Sample EC_AS_AY_C_IN_B1_T1.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Amplification Conditions: C Re amplification of a small sample of B to increase yield.


title: 3rdRndAmpEGenomicInput Sample EC_AS_Spikein_AY_Input_low_B1_new.cel


title: Human MCF7 cells E2F1 Replicate 1

description: Human MCF7


title: 3rdRndAmpEGenomicInput Sample EC_AS_Spikein_AY_Input_low_B2_new.cel


title: Human MCF7 cells Replicate 2

description: Human MCF7


title: Human MCF7 cells AP-2alpha Replicate 2

description: Human MCF7


title: 3rdRndAmpEPool1 Sample EC_AS_Spikein_AY_IP_B1_new.cel


title: 1stRndAmpCGenomicInput Sample EC_AS_AY_C_IN_B1_T2.cel


title: 1stRndAmpCPool2 Sample EC_AS_AY_C_D_B1_T2.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 2 = 96 promoters and random fragments (20ng/uL). Amplification Conditions: C Re amplification of a small sample of B to increase yield.


title: Human MCF7 cells E2F1 Replicate 2

description: Human MCF7


title: 1stRndAmpCPool1 Sample EC_AS_AY_C_C_B1_T1.cel


title: 3rdRndAmpBPool1 Sample EC_AS_Spikein_AY_IP_B2_old.cel


title: 1stRndAmpCPool2 Sample EC_AS_AY_C_D_B1_T1.cel


title: P211 HCT-116, DNMT1 and 3B double knockout, non-treated

status: Public on Aug 01 2006

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

hyb_protocol: ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt’s solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

scan_protocol: arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)

data_processing: raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; two independent array hybridization from every sample were merged; after removal of bad quality clones (marked as - and 0 on array, generalized log2 ratios from 26618 cDNA clones were given in the data table

source_name: cell line HCT-116

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.

growth_protocol: cells were cultivated in McCoy´s 5A with addition of 10% FCS

extract_protocol: total RNA was extracted using Qiagen RNeasy Midi Kit reagents; 2µg total RNA was amplified one round based on T7 RNA Polymerase (Ambion Message Amplification Kit Reagents, 6h IVT)

treatment_protocol: non-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT1 and 3B double knockout, non-treated

source_name: Universal human reference RNA (Stratagene), one round amplified

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column.

tag: common reference sample


title: P207 HCT-116, DNMT1 knockout, U0126-treated

growth_protocol: cells were cultivated in McCoy´s 5A with addition of 10% FCS, 0.1 mg/ml hygromycin

treatment_protocol: 10µM U0126 (MEK-inhibitor), 48h

tag: cell line HCT-116, Ki-RAS-mutation, DNMT1 knockout, U0126-treated

extract_protocol: 2µg total RNA was amplified one round based on T7 RNA Polymerase (Ambion Message Amplification Kit Reagents, 6h IVT)


title: P205 HCT-116, DNMT1 knockout, non-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT1 knockout, non-treated


title: P209 HCT-116, DNMT3B knockout, DMSO-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT3B knockout, DMSO-treated


title: P210 HCT-116, DNMT3B knockout, U0126-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT3B knockout, U0126-treated


title: P206 HCT-116, DNMT1 knockout, DMSO-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT1 knockout, DMSO-treated


title: P213 HCT-116, DNMT1 and 3B double knockout, U0126-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT1 and 3B double knockout, U0126-treated


title: P208 HCT-116, DNMT3B knockout, non-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT3B knockout, non-treated


title: P203 HCT-116, DNMT wildtype, Aza-treated

treatment_protocol: 1µM 5-Aza-CdR, 96h

tag: cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, Aza-treated


title: P212 HCT-116, DNMT1 and 3B double knockout, DMSO-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT1 and 3B double knockout, DMSO-treated


title: P204 HCT-116, DNMT wildtype, Aza-treated

treatment_protocol: 10µM 5-Aza-CdR, 96h


title: 1stRndAmpBPool1 Sample EC_AS_AY_B_C_B1_T1.cel


title: P202 HCT-116, DNMT wildtype, U0126-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, U0126-treated


title: P200 HCT-116, DNMT wildtype, non-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, non-treated


title: P80 dilated cardiomyopathy heart biopsy

description: P80 dilated cardiomyopathy heart biopsy

data_processing: raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; after removal of bad quality spots, two hybridizations of this sample were merged; generalized log2 ratios from 30498 cDNA clones were given in the data table.

source_name: heart, middle septum

tag: Dilated cardiomyopathy


title: P85 dilated cardiomyopathy heart biopsy

description: P85 dilated cardiomyopathy heart biopsy


title: P82 dilated cardiomyopathy heart biopsy

description: P82 dilated cardiomyopathy heart biopsy


title: P81 dilated cardiomyopathy heart biopsy

description: P81 dilated cardiomyopathy heart biopsy


title: P201 HCT-116, DNMT wildtype, DMSO-treated

tag: cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, DMSO-treated


title: NonAmpSpikeInPool2 Sample EC_AS_B_C01_B1_T6.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 2 = 96 promoters and random fragments (20ng/uL)

tag: ChIP


title: P76 dilated cardiomyopathy heart biopsy

description: P76 dilated cardiomyopathy heart biopsy


title: 1stRndAmpBGenomicInput Sample EC_AS_AY_B_IN_B1_T1.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Amplification Conditions: B Struhl lab standard.

tag: Input


title: P75 dilated cardiomyopathy heart biopsy

description: P75 dilated cardiomyopathy heart biopsy

label_protocol: direct fluorescent labelling of 2 µg direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.


title: NonAmpSpikeInPool2 Sample EC_AS_B_CO1_B1_T3.cel


title: P74 dilated cardiomyopathy heart biopsy

description: P74 dilated cardiomyopathy heart biopsy


title: P64 Non failing heart biopsy

description: P64 Non failing heart biopsy

tag: Non failing


title: P70 Non failing heart biopsy

description: P70 Non failing heart biopsy

tag: common reference sample


title: P67 Non failing heart biopsy

description: P67 Non failing heart biopsy


title: P73 dilated cardiomyopathy heart biopsy

description: P73 dilated cardiomyopathy heart biopsy


title: P72 dilated cardiomyopathy heart biopsy

description: P72 dilated cardiomyopathy heart biopsy


title: P83 dilated cardiomyopathy heart biopsy

description: P83 dilated cardiomyopathy heart biopsy


title: NonAmpSpikeInPool2 Sample EC_AS_B_C01_B1_T5.cel


title: NonAmpSpikeInPool2 Sample EC_AS_B_CO1_B1_T1.cel


title: NonAmpSpikeInPool2 Sample EC_AS_B_CO1_B1_T2.cel


title: P78 dilated cardiomyopathy heart biopsy

description: P78 dilated cardiomyopathy heart biopsy


title: P58 Non failing heart biopsy

description: P58 Non failing heart biopsy


title: 1stRndAmpBGenomicInput Sample EC_AS_AY_B_IN_B1_T2.cel


title: NonAmpGenomicInput Sample EC_AS_Genomic_C01_B1_T4.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)).


title: P59 Non failing heart biopsy

description: P59 Non failing heart biopsy


title: P77 dilated cardiomyopathy heart biopsy

description: P77 dilated cardiomyopathy heart biopsy


title: P63 Non failing heart biopsy

description: P63 Non failing heart biopsy


title: P61 Non failing heart biopsy

description: P61 Non failing heart biopsy


title: P62 Non failing heart biopsy

description: P62 Non failing heart biopsy


title: P57 Non failing heart biopsy

description: P57 Non failing heart biopsy


title: P54 Non failing heart biopsy

description: P54 Non failing heart biopsy


title: P55 Non failing heart biopsy

description: P55 Non failing heart biopsy


title: P65 Non failing heart biopsy

description: P65 Non failing heart biopsy


title: NonAmpGenomicInput Sample EC_AS_Genomic_CO1_B1_T2.cel


title: NonAmpSpikeInPool1 Sample EC_AS_A_C01_B1_T6.cel

description: Genomic DNA from HCT116 (total chromatin, crosslinked and reverse crosslinked, phenol/chlor extracted, no Ab treatment (1ug/uL)). Pool 1 = 96 putative novel promoter plasmids (20ng/uL)


title: P50 Non failing heart biopsy

description: P50 Non failing heart biopsy


title: NonAmpSpikeInPool1 Sample EC_AS_A_CO1_B1_T1.cel


title: NonAmpSpikeInPool1 Sample EC_AS_A_CO1_B1_T2.cel


title: NonAmpGenomicInput Sample EC_AS_Genomic_C01_B1_T5.cel


title: NonAmpSpikeInPool1 Sample EC_AS_A_C01_B1_T5.cel


title: NonAmpSpikeInPool1 Sample EC_AS_A_CO1_B1_T3.cel


title: NonAmpGenomicInput Sample EC_AS_Genomic_CO1_B1_T1.cel


title: P53 Non failing heart biopsy

description: P53 Non failing heart biopsy


title: Case A9

city: Toronto

first: Teresa

middle: L

last: Mastracci

state: ON

address: 600 University Ave., room 984

department: Mount Sinai Hospital

country: Canada

institute: Samuel Lunenfeld Research Institute

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A9 (ALH)

source_name: Case A9

tag: Archival early neoplastic breast lesion (atypical lobular hyperplasia; ALH)

source_name: Pooled female genomic DNA

tag: Novagen Catalogue Number


title: Case A14

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A14 (ALH)

source_name: Case A14


title: NonAmpGenomicInput Sample EC_AS_Genomic_CO1_B1_T3.cel


title: Case L10

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L10 (LCIS)

source_name: Case L10

tag: Archival early neoplastic breast lesion (lobular carcinoma in situ; LCIS)


title: Case A8

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A8 (ALH)

source_name: Case A8


title: P52 Non failing heart biopsy

description: P52 Non failing heart biopsy


title: Case A4

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A4 (ALH)

source_name: Case A4


title: Case L5

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L5 (LCIS)

source_name: Case L5


title: Case A18

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A18 (ALH)

source_name: Case A18


title: Case A25

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A25 (ALH)

source_name: Case A25


title: Case A3

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A3 (ALH)

source_name: Case A3


title: Case L7

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L7 (LCIS)

source_name: Case L7


title: Case A7

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A7 (ALH)

source_name: Case A7


title: T64 dilated cardiomyopathy heart biopsy

description: T64 Dilated cardiomyopathy heart biopsy

data_processing: Microarray raw data were normalized using robust multi-array average16 (RMA) implemented in Bioconductor's “affy”-package. Probe sets with “absent” calls (as defined by Bioconductor’s affy-package) in more than 50% of tissue samples in either group (NF and DCM) were excluded

source_name: heart, subendocardial left ventricle

label_protocol: 10 µg of total RNA was processed to produce biotinylated cRNA targets

extract_protocol: total RNA was extracted using Qiagen RNeasy reagents


title: Case L3

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L3 (LCIS)

source_name: Case L3


title: Case L11

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L11 (LCIS)

source_name: Case L11


title: Case L12

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L12 (LCIS)

source_name: Case L12


title: T62 dilated cardiomyopathy heart biopsy

description: T62 Dilated cardiomyopathy heart biopsy


title: T63 dilated cardiomyopathy heart biopsy

description: T63 Dilated cardiomyopathy heart biopsy


title: T61 dilated cardiomyopathy heart biopsy

description: T61 Dilated cardiomyopathy heart biopsy


title: Case L9

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L9 (LCIS)

source_name: Case L9


title: Case A12

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A12 (ALH)

source_name: Case A12


title: Case A11

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A11 (ALH)

source_name: Case A11

source_name: Pooled female genomic DNA


title: Case L13

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L13 (LCIS)

source_name: Case L13


title: Case L2

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L2 (LCIS)

source_name: Case L2


title: T60 dilated cardiomyopathy heart biopsy

description: T60 Dilated cardiomyopathy heart biopsy


title: Case A13

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A13 (ALH)

source_name: Case A13


title: Case L1

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L1 (LCIS)

source_name: Case L1


title: T55 Non failing heart biopsy

description: T55 Non failing heart biopsy


title: T59 dilated cardiomyopathy heart biopsy

description: T59 Dilated cardiomyopathy heart biopsy


title: T56 Non failing heart biopsy

description: T56 Non failing heart biopsy


title: T57 Non failing heart biopsy

description: T57 Non failing heart biopsy


title: T58 Non failing heart biopsy

description: T58 Non failing heart biopsy


title: T65 dilated cardiomyopathy heart biopsy

description: T65 Dilated cardiomyopathy heart biopsy


title: Case L28

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L28 (LCIS)

source_name: Case L28


city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2

data_processing: raw data was GC-RMA normalized using the Bioconductor application for R

organism: Drosophila melanogaster

source_name: Adult whole female flies


title: T54 Non failing heart biopsy

description: T54 Non failing heart biopsy


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 8h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 64h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 4h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 64h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 2h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 1h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 16h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 32h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 16h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate2, 0.25h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 1h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 8h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 0.25h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 2h after 1h heat shock @ 36 dC


title: Drosophila non-selected bioreplicate2

description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2

tag: Drosophila non-selected bioreplicate2


title: Case L8

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L8 (LCIS)

source_name: Case L8


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 32h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 64h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 32h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 16h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 1h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 2h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 8h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 16h after 1h heat shock @ 36 dC


title: P79 dilated cardiomyopathy heart biopsy

description: P79 dilated cardiomyopathy heart biopsy

source_name: heart, middle septum

source_name: Universal human reference RNA (Stratagene), one round amplified


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 32h after 1h heat shock @ 36 dC


title: Case L6

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case L6 (LCIS)

source_name: Case L6


title: SWES_C065_04-15-03

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

institute: Yale University School of Medicine

description: 15 hr unc-79;fem-1 vs reference

data_processing: log base 2 ratio of cy5 to cy3

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: EXP: fem-1 mRNA

tag: fem-1 mRNA

source_name: REF: reference mRNA

tag: reference mRNA


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 4h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 4h after 1h heat shock @ 36 dC


title: SWES_C017_04-15-03

description: 12 hr unc-79mpk-1;fem-1 vs reference

source_name: EXP: mpk-1 mRNA

tag: mpk-1 mRNA


title: SWES_C022_04-04-03

description: 9 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C036_03-27-03

description: 15 hr unc-79mpk-1;fem-1 vs reference


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 8h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila heat resistance selected bioreplicate1, 0.25h after 1h heat shock @ 36 dC


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 2h after 1h heat shock @ 36 dC


title: SWES_C021_04-15-03

description: 12 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C020_04-14-03

description: 15 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C014_04-27-03

description: 15 hr unc-79;fem-1 vs reference


title: SWES_C038_03-27-03

description: 15 hr unc-79;fem-1 vs reference


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 64h after 1h heat shock @ 36 dC


title: Drosophila non-selected bioreplicate1

description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1

tag: Drosophila non-selected bioreplicate1


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 1h after 1h heat shock @ 36 dC


title: SWES_C062_04-24-03

description: 9 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C012_04-27-03

description: 15 hr unc-79mpk-1;fem-1 vs reference


title: Case A21

description: Pooled female genomic DNA competitively hybridized against DNA from archival early neoplastic breast lesion case A21 (ALH)

source_name: Case A21


title: Heat selected line bio. Rep. 2

description: Gene expression data from heat resistance selected flies

source_name: Adult whole female flies of heat selected line 2

tag: Heat resistance selected flies


title: SWES_C028_03-21-03

description: 9 hr unc-79mpk-1;fem-1 vs reference


title: Heat selected line bio. Rep. 3

source_name: Adult whole female flies of heat selected line 3


title: Heat selected line bio. Rep. 4

source_name: Adult whole female flies of heat selected line 4


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate1, 0.25h after 1h heat shock @ 36 dC


title: Heat selected line bio. Rep. 5

source_name: Adult whole female flies of heat selected line 5


title: SWES_C011_06-20-03

description: 6 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C009_06-20-03

description: 3 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C023_04-04-03

description: 6 hr unc-79mpk-1;fem-1 vs reference


title: Heat selected line bio. Rep. 1

source_name: Adult whole female flies of heat selected line 1


title: SWES_C044_03-25-03

description: 12 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C040_04-04-03

description: 3 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C047_03-26-03

description: 6 hr unc-79mpk-1;fem-1 vs reference


title: SWES_C048_03-26-03

description: 3 hr unc-79mpk-1;fem-1 vs reference


title: Control line bio. Rep. 4

description: Gene expression data from non-selected (control) flies

source_name: Adult whole female flies of control line 4

tag: non-selected control flies


title: SWES_C015_06-20-03

description: 0 hr unc-79mpk-1;fem-1 vs reference


title: Control line bio. Rep. 3

source_name: Adult whole female flies of control line 3


title: SWES_C027_03-26-03

description: 0 hr unc-79mpk-1;fem-1 vs reference


title: Control line bio. Rep. 2

source_name: Adult whole female flies of control line 2


title: SWES_C024_04-04-03

description: 0 hr unc-79mpk-1;fem-1 vs reference


title: pre 310701 2

status: Public on Jul 28 2006

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

description: buffer EDTA, SSPE, TWEEN

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

tag: Prostate epithelial cell line


title: Control line bio. Rep. 5

source_name: Adult whole female flies of control line 5


description: Gene expression data from whole adult female Drosophila non-selected bioreplicate2, 4h after 1h heat shock @ 36 dC

source_name: Adult whole female flies


title: Agamb_Fem_19103

status: Public on Jul 15 2006

city: Chicago

first: Joelle

middle: R

last: Perusse

state: IL

address: 920 E. 58th Street

department: Department of Genetics

institute: Yale University

description: Age: 3-5days, Sex: female, Dye: Cy5, Slide: 19103

data_processing: Signal Median

organism: Anopheles gambiae

source_name: Whole adult female

tag: Age

value: 3-5days, Sex:female, Dye:Cy5, Slide:19103


title: Agamb_Fem_19239

description: Age: 3-5days, Sex: female, Dye: Cy3, Slide: 19239

value: 3-5days, Sex:female, Dye:Cy3, Slide:19239


title: SWES_C013_04-27-03

description: 0 hr unc-79;fem-1 vs reference prep 3


title: Agamb_Male_19103

description: Age: 3-5days, Sex: male, Dye: Cy3, Slide: 19103

source_name: Whole adult male

value: 3-5days, Sex:male, Dye:Cy3, Slide:19103


title: pre 030801 1

description: buffer EDTA, SSPE, TWEEN

tag: prostate epithelial cell line


title: Control line bio. Rep. 1

source_name: Adult whole female flies of control line 1


title: pre 310701 1

description: buffer EDTA, SSPE, TWEEN


title: Agamb_Fem_19104

description: Age: 3-5days, Sex: female, Dye: Cy5, Slide: 19104

value: 3-5days, Sex:female, Dye:Cy5, Slide:19104


title: Agamb_Male_19104

description: Age: 3-5days, Sex: male, Dye: Cy3, Slide: 19104

value: 3-5days, Sex:male, Dye:Cy3, Slide:19104


title: DMSO3

status: Public on Jul 07 2006

city: Cambridge

first: Dave

last: Peck

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: HL60 cells were treated with dimethylsulfoxide (DMSO; final concentration 0.1%) and incubated for 5 days

label: SAPE

source_name: HL60 cell line

tag: human promyelocytic leukemia cells


title: Agamb_Fem_19101

description: Age: 3-5days, Sex: female, Dye: Cy3, Slide: 19101

value: 3-5days, Sex:female, Dye:Cy3, Slide:19101


title: DMSO2


title: Agamb_Male_19238

description: Age: 3-5days, Sex: male, Dye: Cy5, Slide: 19238

value: 3-5days, Sex:male, Dye:Cy5, Slide:19238


title: DMSO1


title: Agamb_Fem_19238

description: Age: 3-5days, Sex: female, Dye: Cy3, Slide: 19238

value: 3-5days, Sex:female, Dye:Cy3, Slide:19238


title: Agamb_Male_19239

description: Age: 3-5days, Sex: male, Dye: Cy5, Slide: 19239

value: 3-5days, Sex:male, Dye:Cy5, Slide:19239


title: Agamb_Male_19101

description: Age: 3-5days, Sex: male, Dye: Cy5, Slide: 19101

value: 3-5days, Sex:male, Dye:Cy5, Slide:19101


title: SWES_C037_03-27-03

description: 0 hr unc-79;fem-1 vs reference

source_name: EXP: fem-1 mRNA

source_name: REF: reference mRNA


title: Tretinoin3

description: Hl60 cells were treated with 1µM tretinoin in dimethylsulfoxide (DMSO; final concentration 0.1%) for 5 days


title: Testis from adult rat treated with 50 mg/kg b.w. Adjudin 4 d-2

city: New York

first: Weiliang

last: Xia

state: NY

address: 1230 York Avenue

institute: Population Council

description: normal adult rat testis

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Testis

label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: 0.1 gram of frozen testis tissue extracted using Trizol (Invitrogen) and followed by RNeasy cleanup (Qiagen)

tag: Adult rats were treated with 50 mg/kg b.w. Adjudin [1-(2,4-dichlorobenzyl)-indazole-3-carbohydrazide] by gavage for 4 days


title: Testis from adult rat treated with 50 mg/kg b.w. Adjudin 4 d-1

description: normal adult rat testis


title: Tretinoin1


title: Zebrafish Heart array normoxia N5

status: Public on Jul 06 2006

city: Leiden

first: Christoph

middle: Peter

last: Bagowski

country: Netherlands

institute: Leiden University

description: Normoxia array No5; Technical replicate to sample Normoxia No2

data_processing: Rosetta Resolver

organism: Danio rerio

source_name: zebrafish heart normoxia

tag: Tuebingen wt


title: PGC-1alpha -/- differentiated brown fat cells expressing a siRNA specific for PGC-1beta knockdown (rep2)

city: Boston

first: Marc

last: Uldry

address: 1 Jimmy Fund Way

institute: Dana Farber Cancer Institute

description: Cells immortalized through SV40 driven largeT antigen expression

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.

label: biotinylation

source_name: brown fat cells differentiated for seven days

tag: immortalized cells derived from brown fat tissue of PGC-1alpha KO mouse (mixed background), expressing a siRNA specific for PGC-1beta knockdown.


title: Zebrafish Heart array normoxia N2

description: Normoxia array No2; Biological sample


title: PGC-1alpha -/- differentiated brown fat cells expressing a control siRNA (rep2)

description: Cells immortalized through SV40 driven largeT antigen expression.

tag: immortalized cells derived from brown fat tissue of PGC-1alpha KO mouse (mixed background), expressing a control siRNA.


title: Zebrafish Heart array normoxia N3

description: Normoxia array No3; Biological sample


title: Tretinoin2


title: PGC-1alpha -/- differentiated brown fat cells expressing a siRNA specific for PGC-1beta knockdown (rep1)


title: Adult rat testis-normal 1

description: normal adult rat testis

tag: normal adult rat testis


title: Adult rat testis-normal 3

description: normal adult rat testis


title: Testis from adult rat treated with 50 mg/kg b.w. Adjudin 4 d-3

description: normal adult rat testis


title: Zebrafish Heart array hypoxia Y5

description: Hypoxia array No4; Technical replicate to sample Hypoxia No2

source_name: zebrafish heart hypoxia


title: Testis from adult rat treated with 50 mg/kg b.w. Adjudin  8 h-1

description: normal adult rat testis

tag: Adult rats were treated with 50 mg/kg b.w. Adjudin [1-(2,4-dichlorobenzyl)-indazole-3-carbohydrazide] by gavage for 8 hour


title: PGC-1alpha -/- differentiated brown fat cells treated 4h cAMP (rep2)

tag: immortalized cells derived from brown fat tissue of PGC-1alpha KO mouse (mixed background). passage number


title: Zebrafish Heart array hypoxia Y3

description: Hypoxia array No3; Biological sample


title: Adult rat testis-normal 2

description: normal adult rat testis


title: Zebrafish Heart array hypoxia Y2

description: Hypoxia array No2; Biological sample


title: PGC-1alpha -/- differentiated brown fat cells treated 4h cAMP (rep1)


title: PGC-1alpha -/- differentiated brown fat cells (rep1)

tag: immortalized cells derived from brown fat of PGC-1alpha KO mouse (mixed background). passage number


title: PGC-1alpha -/- differentiated brown fat cells (rep2)


title: Zebrafish Heart array hypoxia Y1

description: Hypoxia array No1; Biological sample


title: Zebrafish Heart array hypoxia Y4

description: Hypoxia array No4; Biological sample


title: Zebrafish Heart array normoxia N4

description: Normoxia array No4; Biological sample


title: Zebrafish Heart array normoxia N1

description: Normoxia array No1; Biological sample


title: WT differentiated brown fat cells treated 4h cAMP (rep2)

source_name: brown fat cells differentiated for 7 days

tag: immortalized cells derived from brown fat tissue of mouse of mixed background. passage number


title: WT differentiated brown fat cells (rep2)


title: IL-18 K/O Sham Operated Signal

status: Public on Jul 04 2006

city: San Antonio

first: James

middle: T.

last: Colston

address: 7703 Floyd Curl Drive

department: Medicine

institute: UTHSCSA

description: Total RNA isolated from cardiac muscle (left ventricle) of sham-operated IL-18 knockout mice (N=5).

data_processing: GCRMA Normalization


title: WT_Banded_Signal

description: WT Banded Signal

source_name: WT Transaortic Constriction Banded Signal

tag: Wild-type littermate


title: Peripheral Blood Mononuclear cells (AF1)

status: Public on Jul 01 2006

first: David

middle: Lawrence

last: Newsom

address: 700 Children's Drive

department: Microbial Pathogenesis

institute: Nationwide Children's Hospital

description: Peripheral Blood Mononuclear cells

hyb_protocol: Please see the protocols at the Functional Genomics Core website of the Columbus Children's Hospital. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: The data was analyzed with ArrayAssist Lite RMA version 3.4.

source_name: Peripheral Blood Mononuclear cells

extract_protocol: Spin Doctor Genomic DNA Isolation kit (Gerard Biotech, Oxford, OH).

tag: Female, AfricanAmerican


title: Twice weekly physical activity, cardiac tissue, 16  months old 3

city: Oxford

first: Natalie

last: Schweitzer

institute: Miami University

description: Gene expression data from female Sprague-Dawley rats that had atwice weekly 1 hr physical activity in a large box (PA)

hyb_protocol: High integrity RNA was hybridized to the Affymetix GeneChip® Rat Genome 230 2.0 Array

scan_protocol: Arrays were scanned using the GeneArray scanner (Agilent Technologies)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and RMA Express.

source_name: Heart left ventricle in female Sprague-Dawley rats after physical activity twice-weekly

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Reference Schweitzer et al. Access to exercise and its relation to cardiovascular health and gene expression in laboratory animals. Life Sciences 77: 2246-2261, 2005.

extract_protocol: Total RNA extraction was performed using a RNeasy Fibrous Tissue Mini kit (Qiagen) according to the manufacturer's recommendations.

tag: Gender

value: Female, Strain:Sprague-Dawley (Charles River)

value: 16 months; Tissue:Heart left ventricle


title: Peripheral Blood Mononuclear cells (AF3)

description: Peripheral Blood Mononuclear cells

data_processing: The data were analyzed with ArrayAssist Lite RMA version 3.4.

label_protocol: Please see the protocols at the Functional Genomics Core website of the Columbus Children's Hospital.


title: WT Sham-operated Signal

description: Total cardiac muscle RNA isolated from sham-operated wild-type mouse hearts

source_name: cardiac muscle, WT Sham-operated


title: Sedentary, cardiac tissue, 16  months old 3

description: Gene expression data from female Sprague-Dawley rats that esided soley in a standard cage (SED).

source_name: Heart left ventricle in female Sprague-Dawley rats kept in a sedentary environment

treatment_protocol: Reference Schweitzer et al. Access to exercise and its relation to cardiovascular health and gene expression in laboratory animals. Life Sciences 77: 2246-2261, 2005.


title: Sedentary, cardiac tissue, 16  months old 4


title: Twice weekly physical activity, cardiac tissue, 16  months old 2


title: Peripheral Blood Mononuclear cells (AS2)

description: Peripheral Blood Mononuclear cells

data_processing: The data was analyzed with ArrayAssist Lite RMA Version 3.4.

tag: Female, AsianAmerican


title: Brain genonmic DNA

description: Brain Genomic DNA

source_name: Brain

tag: Male, AsianAmerican


title: Peripheral Blood Mononuclear cells (C5)

description: Peripheral Blood Mononuclear cells

tag: Female, Caucasian


title: Twice weekly physical activity, cardiac tissue, 16  months old 1

tag: Age


title: Voluntary exercise, cardiac tissue, 16  months old 2

description: Gene expression data from female Sprague-Dawley rats that had access to regular exercise (EX)

source_name: Heart left ventricle in female Sprague-Dawley rats after lifelong exerise


title: Sedentary, cardiac tissue, 16  months old 1


title: Voluntary exercise, cardiac tissue, 16  months old 3


title: IL18_KO_Banded

description: Total RNA isolated from left ventricles of IL-18 K/O mouse hearts (N=6, pooled) each with surgical transaortic constriction for 1 wk

data_processing: GCRMA normalization and background correction

source_name: IL-18 K/O cardiac muscle (N=6, pooled), transaortic constriction 1 wk

tag: Strain

value: IL-18 null on C57BL/6 background

tag: Tissue

value: cardiac muscle


title: Voluntary exercise, cardiac tissue, 16  months old 4


title: Sedentary, cardiac tissue, 16  months old 2


title: Twice weekly physical activity, cardiac tissue, 16  months old 4


title: Peripheral Blood Mononuclear cells (C2)

description: Peripheral Blood Mononuclear cells


title: Peripheral Blood Mononuclear cells (C6)

description: Peripheral Blood Mononuclear cells


title: Voluntary exercise, cardiac tissue, 16  months old 1


title: SWES_C050_04-15-03

description: 0 hr unc-79;fem-1 vs reference prep 2

tag: fem-1 mRNA

tag: reference mRNA


title: PGC-1alpha -/- differentiated brown fat cells expressing a control siRNA (rep1)

tag: immortalized cells derived from brown fat tissue of PGC-1alpha KO mouse (mixed background), expressing a control siRNA.


title: Peripheral Blood Mononuclear cells (C4)

description: Peripheral Blood Mononuclear cells


title: WT differentiated brown fat cells treated 4h cAMP (rep1)


title: MCF7/BUS, 3 nM PPT, 48 hours, biological replication 2

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: Gene expression data from MCF7 (BUS stock) exposed to 3 nM PPT for 48 hours.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: MCF7/BUS cells, human breast adenocarcinoma cell line, estrogen receptor-positive

extract_protocol: QIAGEN RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 3 nM PPT. Total RNA was isolated 48 hours after E2 treatment.

tag: 3 nM PPT


title: MCF7/BUS, 3 nM PPT, 48 hours, biological replication 3


title: Neuroblastoma cell line IMR32

description: neuroblastoma cell line IMR32 (ATCC)

source_name: IMR32 neuroblastoma cells (ATCC)

tag: Male, Caucasian. The tumor was diagnosed as a neuroblastoma with rare areas of organoid differentiation.


title: MCF7/BUS, 10 nM para-nonylphenol, 48 hours, biological replication 3

description: Gene expression data from MCF7 (BUS stock) exposed to 10 nM para-nonylphenol for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 10 nM para-nonylphenol. Total RNA was isolated 48 hours after E2 treatment.

tag: 10 nM para-nonylphenol


title: MCF7/BUS, 10 nM para-nonylphenol, 48 hours, biological replication 1


title: MCF7/BUS, 1 micromolar daidzein, 48 hours, biological replication 2

description: Gene expression data from MCF7 (BUS stock) exposed to 1 micromolar daidzein for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 1 micromolar daidzein. Total RNA was isolated 48 hours after E2 treatment.

tag: 1 micromolar daidzein


title: MCF7/BUS, 1 nM bisphenol A, 48 hours, biological replication 3

description: Gene expression data from MCF7 (BUS stock) exposed to 1 nM bisphenol A for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 1 nM bisphenol A. Total RNA was isolated 48 hours after E2 treatment.

tag: 1 nM bisphenol A


title: MCF7/BUS, 1 nM bisphenol A, 48 hours, biological replication 2


title: MCF7/BUS, 3 nM PPT, 48 hours, biological replication 1


title: MCF7/BUS, 1 nM bisphenol A, 48 hours, biological replication 1


title: MCF7/BUS, 1 micromolar daidzein, 48 hours, biological replication 3