title: MC9 cells from H2O2 conditions_rep 3

city: Gothenburg

first: Hadi

last: Valadi

address: Guldhedsgatan 10A

department: Dept. of Rheumatology and Inflammation Research

country: Sweden

institute: University of Gothenburg

description: Gene expression data from MC/9 cells that have received H2O2 exosomes

hyb_protocol: The microarray experiments were performed by SweGene (www.swegene.org/) according to Affymetrix recommendation. Briefly, a hybridisation cocktail was prepared with the biotinylated and fragmented cRNA, control oligonucleotide B2, herring sperm DNA, acetylated BSA, 4-morpholinepropanesulfonic acid (MES), Tween 20, and bacterial cRNA controls respectively. The hybridisation cocktail was heated to 99°C for 5 min and to 45°C for 5 min, and was briefly centrifuged before hybridization. The prewet GeneChipTM probe array cartridge was filled with the hybridisation cocktail and incubated on rotation, 60 rpm at 45°C for 16–18 h. The cartridge was then subjected to an automated washing procedure, using the GeneChipTM Fluidics Station 400 and with a non stringent wash buffer, containing saline, sodium, phosphate, EDTA (SSPE), Tween 20 and antifoam according to the Affymetrix manual. A final wash with the stringent buffer, containing MES-sodium salt and Tween 20 was performed. The probe array was then stained with a solution of acetylated BSA, streptavidin and R-phycoerythrin in stain buffer, containing sodium-MES and Tween 20 and antifoam, followed by non stringent wash buffer. A second stain was performed with a solution of acetylated BSA, normal goat IgG and biotinylated goat antistreptavidin antibody in stain buffer. A third staining step with streptavidin R-phycoerythrin was performed as described above, before a final one with non-stringent wash buffer at 30°C.

scan_protocol: The probe arrays were scanned with the Gene Array Scanner (Affymetrix, Inc. www.affymetrix.com) and controlled by the software GenChip Operating System 1.2 (GCOS; Affymtrix Inc.).

data_processing: The expression level Signals were scaled in GCOS 1.2 to give a median array intensity of 100. This was done to enable different arrays to be compared. The program Spotfire DecisionSite 8.2 (www.spotfire.com) was used for gene-profiling analysis, genes only presences in exosomes and expression differences. For the network analysis to identify biological mechanisms, the program Ingenuity was used (www.ingenuity.com).

source_name: Mouse mast cell line MC/9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix). The microarray experiments were performed by SweGene (www.swegene.org/)

growth_protocol: MC/9 cells were cultured in DMEM, 10% FBS, 100 µg/ml penicillin-streptomycin, 10% Rat T-Stim, 2 mM L-glutamine and 0,05 mM 2-mercaptoethanol at 37°C and 5% CO2.

treatment_protocol: To induce oxidative stress cells were exposed to 125µM H2O2 for 24h under culture conditions.  For isolation of exosomes, MC/9 cell suspension was centrifuged for 10 minutes at 300g, this to pellet the cells, and the exosomes were prepared from the supernatant. First the debris and organelles of the culture were precipitated by centrifugation; 20min at 16,500g, 4°C, and the supernatant was filtered through a 0.22 µm filter, to remove any molecules larger than 200 nm. The exosomes were then pelleted by an ultracentrifugation at 120,000g, 70min, 4°C.

tag: cell type

tag: condition

tag: cell line

value: Mouse mast cell line MC/9


title: 14 day Placebo: 244

status: Public on Jan 07 2011

type: RNA

city: Neuherberg

first: Christine

last: von Toerne

address: Ingoldstädter Landstraße 1

department: Proteinanalytik

country: Germany

institute: HelmholtzZentrum

description: Gene expression data from transplanted rat kidneys (14d post-transplantation)

hyb_protocol: We used standard Affymetrix procedures for hybridization

scan_protocol: Reactions were performed essentially according to the Affymetrix protocol.

data_processing: The resultant .CEL files were analyzed using the ChipInspector software V.0.92 (CI; Genomatix Software GmbH, Munich, Germany). CI does not supply probeset signal intensitites for individual arrays.  Processed log2 (placebo/control) ratio data provided as supplementary files on the Series record.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: transplanted kidney

label_protocol: Standard Affymetrix protocol.  20µg of total RNA were reverse-transcribed and used for biotinylation.

extract_protocol: Total RNA was isolated by the method of Chomczynski and Sacci. RNA quality was characterized using a RNA6000 Nanochip (Agilent

treatment_protocol:
transplantation protocol: Inbred male rats were purchased from Charles River Laboratories GmbH (Sulzfeld, Germany) and were used in all experiments. Kidney transplantation was performed by a modified technique originally described by Lee (1967) under general ether anaesthesia. Unlike the original model, the recipient's right kidney was left in place and no immunosuppressive agent was given, in order to enhance the contribution of rejection to CAD.
Rats were not treated with any medication including Cyclosporine A.

tag: Transplants

value: F344 RT1lvl

tag: Recipients

value: LEW RT1l


title: B Cells, fresh, replicate #2

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

country: USA

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v1GeneChip 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 RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

organism: Mus musculus

source_name: Unactivated B Cells

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

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

treatment_protocol: In brief, the experimental protocol is as follows: splenocytes are isolated from C57Bl/6 mice (6-10 wks old) and cultured for 0, 24, 48 and 72 hrs. Cultures containe either anti-CD3/IL2/IL4 or anti-IgM/IL4 to activate T cells and B cells respectively. At each time point, B, CD4+ and CD8+ cells are purified by positive selection using magnetic beads and total RNA is prepared from each cell type.

tag: Sex

value: unknown

tag: genotype

value: wild-type

tag: strain

tag: disease state

value: healthy

tag: age

value: 3 months


title: B Cells, fresh, replicate #1


title: MC9 cells from H2O2 conditions_rep 1


title: MC9 cells from H2O2 conditions_rep 4


title: 13970009 - Tor 5-2 polysome 24h repet1 vs. Tor 5-2 total 24h repet1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: The impact of the TOR pathway on growth and stress responses.

hyb_protocol: Tor 5-2 total 24h repet1 Cy5 / Tor 5-2 polysome 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 480V, laser power 35%. Cy5: 635nm, pmt voltage 480V, laser power 30%.

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the Loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock. Analyses were performed in R.

organism: Arabidopsis thaliana

source_name: Tor 5-2 total 24h

label_protocol: Labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: Seedling. Media=MS(1/5). Hygrometry=75%. Temperature=20°C.

extract_protocol: Tor 5-2 total 24h repet1:40ug.

treatment_protocol: Name: Induction 24h - compound based treatment - compound addition, ethanol:time 24hour. inducible RNAi

tag: ecotype

value: landsberg erecta

value: AtTor

tag: sample type

value: tor RNAi mutant

tag: tissue

value: seedling

tag: developmental stage

value: Boyes 1.02 (Boyes et al. Plant Cell 2001)

tag: time

source_name: Tor 5-2 polysome 24h

extract_protocol: Tor 5-2 polysome 24h repet1:2ug.


title: 13970008 - Tor 6-3 total 24h repet1 vs. Tor 6-3 polysome 24h repet1

hyb_protocol: Tor 6-3 polysome 24h repet1 Cy5 / Tor 6-3 total 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Tor 6-3 polysome 24h

extract_protocol: Tor 6-3 polysome 24h repet1:2ug.

source_name: Tor 6-3 total 24h

extract_protocol: Tor 6-3 total 24h repet1:40ug.


title: 7 day Placebo: 540

description: Gene expression data from transplanted rat kidneys (7d post-transplantation)


title: 13970007 - Tor 6-3 polysome 24h repet1 vs. Tor 6-3 total 24h repet1

hyb_protocol: Tor 6-3 total 24h repet1 Cy5 / Tor 6-3 polysome 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: B Cells, Activated with aIgM, replicate #1

source_name: B Cells activated with algM


title: MC9 cells from H2O2 conditions_rep 2


title: MC9 cells from normal conditions_rep 4

description: Gene expression data from MC/9 cells that have received normal exosomes

value: normal


title: 13970010 - Tor 5-2 total 24h repet1 vs. Tor 5-2 polysome 24h repet1

hyb_protocol: Tor 5-2 polysome 24h repet1 Cy5 / Tor 5-2 total 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Exosomes from H2O2 conditions_rep 4

description: Gene expression data from exosomes isolated from H2O2 conditions

value: Exosomes


title: 7 day Placebo: 539


title: 7 day Placebo: 213


title: MC9 cells from normal conditions_rep 2


title: MC9 cells from normal conditions_rep 3


title: MC9 cells from normal conditions_rep 1


title: Control kidney: N4

description: Gene expression data from transplanted rat kidneys (control)


title: 13969996 - GUS polysome 24h repet1 vs. GUS total 24h repet1

hyb_protocol: GUS total 24h repet1 Cy5 / GUS polysome 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: GUS total 24h

extract_protocol: GUS total 24h repet1:40ug. (Extraction-ARNs-totaux.doc)

value: gus

value: GUS control

source_name: GUS polysome 24h

extract_protocol: GUS polysome 24h repet1:2ug. (Extraction-ARNs-polysomaux.doc)


title: 7 day Placebo: 211


title: 27051402_setdb1_3

city: Karp 7

first: Yariv

last: Houvras

state: MA

address: 1 Blackfan Circle

institute: Childrens Hospital Boston

description: This sample is of MiniCoopR-SETDB1 melanoma. It is one of four biological replicates used in the experiment.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Danio rerio

source_name: MiniCoopR-SETDB1_3 melanoma

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Zebrafish of the indicated genotype were mated, and embryos were injected with either MiniCoopR-GFP or MiniCoopR-SETDB1 transposon vectors.  Transgenic zebrafish with melanocytes were raised to adulthood.  Zebrafish with dorsal melanomas were isolated, and melanomas were allowed to grow for 3 weeks from the date of onset.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, USA).

value: p53-M214k; mitf -/-; mitf:BRAF-V600E

value: melanoma

tag: transposon vector


title: 13969997 - GUS total 24h repet1 vs. GUS polysome 24h repet1

hyb_protocol: GUS polysome 24h repet1 Cy5 / GUS total 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 26816402_setdb1_4

source_name: MiniCoopR-SETDB1_4 melanoma


title: Control kidney: N3

value: F344 RT1lvl


title: HeLa U133_Plus2 gene expression

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

description: gene expression profiling of asynchronously growing HeLa cells

hyb_protocol: Hybridizations were performed as directed by the manufacturer.

scan_protocol: The microarray was scanned using a GeneChIP Scanner 3000.

data_processing:
The data was analyed using GeneChIP Operating Software (GCOS; Affymetrix).
Transcript signal was mapped against the chromosome coordinates (probe-by-probe basis) using the HG-U133A_2 Annotations CSV file for hg18 build of the human genome provided by Affymetrix.

organism: Homo sapiens

source_name: HeLa (ATCC CCL-2)

label_protocol: Samples were processed and labeled according to Affymetrix protocols.

growth_protocol: Adherant HeLa (ATCC CCL-2) cells were maintained in DMEM/high glucose (Hyclone, Thermo Scientific) in the presence of 10% DCS and 1X penicillin/streptomycin at in 5% CO2 37 degrees.

extract_protocol: Total RNA extraction is according to the manufacturer's instructions (Invitrogen) using Trizole reagent.

treatment_protocol: No treatment done

value: HeLa (ATCC CCL-2)


title: Control kidney: N2


title: 26809002_setdb1_2

source_name: MiniCoopR-SETDB1_2 melanoma


title: Exosomes from H2O2 conditions_rep 2

value: Mouse mast cell line MC/9


title: Expression profile of  asf1-1 cells

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled mutant cDNA and Cy3-labeled wild-type cDNA were mixed and combined with human Cot1DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (GE2-v5_10_Apr08 protocol) and subjected to combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

organism: Schizosaccharomyces pombe

source_name: log. growing cells

label_protocol: Ribosomal RNA was depleted with RiboMinus kit (Invitrogen) and total RNA reverse-transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Total RNA was extracted using Master Pure Yeast RNA purification kit (Epicenter) according manufacturer's instructions.

value: wild-type


title: Expression profile of  ∆hip1 cells


title: Exosomes from H2O2 conditions_rep 3


title: 26809202_gfp_3

description: This sample is of MiniCoopR-GFP melanoma. It is one of four biological replicates used in the experiment.

source_name: MiniCoopR-GFP_3 melanoma

value: MiniCoopR-GFP


title: Exosomes from normal conditions_rep 4

description: Gene expression data from exosomes isolated from normal conditions


title: Exosomes from H2O2 conditions_rep 1


title: 26809302_gfp_4

source_name: MiniCoopR-GFP_4 melanoma


title: H3K9ac in alp13∆ cells

type: genomic

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_107_Sep09 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

molecule: genomic DNA

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated by appropriate antibody: H3K9ac (Upstate). Immunoprecipitated DNA was recovered by incubation with protein A slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 18˚C.

tag: antibody


title: H3K9ac in asf1-1 cells

tag: cell type


title: Exosomes from normal conditions_rep 2

source_name: Mouse mast cell line MC/9

tag: condition


title: 26692502_gfp_2

source_name: MiniCoopR-GFP_2 melanoma


title: H3K9ac in wild-type cells


title: Subject 014 post surgery

status: Public on Jan 06 2011

city: Cleveland

first: Jonathan

middle: David

last: Smith

state: OH

address: 9500 Euclid Avenue

department: Cell Biology

institute: Cleveland Clinic

description: Collected post surgery

hyb_protocol: Purified labeled cDNA was hybridized to HumanWG–6 v2 Expression BeadChip (Illumina) microarrays according to the manufacturer’s instructions.  The hybridization temperature was reduced to 48oC, following the instructions from NuGEN to adjust the conditions for hybridization of cDNA rather than cRNA.

scan_protocol: The arrays were scanned on the Illumina BeadArray Reader using Illumina BeadScan image data acquisition software.

data_processing: The image data were quantitatively analyzed and quantile normalized without further background subtraction using the BeadStudio Software.

label: Biotin

source_name: Whole blood

label_protocol: Total RNA was amplified using Ovation RNA amplification System V2 (NuGEN). The amplified single stranded cDNA was labeled with biotin following the manufacturer’s protocol.

extract_protocol: Total RNA was isolated using PAXgene Blood RNA Kit (Qiagen) following manufacturer’s guidelines. RNase-Free DNase was used for on-column DNA digestion.  Quality of RNA was evaluated by incubating 200-400 ng of total RNA for each sample at 37oC overnight.

treatment_protocol: 11 obese subjects with type 2 diabetes participated in this study. They all underwent bariatric surgery.

tag: gender

value: Female


title: Subject 014 pre surgery

description: Collected pre surgery


title: Exosomes from normal conditions_rep 3

tag: cell line


title: 26807002_gfp_1

source_name: MiniCoopR-GFP_1 melanoma


title: Subject 013 post surgery

description: Collected post surgery

value: Male


title: Exosomes from normal conditions_rep 1


title: Subject 008 post surgery

description: Collected post surgery


title: Subject 503 pre surgery

description: Collected pre surgery


title: 26645502_setdb1_1

source_name: MiniCoopR-SETDB1_1 melanoma


title: Subject 015 post surgery

description: Collected post surgery


title: Subject 013 pre surgery

description: Collected pre surgery


title: Subject 501 pre surgery

description: Collected pre surgery


title: Subject 005 pre surgery

description: Collected pre surgery


title: Subject 012 pre surgery

description: Collected pre surgery


title: Subject 006 post surgery

description: Collected post surgery


title: Subject 501 post surgery

description: Collected post surgery


title: Subject 006 pre surgery

description: Collected pre surgery


title: Subject 007 post surgery

description: Collected post surgery


title: Subject 005 post surgery

description: Collected post surgery


title: Subject 008 pre surgery

description: Collected pre surgery


title: Subject 503 post surgery

description: Collected post surgery


title: Subject 015 pre surgery

description: Collected pre surgery


title: Subject 007 pre surgery

description: Collected pre surgery


title: Subject 004 pre surgery

description: Collected pre surgery


title: CD4+ Lymphocyte, fresh, replicate #2

source_name: Unactivated CD4 lymphocytes

value: unknown

value: healthy

value: 3 months


title: M.smegmatis_mc2_155_dMSMEG_0166_study_mutant_rep3

city: Portland

first: Melissa

middle: Suzan

last: Standley

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: Oregon Health & Science University

description: This sample is of Mycobacterium smegmatis mc2 155 delta-MSMEG_0166, a triple deletion mutant in which the gene encoding MSMEG_0166 is interupted by the insertion of a hygromycin resistance cassette. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by S. Caprice Rosato at the Center for Genome Research and Biocomputing at Oregon State University, Corvallis, OR, USA, following their standard operating protocol. See http://corelabs.cgrb.oregonstate.edu/.

scan_protocol: Scanning was performed by S. Caprice Rosato at the Center for Genome Research and Biocomputing at Oregon State University, Corvallis, OR, USA, following their standard operating protocol. See http://corelabs.cgrb.oregonstate.edu/.

organism: Mycolicibacterium smegmatis MC2 155

label_protocol:
cDNA was synthesized either using Superscript III First Strand Synthesis Kit (Invitrogen, Carlsbad, CA, USA) followed by treatment with Large Fragment DNA Polymerase I (Invitrogen), and was cleaned up using the MinElute PCR Purification Kit (Qiagen Inc., Valencia, CA, USA) or cDNA was synthesized by S. Caprice Rosato at the Center for Genome Research and Biocomputing at Oregon State University, Corvallis, OR, USA, following their standard operating protocol. See http://corelabs.cgrb.oregonstate.edu/. cDNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer and a Nanodrop ND-1000.
Labeling was performed by S. Caprice Rosato at the Center for Genome Research and Biocomputing at Oregon State University, Corvallis, OR, USA, following their standard operating protocol. See http://corelabs.cgrb.oregonstate.edu/.

growth_protocol:
Mycobacterium smegmatis mc2 155 was grown to mid-log phase (O.D.600nm 0.8) aerobically at 37°C in Middlebrook 7H9 media supplemented with OADC and Tween 80 (Rinsho Biseibutshu Jinsoku Shindan Kenkyukai Shi. 2000;11(2):79-85).
Mycobacterium smegmatis mc2 155 delta-MSMEG_0166 was grown to mid-log phase (O.D.600nm 0.8) aerobically at 37°C in Middlebrook 7H9 media supplemented with OADC and Tween 80 (Rinsho Biseibutshu Jinsoku Shindan Kenkyukai Shi. 2000;11(2):79-85).

extract_protocol: Following treatment with lysozyme and mechanical disruption of the cell wall, total RNA was extracted using TriReagent (Molecular Research Center, Inc., Cincinnati, OH, USA)/chloroform and cleaned up using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) or the High Pure RNA Isolation Kit (F. Hoffmann-La Roche Ltd, Basel, Switzerland). DNA was removed off-column by DNase digestion with the TURBO DNA-free kit (Applied Biosystems/Ambion, Austin, TX, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer and a Nanodrop ND-1000.

tag: genotype/variation

value: Single gene mutant delta-MSMEG_0166

tag: phenotype

value: Ub2 and oxidative stress hypersensitive


title: Subject 004 post surgery

description: Collected post surgery


title: M.smegmatis_mc2_155_dMSMEG_0166_study_mutant_rep2

description: This sample is of Mycobacterium smegmatis mc2 155 delta-MSMEG_0166, a triple deletion mutant in which the gene encoding MSMEG_0166 is interupted by the insertion of a hygromycin resistance cassette. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: M.smegmatis_mc2_155_dMSMEG_0166_study_wild-type_rep2

description: This sample is of wild-type Mycobacterium smegmatis mc2 155. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Mycobacterium smegmatis mc2 155 wild-type

value: Wild-type

value: normal


title: 231-knockdown-rep 3

city: Augusta

first: yong

last: teng

address: 1120 15th Street

institute: Medical College of Georgia

description: highly aggressive cancer cell line

hyb_protocol: All samples passing this quality control were hybridized to a GeneChip® Human Genome U133A 2.0 Array (Affymetrix, CA) probing 18,400 transcripts and variants. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450 (x2)  .

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip Scanner 3000 7G Plus

data_processing: The data were analyzed with Affymetrix Expression Console Software (v.1.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA). The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: WASF3 knockdown single clone 3

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).The probe was generated using the Affymetrix 3’ IVT Express protocol.

growth_protocol: MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol: RNAs were extracted using Trizol reagent (Invitrogen) and the Qiagen RNeasy kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using a Bioanalyzer to assess the quality of the sample.

treatment_protocol: To generate WASF3 stable knockdown MDA-MB-231 cells, the pSM2 retroviral vectors containing a short hairpin RNA against WASF3 (shRNA1 - V2LHS 261688; shRNA2-V2LHS90825; Open Biosystems, Huntsville, AL) were used for infection. As controls the empty pSM2 vector and an shRNA targeting GFP, were used. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and individual drug-resistant clones were collected and expanded.

value: MDA-MB-231 passage 4, puromycin resistant


title: M.smegmatis_mc2_155_dMSMEG_0166_study_wild-type_rep3

description: This sample is of wild-type Mycobacterium smegmatis mc2 155. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 231-knockdown-rep 2

description: highly aggressive cancer cell line

source_name: WASF3 knockdown single clone 2


title: 231-control-rep 2

description: highly aggressive cancer cell line

source_name: control single clone 2


title: 231-control-rep 3

description: highly aggressive cancer cell line

source_name: control single clone 3


title: 231-control-rep 1

description: highly aggressive cancer cell line

source_name: control single clone 1


title: M.smegmatis_mc2_155_dMSMEG_0166_study_wild-type_rep1

description: This sample is of wild-type Mycobacterium smegmatis mc2 155. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 231-knockdown-rep 1

description: highly aggressive cancer cell line

source_name: WASF3 knockdown single clone 1


title: M.smegmatis_mc2_155_dMSMEG_0166_study_mutant_rep1

description: This sample is of Mycobacterium smegmatis mc2 155 delta-MSMEG_0166, a triple deletion mutant in which the gene encoding MSMEG_0166 is interupted by the insertion of a hygromycin resistance cassette. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: G11OH-T_4h-OH2

city: Manhattan

first: Ross

last: Levine

state: NY

address: RRL

institute: MSKCC

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: The data were analyzed with dchip with default parameters.

source_name: Resistant 4OHT

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

value: tumor breast


title: G11OH-T_4h-E2

source_name: Resistant estradiol


title: G11OH-T_4h-E+OH3

source_name: Resistant estradiol+4OHT


title: G11OH-T_4h-E+OH2


title: G11OH-T_4h-E+OH1


title: G11OH-T_4h-OH3


title: 92.1 - siBAP1 - replicate1

city: St. Louis

first: Elisha

last: Roberson

state: MO

address: 660 South Euclid Ave., CB 8045

department: Internal Medicine & Genetics

institute: Washington University in St. Louis

description: replicate 1 - separate transfection

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were analyzed using beadarray and limma R packages. Raw data were log2 transformed and quantile normalized. siBAP1 versus siControl contrast was analyzed against the fitted linear model using eBayes functions in limma.

source_name: 92.1 cells

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion, AMIL1791). Cleanup with DNA Clean-up and Concentrator 5 columns (zymo research).

growth_protocol: Grown in RPMI-1640 (Lonza) supplemented with 10% fetal bovine serum

extract_protocol: Qiagen RNEasy RNA isolation kit according to manufacturer's instructions.

treatment_protocol: All lines transfected using HiPerFect (Qiagen) system according to manufacturer's instructions. Silencing constructs consisted of either control #1 siRNA (Ambion) or Silencer Select BAP1. 5 days post transfection cells were harvested for RNA extraction.

tag: knockdown


title: 92.1 - siBAP1 - replicate3

description: replicate 3 - separate transfection


title: G11OH-T_4h-E3


title: 92.1 - control #1 - replicate2

description: replicate 2 - separate transfection

value: Control


title: G11OH-T_4h-E1


title: G11OH-T_4h-C2

source_name: Resistant control


title: G11OH-T_4h-C1


title: 92.1 - siBAP1 - replicate2

description: replicate 2 - separate transfection


title: B7_4h-E+OH3

source_name: Sensitive estradiol+4OHT


title: 92.1 - control #1 - replicate3

description: replicate 3 - separate transfection


title: B7_4h-E+OH2


title: B7_4h-OH3

source_name: Sensitive 4OHT


title: G11OH-T_4h-OH1


title: G11OH-T_4h-C3


title: 92.1 - control #1 - replicate1

description: replicate 1 - separate transfection


title: B7_4h-OH2


title: B7_4h-C2

source_name: Sensitive control


title: B7_4h-E+OH1


title: B7_4h-E3

source_name: Sensitive estradiol


title: B7_4h-C3


title: B7_4h-OH1


title: B7_4h-E1


title: B7_4h-C1


title: EBNA3CHT LCL C51 HT- day 7 (Non-permissive) replicate4

city: Boston

first: Bo

last: Zhao

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

hyb_protocol: Following Affymetrix's mannual

scan_protocol: Following Affymetrix's mannual

data_processing: Following Affymetrix's mannual

source_name: EBNA3CHT LCLs grown in HT- media for 7 days

label_protocol: Following Affymetrix's mannual

growth_protocol: EBNA3CHT LCLs were grown in the presence (permissive) or the absence (non-permissive) of HT for 7 days, or transcomplemented with an OriP base EBNA3C expression vector and grwon in the absence of HT for 12 weeks.

extract_protocol: Total cellular RNA was prepared using RNABee following manufacturer's mannual.

treatment_protocol: EBNA3CHT LCLs were washed with fresh RPMI media 3 times, incubated at 37C for 30 minutes and washed twice again. The cells were seeded in the HT+ or HT- media and grown for 7 days. The cell concentration was kept around 300,000/ml. EBNA3CHT LCLs were transfected with Ori-P based EBNA 3C expression plasmid and grown in HT- media for 12 weeks.

value: EBNA3CHT recombinant EBV transformed human lymphoblastoid cell line

tag: growth condition

value: HT-

tag: ebna3c epresssion

value: Little EBNA3CHT, Mostly Cytoplasm


title: B7_4h-E2


title: EBNA3CHT LCL C51 HT- day 7 (Non-permissive) replicate3


title: EBNA3CHT LCL C51 HT- day 7 (Non-permissive) replicate2


title: N206_1

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Gene expression data from N206 cells

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: N206 were isolated from NOD mice

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf)

growth_protocol: The T cells were cultured in RPMI medium plus 5% fetal bovine serum and IL2.

extract_protocol: Qiagen RNA extraction kit was used according to manufacturer's guide

value: Treg cells

tag: t cell type

tag: strain

value: NOD mice


title: EBNA3CHT LCL C19 HT- day 7 (Non-permissive) replicate3


title: EBNA3CHT LCL C19 HT- day 7 (Non-permissive) replicate1


title: NR206_1

description: Gene expression data from NR206 cells.

source_name: NR206 were isolated from NOR mice

value: NOR mice


title: EBNA3CHT LCL C51 HT- day 7 (Non-permissive) replicate1


title: EBNA3CHT LCL C19 HT- day 7 (Non-permissive) replicate2


title: BDC_2

description: Gene expression data from BDC cells

source_name: BDC cells were isolated from BDC NOD mice

value: Tpath cells

value: BDC


title: EBNA3CHT LCL C15 HT- day 7 (Non-permissive) replicate4


title: EBNA3CHT LCL C15 HT- day 7 (Non-permissive) replicate3


title: N79_2

description: Gene expression data from N79 cells

source_name: N79 were isolated from NOD mice

value: T cells (neutral control cells)


title: N79_1

description: Gene expression data from N79 cells


title: EBNA3CHT LCL C19 HT- day 7 (Non-permissive) replicate4


title: EBNA3CHT LCL C15 HT- day 7 (Non-permissive) replicate2


title: EBNA3CHT LCL C51 HT+ day 7 (Permissive) replicate4

source_name: EBNA3CHT LCLs grown in HT+ media for 7 days

value: HT+

value: EBNA3CHT, Nucleus


title: N206_2

description: Gene expression data from N206 cells


title: BDC_1

description: Gene expression data from BDC cells


title: NR206_2

description: Gene expression data from NR206 cells.


title: EBNA3CHT LCL C51 HT+ day 7 (Permissive) replicate2


title: EBNA3CHT LCL C15 HT- day 7 (Non-permissive) replicate1


title: EBNA3CHT LCL C51 HT+ day 7 (Permissive) replicate3


title: EBNA3CHT LCL C51 HT+ day 7 (Permissive) replicate1


title: EBNA3CHT LCL C19 HT+ day 7 (Permissive) replicate3


title: EBNA3CHT LCL C19 HT+ day 7 (Permissive) replicate2


title: EBNA3CHT LCL C19 HT+ day 7 (Permissive) replicate4


title: EBNA3CHT LCL C19 HT+ day 7 (Permissive) replicate1


title: EBNA3CHT LCL C15 HT+ day 7 (Permissive) replicate3


title: M8 114C-2

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

institute: Institute for Medical Microbiology

hyb_protocol: Portions of 20 µg cRNA were subjected to fragmentation in the presence of Mg2+. Subsequently 10 µg fragmented cRNA (target) was loaded onto CodeLink Mouse Whole Genome Microarray glass slides containing 36.227 probe sets (Applied microarrays, Tempe AZ, USA) and hybridised for 18 h in a Minitron shaker incubator (Infors AG, Bottmingen, Germany) at 37Co/300rpm (n = 2 arrays per sample). Washing and dyeing with Cy-5 coupled streptavidin was done according to the original protocol for CodeLink arrays (Applied microarrays, Tempe AZ, USA)

scan_protocol: Arrays were scanned using a GenePix 4000 B scanner and GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA)

data_processing: Spot signals of CodeLink bioarrays were quantified using CodeLink System Software consisting of Batch Submission (V2.2.27) and Expression Analysis (V2.2.25) (GE Healthcare) as outlined in the user's manual. CodeLink Expression Software 1.21 generated background corrected raw as well as median centered intra-slide normalized data. The intra-slide normalized data were used for further analysis. These data were checked for quality control. Qutlier values were discarded. Missing values were imputed using sequential K-nearest neighbour (SKNN) imputation. Resulting data were quantile normalized and logged to base 2. Differentially regulated genes between KO and WT mice were identified using a novel two-class rank statistics (Rank products, RP). For each gene, a false discovery rate (FDR) < 0.05 was defined as the significance level.

source_name: testicular tissue

label_protocol: 1 µg total RNA were used in cDNA synthesis reaction with a poly-A binding primer containing the T7-polymerase promoter. Resulting cDNA was transcribed into cRNA in one round amplification in the presence of 11-Bio-UTP. Double stranded cDNA and biotin labelled cRNA were purified using the mini columns included in the kit.

growth_protocol: Breeding strategy, genotyping and confirmation of Cx43-gene loss by b-gal immunohistochemistry (IHC) of WT and homozygous SCCx43KO-/- mice were realized as described previously [Brehm et al. Am J Pathol, 2007. 171 (1):19-31]. For all experiments, eight day old mice were used, except for immunofluorescence (IF) where fifteen day old mice were utilised, since DMRT7 protein is known to be first detectable from day 13.5 onwards

extract_protocol: To carry out Microarray analysis, one testis of three mice of each genotype was used. Total RNA was prepared from dissected testis tissues using RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: Mice were anesthetized and sacrificed by intraperitoneal injection of an overdose cocktail of ketamine hydrochloride (Medistar, Holzwickede, Germany) and xylazine (Serumwerk Bernburg, Bernburg, Germany). The body and testis weights were defined. Both testes were removed immediately. One testis was snap-frozen in liquid nitrogen and then stored at -80°C until RNA extraction, the other was placed in Bouin´s solution over night for IHC and hematoxylin and eosin staining (H&E), followed by paraffin embedding. For IF the second testis was placed in formalin for two hours before paraffin embedding.

value: Knock-out (SCCx43KO-/-)


title: B781_V71_DF2

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean, done by Partek Genomics suite (version 6.5 Copyright © 2010)

extract_protocol: Trizol reagent (Invitrogen)

tag: treatment

tag: differentiation

value: differentiated


title: EBNA3CHT LCL C15 HT+ day 7 (Permissive) replicate1


title: EBNA3CHT LCL C15 HT+ day 7 (Permissive) replicate4


title: EBNA3CHT LCL C51 transcomplemented with EBNA3C (Trans) replicate 3

source_name: EBNA3C transcomplemented for 12 weeks and grown in HT- media

value: WT EBNA3C, Nucleus


title: EBNA3CHT LCL C51 transcomplemented with EBNA3C (Trans) replicate 1


title: B777_V71_NDF3

scan_protocol: according to the instruction manual, as described in the Affymetrix website

value: undifferentiated


title: M8 114C-1


title: EBNA3CHT LCL C19 transcomplemented with EBNA3C (Trans) replicate 1


title: M7 114B-2

value: Wild Type


title: B780_V71_DF1

label_protocol: according to the instruction manual, as described in the Affymetrix website

value: Control


title: EBNA3CHT LCL C19 transcomplemented with EBNA3C (Trans) replicate 2

value: EBNA3CHT recombinant EBV transformed human lymphoblastoid cell line


title: B778_PLKO_DF1

value: IKBKAP shRNA


title: EBNA3CHT LCL C19 transcomplemented with EBNA3C (Trans) replicate 3

value: HT-


title: M8 114A-1


title: B776_V71_NDF2


title: M7 112B-1


title: EBNA3CHT LCL C15 HT+ day 7 (Permissive) replicate2


title: M7 114B-1


title: EBNA3CHT LCL C15 transcomplemented with EBNA3C (Trans) replicate 2


title: EBNA3CHT LCL C51 transcomplemented with EBNA3C (Trans) replicate 2


title: M8 114A-2


title: UK-Affy_small intestine

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

description: Gene expression data from Mus musculus small intestine

hyb_protocol: according to the Mouse 430 2.0 protocol by Affymetrix

data_processing: Normalization was performed using Spotfire DSMA, method: GCRMA

source_name: Mus musculus small intestine biopsy

extract_protocol: RNA extraction performed with Qiagen RNeasy according to the manufacturers protocol, quality control using an Agilent Bioanalyzer

tag: tissue

value: small intestine

tag: genotype

value: wild-type

tag: age

value: adult


title: B775_PLKO_NDF3


title: B774_PLKO_NDF2


title: Subject 012 post surgery

description: Collected post surgery

source_name: Whole blood

value: Male


title: EBNA3CHT LCL C15 transcomplemented with EBNA3C (Trans) replicate 1


title: UK-Affy_colon

description: Gene expression data from Mus musculus colon

scan_protocol: according to the Mouse 430 2.0 protocol by Affymetrix

source_name: Mus musculus colon biopsy

value: colon


title: B779_PLKO_DF2


title: M7 112B-2


title: p73_ChIP_Veh_B

status: Public on Jan 05 2011

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

institute: Vanderbilt University Medical Center

description: p73 Rh30 Vehicle ChIP, array B

hyb_protocol: see GenPathway Inc. FactorPath protocol

scan_protocol: see GenPathway Inc. FactorPath protocol

data_processing:
The CEL files were analyzed using Affymetrix' Tiling Analysis Software.  A two-sample analysis was performed to generate BAR files that contain the signal values for all probes on the arrays (moving statistic, ratio in linear scale ChIP/input).  MaxGap = 400 bp, MinRun = 180 bp, intervals had signals >= 2.5.
Results file descriptions: The .bar files contain signals generated using Affymetrix' Tiling Analysis Software (moving statistic, ratio ChIP/input).  The GSE15703_intervalbed.bed file contains p73 binding site intervals and peaks for the vehicle and rapamycin-treated samples. The BED file is available on the GSE15703 Series record.

source_name: p73 ChIP DNA from Rh30, vehicle

label_protocol: see GenPathway Inc. FactorPath protocol

growth_protocol: Cells were cultured in RPMI (Invitrogen) containing 10% Fetal Bovine Serum.

extract_protocol: Rh30 cells were crosslinked with formaldehyde, crosslinks were reversed, and samples were lysed according to GenPathway, Inc. FactorPath protocols.

treatment_protocol: Rh30 cells were treated with vehicle or 40 nM rapamycin in serum-free media for 24 h.

tag: cells

value: Rh30 rhabdomyosarcoma cells

value: Vehicle

tag: antibody

value: Bethyl A300-126A anti-p73

source_name: input DNA from Rh30


title: EBNA3CHT LCL C15 transcomplemented with EBNA3C (Trans) replicate 3

tag: cell type


title: p73_ChIP_Rap_B

description: p73 Rh30 Rapamycin ChIP, array B

source_name: p73 ChIP DNA from Rh30, rapamycin

value: 40 nM rapamycin


title: p73_ChIP_Rap_D

description: p73 Rh30 Rapamycin ChIP, array D


title: p73_ChIP_Rap_C

description: p73 Rh30 Rapamycin ChIP, array C


title: p73_ChIP_Veh_C

description: p73 Rh30 Vehicle ChIP, array C


title: p73_ChIP_Veh_D

description: p73 Rh30 Vehicle ChIP, array D


title: p73_ChIP_Veh_A

description: p73 Rh30 Vehicle ChIP, array A


title: p73_ChIP_Rap_A

description: p73 Rh30 Rapamycin ChIP, array A


title: IMR90, biological rep1

city: Singapore

first: Yee Jiun

last: Kok

address: 20 Biopolis Way, #06-01 Centros

country: Singapore

institute: Bioprocessing Technology Institute

hyb_protocol: Hybridisations were carried out at 45°C for 16h with reagents from Affymetrix “GeneChip Hybridization, Wash, and Stain Kit”, with subsequent washing and staining of arrays automated and preprogrammed (FS450_0001) on GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 using default settings.

data_processing: Images were extracted and analyzed by MAS5.0 workflow with default settings in Expression Console v1.1.

source_name: Trancripts from IMR90

label_protocol: Total RNA was reversed transcribed and biotinylated using Affymetrix 3' IVT Express Kit.

growth_protocol: HES-3 and ESIMR90 were cultured on BD Matrigel in mTeSR1 media; IMR90 was cultured in DMEM media supplemented with 10% FBS, 2mM L-glutamine, and 20 units each of penicillin and streptomycin.

extract_protocol: Total RNA was extracted from cell pellets using TRIzol reagent (Invitrogen) as per manufacturer's protocol. RNA extracted into the aqueous phase was concentrated by precipitation in equal volume of isopropnaol at -20°C overnight, and subsequently purified using Qiagen Rneasy Mini Kit according to manufacturer's protocol.

value: female fetal lung fibroblasts from ATCC (CCL-186)


title: ES4SKIN, biological rep 1

source_name: Trancripts from ESIMR90

growth_protocol: HES-3 and ES4SKIN were cultured on BD Matrigel in mTeSR1 media; FORESKIN was cultured in DMEM media supplemented with 10% FBS, 2mM L-glutamine, and 20 units each of penicillin and streptomycin.

value: iPS cells derived from FORESKIN


title: FORESKIN, biological rep 2

source_name: Trancripts from FORESKIN

value: newborn foreskin fibroblasts from ATCC (CRL-2097)


title: HES-3, biological rep2

source_name: Trancripts from HES-3

value: embryonic stem cells from ESI


title: ESIMR90, biological rep2

value: iPS cells derived from IMR90


title: INPUT

city: Los Angeles

first: Tasuku

last: Kitada

address: 611 Charles E Young Dr East

institute: University of California, Los Angeles

hyb_protocol: Affymetrix 500K.

scan_protocol: Affymetrix 500K.

data_processing: Two sample comparison (input DNA as the control group) with the Affymetrix® Tiling Analysis Software (TAS) v1.1.

organism: Saccharomyces cerevisiae

source_name: INPUT DNA

label_protocol: Affymetrix 500K.

growth_protocol: YPD at 30 degrees C.

extract_protocol: Hecht et al., Nature 1996.

treatment_protocol: Formaldehyde fixed.

tag: fraction

value: Input


title: HES-3, biological rep 1


title: HES-3, biological rep1


title: ES4SKIN, biological rep 2


title: RNA polymerase II

data_processing:
Two sample comparison (input DNA as the control group) with the Affymetrix® Tiling Analysis Software (TAS) v1.1.
Corresponding input record: GSM543122

source_name: RNAP II ChIP DNA

value: RNAP II, monoclonal

tag: antibody manufacturer

value: Covance

tag: antibody catalog

value: ChIP DNA


title: FORESKIN, biological rep 1


title: ESIMR90, biological rep1


title: IMR90, biological rep2


title: HES-3, biological rep 2


title: INPUT_6


title: INPUT_4


title: INPUT_3


title: INPUT_1


title: gH2A

data_processing:
Two sample comparison (input DNA as the control group) with the Affymetrix® Tiling Analysis Software (TAS) v1.1.
Corresponding input records: GSM543115, GSM543116, GSM543117, GSM543118, GSM543119, GSM543120

source_name: gamma-H2A ChIP DNA

value: gamma-H2A, polyclonal

value: Abcam

value: ChIP


title: Soybean_Tamahomare_Podelongation1

city: Bunkyo-ku yayoi

first: Tomoyo

last: Narikawa

state: Tokyo

country: Japan

institute: University of Tokyo

description: Gene expression data from pods of Tamahomare at reproductive development

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AFFYMETRIX GeneChip Scanner 3000.

data_processing:
CEL files processed with Algorithm: ExpressionStat 5.0
The data were analyzed with Distribution Free Weighted method (DFW) using Bioconductor and R

organism: Glycine max

source_name: soybean pod at the beginning of Pod elongation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: tRNAwas extracted using RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: Samples were stored at -80C until RNA extraction.

tag: cultivar

value: Tamahomare

tag: developmental stage

value: Pod elongation


title: Soybean_Tamahomare_Bean2mm2

description: Gene expression data from pods and beans of Tamahomare at reproductive development

source_name: soybean seed and pod when the bean's length is 2mm

value: Bean 2mm


title: Soybean_Tamahomare_Bean2mm1


title: Soybean_Tamahomare_Podelongation2


title: Male WSP-1 EtOH Pool 2 21d

first: Marina

last: Guizzetti

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

hyb_protocol: Hybridization with complex labeled RNA probe was performed overnight at 50 degrees C with 20 ml Ultra-Array hybridization buffer (Ambion).  The final post hybridization wash was at 50 degrees C in 0.5 x SSC, 0.5% SDS.

scan_protocol: Microarrays were exposed to storage phosphor screens for 2 h and scanned at high resolution with a Cyclone phosphorimager and OptiQuant software (Perkin Elmer).

data_processing: Raw expression values were obtained using Pathways v4 Software (Research Genetics) and exported. The raw values were imported into Vector Expression 3.1 where log2-transformation, conversion to z-scores, multiplied by 2 and added to eight so that each array has a mean of 8, a variance of 4, and a standard deviation of 2.

source_name: prefrontal cortex

label_protocol: Rnase treated total RNA isolated from the PFC of two animals (2.5 micrograms each) was pooled for each complex probe labeling reaction.  Probe labeling from the total RNA mixture was performed by linear synthesis with 33P-dATP incorporation using the Array Advantage kit (Ambion) using anchored oligo-dT primers and M-MLV reverse transcriptase with a 42 degree C incubation for 2 hours.  Complex probes were purified by passage through a NucAway spin column.

extract_protocol: Total RNA was extracted from the PFC using RNA  STAT-60 (Tel-Test, Inc.) according to the manufacturers protocol.  Contaminating genomic DNA was  removed by digestion with Rnase free Dnase followed by Zymo-spin column purification according to the manufacturer's recommendations (Zymo Research).

treatment_protocol: Two independently derived replicate Withdawal-Seizure Prone (WSP) and Withdrawal-Seizure Resistant (WSR) were derived by selective breeding for divergent withdrawal severity from genetically heterogeneous HS/Ibg mice.  Female and male mice from both replicates were tested for expression differences.  To identify phenotype-specific differences, expression analysis was collapsed on replicate for each selected line.  Mice were maintained under a light/dark cycle of 0600-1800 light with water and Purina Lab Diet Chow available ad libitum.  Room temperatures were maintained at 22 +/- 1 degree celcius.  All animal procedures were approved by the Portland Oregon VA Medical Center Institutional Animal Care and Use committee and followed US National Institutes of Health animal welfare guidelines.  Mice were made dependent upon Ethanol (EtOH) using a method of vapor inhalation in chambers manufactured in-house, with modifications previously published (Beadles-Bohline and Wiren, 2006).  Drug-naive adult mice from selected generation 26 (filial generation G87-G116) were used.  EtOH exposure was initiated at 0800 h.  On day one EtOH mice were weighed, injected i.p. with EtOH at 1.5 g/kg for WSP-1, WSR-1, WSR-2 and1.75 g/kg for WSP-2 animals, necessary to maintain similar blood EtOH concentrations between the selected lines, and 68.1 mg/kg pyrazole HCl.  Control animal were placed into air chambers and received pyrazole only.  All mice again received pyrazole (68.1 mg/kg) at 24 h and 48 h to reduce fluctuations in BEC.  EtOH exposed mice had 20 microliters of blood take from the tail for daily BEC determination.  Following 72 h of constant EtOH vapor exposure, all mice were removed from the chambers, weighed, and had tail blood samples drawn for BEC determination by gas chromatography as previously described.  Prefronal cortex (PFC) was isolated by dissection from whole brain by first discarding the olfactory bulb and making a coronal slice 2 mm into the frontal region of the cortex.  Lateral regions were removed by cutting the tissue at a 45 degree angle with the lobes facing upward.

tag: sex

value: Male

tag: selected line

value: WSP

tag: selected line rep

value: Ethanol vapor

tag: biological replicate

tag: time point

value: 21d withdrawal


title: Male WSR-1 EtOH Pool 2 21d

value: WSR

tag: treatment


title: Male WSR-2 Air Pool 2 21d

value: Control


title: Male WSR-2 EtOH Pool 2 21d


title: Male WSR-2 EtOH Pool 1 21d


title: Male WSR-1 EtOH Pool 1 21d


title: Male WSR-1 Air Pool 2 21d


title: Male WSR-2 Air Pool 1 21d


title: Male WSP-1 EtOH Pool 1 21d


title: Male WSP-1 Air Pool 2 21d


title: Male WSP-1 Air Pool 1 21d


title: Female WSR-2 EtOH Pool 2 21d

value: Female


title: WT_2

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.10). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's test. Only data with a false discovery rate (FDR) adjusted p-value <0.05 and at least 2x differential expression were included in the analysis. Data underwent z-score transformation for display.

source_name: Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

tag: strain

tag: genotype/variation

value: Wild type

value: Regulatory T-cells CD4+CD25+


title: Male WSP-2 EtOH Pool 1 21d


title: SC_1

value: Conditional Sirt1 knockout (CD4 cre recombinase)


title: Male WSP-2 Air Pool 1 21d


title: Male WSP-2 Air Pool 2 21d


title: SF_2

value: Conditional Sirt1 knockout (Foxp3 cre recombinase)


title: SF_3


title: WT_3


title: Male WSP-2 EtOH Pool 2 21d


title: SC_3


title: SC_2


title: Male WSR-1 Air Pool 1 21d


title: SF_1


title: WT_1


title: Female WSR-2 EtOH Pool 1 21d


title: Female WSR-2 Air Pool 2 21d


title: Female WSR-1 EtOH Pool 2 21d


title: Female WSR-2 Air Pool 1 21d


title: Female WSR-1 EtOH Pool 1 21d


title: Female WSR-1 Air Pool 1 21d


title: Female WSP-2 EtOH Pool 2 21d


title: Female WSR-1 Air Pool 2 21d


title: Female WSP-2 Air Pool 2 21d


title: Female WSP-2 EtOH Pool 1 21d


title: Female WSP-1 EtOH Pool 2 21d


title: Female WSP-1 Air Pool 2 21d


title: Female WSP-1 EtOH Pool 1 21d


title: Female WSP-1 Air Pool 1 21d


title: Female WSP-2 Air Pool 1 21d


title: ∆ohkA vs. M145(88h)

city: Shanghai

first: Yinhua

last: Lu

address: 300 Fenglin Road

department: Institute of Plant physiology and ecology

country: China

institute: Shanghai Institutes for Biological Sciences

hyb_protocol: Hybridization was carried out at 65°C for 17h with constant rotation at 10rpm.

scan_protocol: Arrays were scanned with 3um resolution using Agilent DNA Microarray scanner (Agilent Technologies, Palo Alto,CA).

data_processing: Microarray data were normalized in the Agilent's Feature Extraction software using total array signals and LOWESS algorithm options. The gene expression ration (n-fold change from ohkA strain to the wild-type strain M145) was calculated from the noramlized signal intensities.

organism: Streptomyces coelicolor A3(2)

source_name: Streptomyces coelicolor A3(2) M145

label_protocol: RNA samples were reverse transcribed to cDNA using MMLV reverse transcriptase (Invitrogen, Carlsbad, CA), followed by transcription with T7 RNA polymerase (New England Biolabs, Beverly, MA) resulting in aaUTP(Ambion, Austin,TX)-labeled cRNA. After cRNA purification with RNeasy mini kit (Qiagen),cRNA with further labeled with cy3 (for the wild-type strain M145) and cy5 (for the ohkA mutant),respectively.

growth_protocol: Cultures of Streptomyces coelicolor wild-type strain M145 and the ohkA mutant incubated on MS solid medium with plastic cellophane were collected at three time points (48,64 and 88h) .

extract_protocol: RNA isolation was performed with Trizol(Invitrogen,  Carlsbad, CA) following the procedures recommended by the manufacturer. RNA samples were digested with DNA I (Takara) followed by purification with RNAeasy mini kit (QIAGEN, Valencia, CA) to remove the contamination of chromosomal DNA.

treatment_protocol: The collected samples were frozen immediately in liquid nitrogen and then ground into powder.

tag: genetic background

tag: genotype

value: the ohkA mutant

value: 88h after incubation

source_name: Streptomyces coelicolor A3(2)

value: wild type


title: ∆ohkA vs. M145(64h)

value: 64h after incubation


title: pESK II

city: Columbia

first: Bhanu

last: Telugu

address: 1201 E.Rollins St

department: Animal Sciences

institute: University of Missouri

description: Genomic DNA extracted from pESK II cells was genotyped using Illumina's Porcine SNP60 BeadChip.

hyb_protocol: a service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/

data_processing: The processed and raw data files were provided as a service by "GeneSeek". According to the information provided, the matrix is generated using GSGT Version 1.6.3 (Gene Spring, Agilent, CA). The "Genotype Summary" matrix file was generated by importing the genotypes into Microsoft Access which was used to identify the total number of valid ("nocalls" excluded) pairwise genotypes between samples and identify the total number of discordant genotypes between samples.

label: C-Bio and A-DNP

organism: Sus scrofa

source_name: ICMs isolated by immunosurgery from in vitro-produced d 5.5 porcine blastocysts were transduced with human KLF4 by lentiviral and stem cell colonies were derived.

growth_protocol: pESK cells cultured in KP/CH medium on MEF feeder

extract_protocol: Extraction of genomic DNA fromgrowing cultered cells was performed using proteinase K and repeated phenol-chloroform extraction.

treatment_protocol: ICMs were subjected lentiviral transduction with hKLF4 and M2rtTA virus under 4% O2 and 5% CO2 air at 38.5ºC. Two days following transduction the blastomeres were plated onto irradiated MEF feeders and cultured two weeks for development of stem cell colonies.

tag: breed

value: Landrace

tag: gender

value: male


title: ∆ohkA vs. M145(48h)

value: 48h after incubation


title: H3Cter, rep 2

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

description: ChIP on chip

hyb_protocol: Robyr, D. and Grunstein, M. (2003) Genomewide histone acetylation microarrays. Methods, 31, 83-89

scan_protocol: ImaGene 4.2

data_processing: Genespring 7.3

source_name: S.pombe wt

label_protocol: Spotted microarrays were hybridized using Cy3 and Cy5

growth_protocol: YES media at 30 degree

tag: antibody


title: input, rep 1

description: ChIP on chip

extract_protocol: Robyr, D. and Grunstein, M. (2003) Genomewide histone acetylation microarrays. Methods, 31, 83-89

value: input


title: input, rep 2

description: ChIP on chip


title: input, rep 8

description: ChIP on chip


title: B6AF1 male, biological rep2

city: Chapel Hill

first: Arlin

middle: B

last: Rogers

state: NC

address: Campus Box 7431

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

description: Gene expression data from 9-month-old mouse liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430A 2.0 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 100.

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

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

treatment_protocol: F1 mice were raised on chow diet under standard conditions in SPF facility. There was no experimental intervention.

value: B6 dam x AJ sire

tag: tissue

value: Liver

tag: age

value: 9 months


title: H3Cter, rep 1

description: ChIP on chip


title: input, rep 4

description: ChIP on chip


title: input, rep 3

description: ChIP on chip


title: pESK I

description: Genomic DNA extracted from pESK I cells was genotyped using Illumina's Porcine SNP60 BeadChip.

scan_protocol: a service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/

source_name: Physically dissociated ICMs from in vitro-produced d 5.5 porcine blastocysts were transduced with human KLF4 by lentiviral and stem cell colonies were derived.


title: input, rep 5

description: ChIP on chip


title: input, rep 6

description: ChIP on chip


title: B6AF1 male, biological rep1


title: H4K16ac, rep 2

description: ChIP on chip


title: input, rep 7

description: ChIP on chip


title: S.pombe wt expression, rep 3

description: Expression analysis of WT strain.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Genespring GX 7.3

source_name: IS 3 Hu303 wt sample 3

label_protocol: Affymetrix

extract_protocol: Affymetrix


title: AB6F1 male, biological rep2

value: AJ dam x B6 sire


title: H4K16ac, rep 1

description: ChIP on chip


title: H4K12ac, rep 2

description: ChIP on chip


title: AB6F1 male, biological rep1


title: H4K8ac, rep 2

description: ChIP on chip


title: H4K12ac, rep 1

description: ChIP on chip


title: S.pombe wt expression, rep 2

description: Expression analysis of WT strain.

source_name: KE 02 Hu303 wt sample 2


title: S.pombe wt expression, rep 1

description: Expression analysis of WT strain.

source_name: KE 01 Hu303 wt sample 1


title: Room_Temp_Larvae_rep3

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

description: Room Temp, D.melangaster Larvae (dp cn bw) rep3

hyb_protocol: According to NimbleGen protocol

scan_protocol: According to NimbleGen protocol

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila melanogaster

label_protocol: According to NimbleGen protocol

growth_protocol:
Kc167 cells were grown at 22C in Schneider's medium supplemented with 5% heat-inactivated FBS and 20ug/ml gentamicin in tissue culture flasks to a final concentration of ~1x10^7 cells per ml
larvae were grown at 25C under a 12h light/dark cycle on Bloomington's food

extract_protocol: total RNA was extracted with TRIzol reagent according to the manufacture's protocol

tag: cell type

value: 3rd instar larvae


title: H4K5ac, rep 2

description: ChIP on chip


title: H4K5ac, rep 1

description: ChIP on chip


title: H3K56ac, rep 2

description: ChIP on chip


title: Room_Temp_Larvae_rep2

description: Room Temp, D.melangaster Larvae (dp cn bw) rep2


title: Room_Temp_Larvae_rep1

description: Room Temp, D.melangaster Larvae (dp cn bw) rep1


title: H4K8ac, rep 1

description: ChIP on chip


title: S.pombe set1 expression, rep 1

description: Expression analysis of Set1 mutant strain.

source_name: CB 13 Hu1221 set1 sample 1

value: p14-p10, sp_set1::KanMX6


title: s.pombe set2 expression, rep 2

description: Expression analysis of Set2 mutant strain.

source_name: Hu1227 set2


title: s.pombe set2 expression, rep 1

source_name: Hu1227 set2 sample 1


title: S.pombe set1 expression, rep 2

source_name: K3 03 Hu1221 set1 sample 2


title: H3K56ac, rep 1

description: ChIP on chip


title: Heat_Shock_Larvae_rep3

description: Heat Shock, D.melangaster Larvae (dp cn bw) rep3


title: Heat_Shock_Larvae_rep1

description: Heat Shock, D.melangaster Larvae (dp cn bw) rep1


title: H3K36me2, rep 1

description: ChIP on chip


title: H3K36me2, rep 2

description: ChIP on chip


title: Room_Temp_KC167_Cells_rep3

description: Room Temp, D.melaogaster KC167 Cells rep3

value: Kc167 cell line


title: H3K27ac, rep 1

description: ChIP on chip


title: H3K23ac, rep 2

description: ChIP on chip


title: H3K18ac, rep 2

description: ChIP on chip


title: Room_Temp_KC167_Cells_rep1

description: Room Temp, D.melaogaster KC167 Cells rep1


title: Heat_Shock_KC167_Cells_rep1

description: Heat Shock, D.melaogaster KC167 Cells rep1


title: Heat_Shock_KC167_Cells_rep3

description: Heat Shock, D.melaogaster KC167 Cells rep3


title: Room_Temp_KC167_Cells_rep2

description: Room Temp, D.melaogaster KC167 Cells rep2


title: Heat_Shock_Larvae_rep2

description: Heat Shock, D.melangaster Larvae (dp cn bw) rep2


title: Heat_Shock_KC167_Cells_rep2

description: Heat Shock, D.melaogaster KC167 Cells rep2


title: H3K27ac, rep 2

description: ChIP on chip


title: Kc167Cells_MOCK_HSFIP_1sthalf_rep1

description: mock immunoprecipitated chromosomal DNA

hyb_protocol: According to Agilent protocol

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1) according to Agilent protocol.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction, Blank subtraction normalization, Inter-array median normalization, Intra-array (dye-bias) median normalization

label: Alexa 647

source_name: mock IP

label_protocol: Anti-HSF or mock immunoprecipitated chromosomal DNA was subjected to two rounds of amplification by LM-PCR as described by Ren et al. 2000 and Birch-Machin et al. 2005 with amino-allyl modified nucleotides being incorporated into the amplified product in the second round. Fluorescent dye conjugation and probe clean-up and precipitation was performed as described on the CDMC web site (www.flyarrays.com).

growth_protocol: Kc167 cells were grown at 22C in Schneider's medium supplemented with 5% heat-inactivated FBS and 20ug/ml gentamicin in tissue culture flasks to a final concentration of ~1x10^7 cells per ml.

extract_protocol: According to Agilent protocol

treatment_protocol:
ip: chromosal DNA was obtained by chromatin-imunoprecipitation as described by Weinmann and Farnham 2002 with an anti-HSF antibody
mock: chromosal DNA was obtained by mock chromatin-imunoprecipitation as described by Weinmann and Farnham 2002 with no antibody
WCE: chromosal DNA was obtained as described by Weinmann and Farnham 2002 with an anti-HSF antibody

label: Alexa 555

source_name: Whole Cell Extract (WCE)

value: none (whole cell extract)


title: INPUT_5

source_name: INPUT DNA

tag: fraction

value: Input


title: H3K14ac, rep 2

description: ChIP on chip


title: H3K14ac, rep 1

description: ChIP on chip


title: Kc167Cells_MOCK_HSFIP_2nd_half_rep2

description: mock immunoprecipitated chromosomal DNA


title: 40 nM rapamycin, sh p73-1, A

description: To identify mTOR/p73 target genes, files were imported into GeneSpring GX 9.0.6.  The ExonPlier16 summarization algorithm was used, with Core meta probeset level and baseline transformation to the median of all samples.  Pairwise comparisons were made between the four categories of samples (Control, sh p73, Rapamycin, Rapamycin + sh p73).

hyb_protocol: see Vanderbilt Microarray Shared Resource, Affymetrix

source_name: Rh30 cells, rapamycin, sh p73-1

extract_protocol: Total RNA was harvested using the Aurum Total RNA Mini Kit (Bio-Rad) using lysis buffer without beta-Mercaptoethanol.

treatment_protocol: Rh30 cells were infected with lentivirus expressing RNAi targeting p73 or GFP (control) for 3d, then treated with vehicle or 40 nM rapamycin in serum-free media for 24 h.

tag: cells

value: Rh30 rhabdomyosarcoma cells

value: 40 nM rapamycin

tag: rnai


title: Kc167Cells_HSFIP_1sthalf_rep2

description: Anti-HSF immunoprecipitated chromosomal DNA

source_name: anti-HSF

value: anti-HSF


title: KYSE170-ncRNA

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

institute: Kumamoto University

description: KYSE-170 cells were transfected with oligoribonucleotides for ncRNA (Ambion, Austin, TX) using Hiperfect (Qiagen, Valencia, CA) according to the provider’s protocol for overexpression. Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method and was labeled and prepared for hybridization to human Oligo chip 25k (Toray, Kamakura, Japan) using standard methods.

hyb_protocol: According to manufacture’s instructions, labeled and fragmented RNA was hybridized on the human Oligo chip 25k for 16 hour at 37˚C.

scan_protocol: Human Oligo chip 25k was scanned using ProScanArray (PerkinElmer).

data_processing: GenePix Pro 4.0.0.54 default settings.  No further data processing was performed.

label_protocol: According to manufacture’s instructions, aminoallyl-cRNA was prepared from 500 ng of total RNA and was labeled with Cy5.

growth_protocol: KYSE-170 cels were maintained in Ham’s F-12/RPMI 1640 (Invitrogen, San Diego, CA) containing 5% fetal bovine serum at 37 ˚C in a fully-humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

tag: cell line


title: H3K18ac, rep 1

description: ChIP on chip


title: 40 nM rapamycin, sh p73-2, B

scan_protocol: see Vanderbilt Microarray Shared Resource, Affymetrix

data_processing: To identify mTOR/p73 target genes, files were imported into GeneSpring GX 9.0.6.  The ExonPlier16 summarization algorithm was used, with Core meta probeset level and baseline transformation to the median of all samples.  Pairwise comparisons were made between the four categories of samples (Control, sh p73, Rapamycin, Rapamycin + sh p73).

source_name: Rh30 cells, rapamycin, sh p73-2


title: KYSE170-miR-210

description: KYSE-170 cells were transfected with oligoribonucleotides for miR-210 (Ambion, Austin, TX) using Hiperfect (Qiagen, Valencia, CA) according to the provider’s protocol for overexpression. Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method and was labeled and prepared for hybridization to human Oligo chip 25k (Toray, Kamakura, Japan) using standard methods.


title: Kc167Cells_HSFIP_1sthalf_rep1


title: H3K23ac, rep 1

description: ChIP on chip


title: Kc167Cells_MOCK_HSFIP_2nd_half_rep1

description: mock immunoprecipitated chromosomal DNA


title: H3K9ac, rep 2

description: ChIP on chip


title: Kc167Cells_HSFIP_2nd_half_rep1


title: p73_ChIP_Rap_G

description: p73 Rh30 Rapamycin ChIP, array G

data_processing:
The CEL files were analyzed using Affymetrix' Tiling Analysis Software.  A two-sample analysis was performed to generate BAR files that contain the signal values for all probes on the arrays (moving statistic, ratio in linear scale ChIP/input).  MaxGap = 400 bp, MinRun = 180 bp, intervals had signals >= 2.5.
Results file descriptions: The .bar files contain signals generated using Affymetrix' Tiling Analysis Software (moving statistic, ratio ChIP/input).  The GSE15703_intervalbed.bed file contains p73 binding site intervals and peaks for the vehicle and rapamycin-treated samples. The BED file is available on the GSE15703 Series record.

source_name: p73 ChIP DNA from Rh30, rapamycin

value: Bethyl A300-126A anti-p73

source_name: input DNA from Rh30


title: INPUT_2


title: Kc167Cells_HSFIP_2nd_half_rep2


title: p73_ChIP_Veh_E

description: p73 Rh30 Vehicle ChIP, array E

source_name: p73 ChIP DNA from Rh30, vehicle

value: Vehicle


title: wild-type_lactate-growth_cDNA_vs_gDNA

type: mixed

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

institute: University of Calgary

hyb_protocol: Dried probes from the treatment condition (cDNA) and universal reference (gDNA) were mixed and diluted to 40 µl using a hybridization solution containing 50% (vol/vol) formamide, 5x SSC, 0.1% (wt/vol) SDS and 0.1 mg/ml herring sperm DNA. This solution was then incubated at 98 °C for 5 minutes and then kept at 60 °C. 16 ul of 3x SSC solution was added to the wells at the ends of the microarray slides to maintain proper chamber humidity, and then the hybridization solution was applied to the Corning UltraGAPS microarray slide which had been pre-washed according to manufacturer specification (Corning, New York). The slides were incubated for 17 hours in Corning hybridization chambers and then washed according the manufacturer’s specifications and dried in a centrifuge.

scan_protocol: The hybridized slides were scanned on a PerkinElmer Scanarray 5000 scanner (PerkinElmer, Massachusetts).

data_processing: Raw data from 4 arrays (with duplicate spots) were used to generate 8 columns of data. The data is the ratio of RNA (cDNA) intensity versus genomic DNA (gDNA) intensity. The gDNA was used as a universal reference to control for spot morphology and density. This data underwent a lowpass filter and total intensity normalization in both the RNA and gDNA channels. These normalized data columns were then analyzed with Stanford Tools SAM (Significance Analysis of Microarrays) which median centered the data averaged the duplicate spots and replicate arrays and generated a q-value to represent the probability that the if the spot is included as differentially expressed that it is a false positive.

label: Alexa fluor 647

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: cDNA, wild-type strain

label_protocol: Amino modified cDNA was generated from 10 ug of total RNA using indirect cDNA labeling and random hexamers utilizing the Indirect SuperScript labeling kit from invitrogen. Amino-modified gDNA was generated using 1 µg of gDNA using indirect labeling with random hexamers utilizing the Bioprime indirect labeling kit from Invitrogen. The amino-modified cDNA was then coupled with Alexa fluor 647 and the amino-modified gDNA with Alexa fluor 555.

growth_protocol: D. vulgaris was cultured at 30 °C in 1 L Erlenmeyer flasks containing 500 ml of defined Widdel-Pfenning (WP) medium containing 3 mM acetate and 28 mM sulfate and 68mM lactate. The medium was bubbled with oxygen-free mixed gas consisting of 10% CO2 and 90% N2. Gas was delivered at 100 ml/min after passing through a heated (325 °C) copper reduction tube for oxygen removal.

extract_protocol: Total RNA was extracted from mid-log phase cells using Invitrogen Trizol and Bacterial Max reagents. The RNA was purified with the Qiagen RNA Easy kit with on column DNase digestion. RNA quality and quantity were assessed using the absorbance ratio at 260 and 280 nm (A260/A280), denaturing agarose gel electrophoresis with ethidium bromide staining and with a Qubit fluorometer. To extract genomic DNA (gDNA) cell pellets were resuspended in NaCl-EDTA with lysozime, SDS, NaCL04, and chloroform:isoamylalcohol. This solution was centrifuged for 3 minutes at 10xg and the supernatant was added to 2 volumes of 95% EtOH to precipitate the DNA. Once the ethanol was removed the DNA is dissolved in TE and DNAse-Free RNAase and Proteinase K are used to remove contaminates. A phenol extraction and ethanol precipitation is then used to isolate the purified DNA. Quantification of DNA was conducted using absorbance ratio at 260 and 280 nm (A260/A280), agrose gel electrophoresis and with a Qubit fluorometer.

value: wild-type

label: Alexa Fluor 555

source_name: gDNA reference, wild-type strain


title: p73_ChIP_Veh_G

description: p73 Rh30 Vehicle ChIP, array G


title: PerR_lactate-growth_cDNA_vs_gDNA

source_name: cDNA, PerR mutant strain

value: PerR mutation


title: H3K4me2, rep 2

description: ChIP on chip

source_name: S.pombe wt


title: H3K4me2, rep 1

description: ChIP on chip


title: 40 nM rapamycin, sh GFP, A

source_name: Rh30 cells, rapamycin, sh GFP

label_protocol: see Vanderbilt Microarray Shared Resource, Affymetrix

value: sh GFP


title: p73_ChIP_Rap_E

description: p73 Rh30 Rapamycin ChIP, array E


title: 40 nM rapamycin, sh GFP, B


title: Vehicle control, sh GFP, A

source_name: Rh30 cells, vehicle, sh GFP


title: Vehicle control, sh p73-2, B

source_name: Rh30 cells, vehicle, sh p73-2


title: p73_ChIP_Veh_F

description: p73 Rh30 Vehicle ChIP, array F


title: Room Temp hsf4 Larvae rep 3

description: Room Temp

scan_protocol: According to NimbleGen protocol Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

source_name: hsf4 Larvae

growth_protocol: Kc167 cells were grown at 22C in Schneider's medium supplemented with 5% heat-inactivated FBS and 20ug/ml gentamicin in tissue culture flasks to a final concentration of ~1x10^7 cells per ml

tag: developmental stage

value: Room Temp

value: hsf4 mutant

value: larvae


title: Room Temp hsf4 Larvae rep 2

description: Room Temp


title: Vehicle control, sh GFP, B


title: 30 min Heat Shock hsf4 Larvae rep 2

description: 30 min Heat Shock

value: 30 min Heat Shock


title: WT heart 2

city: Cincinnati

first: John

last: Elrod

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital and Medical Center

description: Gene expression data from wildtype mouse hearts.

hyb_protocol: Hybridization cocktail for a single probe array contained 2.5 ug of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer. GeneChip Mouse Gene 1.0 ST Array (Affymetrix) was hybridized at 45C for 18 hours in the GeneChip Hybridization Oven 640 (Affymetrix).

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

data_processing: The data was RMA normalized using GeneSpring GX 7.3.

source_name: Heart sample from 8-week-old C57BL/6 mice

label_protocol: The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin-labeled sense-strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

extract_protocol: RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Mice were euthanized and hearts were rapidly removed and placed in RNAeasy for 48hr at 4C in preparation for RNA extraction.

value: wildtype

value: heart

value: 8 weeks


title: WT heart 3


title: 30 min Heat Shock hsf4 Larvae rep 1

description: 30 min Heat Shock

value: 3rd instar larvae


title: WT heart 1


title: p73_ChIP_Rap_F

description: p73 Rh30 Rapamycin ChIP, array F

hyb_protocol: see GenPathway Inc. FactorPath protocol

scan_protocol: see GenPathway Inc. FactorPath protocol

extract_protocol: Rh30 cells were crosslinked with formaldehyde, crosslinks were reversed, and samples were lysed according to GenPathway, Inc. FactorPath protocols.


title: Room Temp hsf4 Larvae rep 1

description: Room Temp


title: Vehicle control, sh p73-1, A

source_name: Rh30 cells, vehicle, sh p73-1


title: 30 min Heat Shock hsf4 Larvae rep 3

description: 30 min Heat Shock


title: H3K9ac, rep 1

description: ChIP on chip


title: Ppif-/- heart 3

description:
Gene expression data from Ppif-/- mouse hearts.
Ppif-/- mice were back-crossed to C57BL/6 from an original Sv129 background. See original description in Baines et al. Nature. 2005; 434:658-662 (PMID 15800627).

source_name: Heart sample from 8-week-old Ppif-/- mice

value: Ppif-/- (global gene knockout)


title: Wildtype (Col-0) - treatment (salt stress) - rep1

status: Public on Jan 04 2011

city: Beijing

first: Zhaoliang

last: Zhang

state: Beijing

address: datun road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of sciences

description: Data in table represents LuxScan 3.0-processed Cy5 channel of 10.6.4 10313A_wt-6-1 Cy5+10313A_mu-6-1 Cy3 1080.LSR (Cy3 intensity not used in final analysis)

hyb_protocol: standard CapitalBio Methods

scan_protocol: GeneChips were scanned using LuxScan 10KA (CapitalBio)

data_processing: The data were analyzed with LuxScan 3.0 (CapitalBio)

source_name: 11-day-old seedling of Col-0 at salt stress treatment condition

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Col-0 and skb1-1 mutant were grown at 22°C on MS plates containing 2% sucrose for 11 days.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, Gaithersburg, MD, USA) and purified using NucleoSpin® RNA clean-up kit (MACHEREY-NAGEL, Germany) according to the manufacturer’s instructions.

treatment_protocol: Samples were incubated for 6 h in MS medium (control) or MS medium containing 200 mM NaCl (treatment) and then collected for RNA extraction.

value: seedling

value: 11 day old

value: incubated in MS medium containing 200 mM NaCl for 6 h


title: Wildtype (Col-0) - control - rep2

description: Data in table represents LuxScan 3.0-processed Cy5 channel of 10.6.2 10313A_wt-0-2 Cy5+10313A_mu-0-2 Cy3 1071.LSR

source_name: 11-day-old seedling of Col-0 at control condition

value: incubated in MS medium for 6 h


title: Ppif-/- heart 2


title: Wildtype (Col-0) - control - rep1

description: Data in table represents LuxScan 3.0-processed Cy5 channel of 10.6.2 10313A_wt-0-1 Cy5+10313A_mu-0-1 Cy3 1001.LSR


title: Wildtype (Col-0) - treatment (salt stress) - rep2

description: Data in table represents LuxScan 3.0-processed Cy5 channel of 10.6.4 10313A_wt-6-2 Cy5+10313A_mu-6-2 Cy3 1081.LSR (Cy3 intensity not used in final analysis)


title: Mutant (skb1-1) - control - rep2

description: Data in table represents LuxScan 3.0-processed Cy3 channel of 10.6.2 10313A_wt-0-2 Cy5+10313A_mu-0-2 Cy3 1071.LSR

source_name: 11-day-old seedling of skb1-1 at control condition


title: EAC_064

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48702 probes on the Human-6 beadChip ver.2 were used. Clinical data provided as a supplementary file on Series record:GSE13898_EAC_MDACC_DepSysB_ClinicalInformation.txt.gz

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Esophagus

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina?? TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

growth_protocol: Specimen from Primary Human esophageal Tumor biopsy

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

treatment_protocol: No treatment. Disease state only

tag: Patient #51393


title: F.pla_acetate_rep 1

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

description: F. placidus grown with 10 mM acetate. First biological replicate.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

organism: Ferroglobus placidus DSM 10642

source_name: 10 mM acetate as electron donor and 56 mM ferric citrate as acceptor

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with either 1 mM benzoate or 10 mM acetate as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85 C in the dark.

extract_protocol: Total RNA was extracted according to the HG protocol described in Holmes et al (in preparation)

treatment_protocol: Cultures (100 ml in 156 ml serum bottles) were divided into 50 ml conical tubes (Falcon), and cells were pelleted with centrifugation at 3,000 xg for 15 min. Pellets were then immediately frozen in liquid nitrogen and stored at –80 °C

tag: type of electron donor

value: short organic acid


title: EAC_062

tag: Patient #50512


title: Ppif-/- heart 1

tag: strain


title: Mutant (skb1-1) - control - rep1

description: Data in table represents LuxScan 3.0-processed Cy3 channel of 10.6.2 10313A_wt-0-1 Cy5+10313A_mu-0-1 Cy3 1001.LSR

tag: treatment


title: EAC_063

tag: Patient #50714


title: F.pla_acetate_rep 2

description: F. placidus grown with 10 mM acetate. Second biological replicate.


title: EAC_059

tag: Patient #49403


title: EAC_060

tag: Patient #49668


title: EAC_061

tag: Patient #50492


title: EAC_057-2

tag: Patient #48253


title: EAC_058

tag: Patient #49299


title: EAC_055-1

tag: Patient #46682


title: EAC_054-1

tag: Patient #46663


title: EAC_054-2


title: EAC_055-2


title: EAC_053

tag: Patient #41411


title: EAC_057-1


title: EAC_051

tag: Patient #38700


title: EAC_050

tag: Patient #35855


title: EAC_052-1

tag: Patient #41113


title: Kc167Cells_HSFIP_RT_rep1

scan_protocol: According to Agilent protocol Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction, Blank subtraction normalization, Inter-array median normalization, Intra-array (dye-bias) median normalization, quantified data was reformatted for analysis with ChIP Analytics software

source_name: Kc167 Cells, ChIP

label_protocol:
Anti-HSF immunoprecipitated chromosomal DNA was subjected to two rounds of amplification by LM-PCR as described by Ren et al. 2000 and Birch-Machin et al. 2005 with amino-allyl modified nucleotides being incorporated into the amplified product in the second round. Fluorescent dye conjugation and probe clean-up and precipitation was performed as described on the CDMC web site (www.flyarrays.com).
chromosomal DNA was subjected to two rounds of amplification by LM-PCR as described by Ren et al. 2000 and Birch-Machin et al. 2005 with amino-allyl modified nucleotides being incorporated into the amplified product in the second round. Fluorescent dye conjugation and probe clean-up and precipitation was performed as described on the CDMC web site (www.flyarrays.com).

extract_protocol:
ip: chromosal DNA was obtained by chromatin-imunoprecipitation as described by Weinmann and Farnham 2002 with an anti-HSF antibody
WCE: chromosal DNA was obtained as described by Weinmann and Farnham 2002 with an anti-HSF antibody

value: cells were aerated for 4 hours at 22C by gentle shaking

tag: sample type

tag: antibody

value: Rabbit polyclonal anti-HSF serum 943 (Westwood et al., 1991)

tag: cell line

source_name: Kc167 Cells, input

tag: label


title: EAC_043

tag: Patient #33413


title: EAC_036

tag: Patient #49236


title: EAC_046

tag: Patient #34129


title: EAC_052-2


title: EAC_037

tag: Patient #49764


title: EAC_048

tag: Patient #35577


title: EAC_049

tag: Patient #35813


title: EAC_045

tag: Patient #33529


title: EAC_034

tag: Patient #48917


title: EAC_056

tag: Patient #46956


title: EAC_041

tag: Patient #50161


title: EAC_042

tag: Patient #32964


title: EAC_038

tag: Patient #49793


title: EAC_031-1

tag: Patient #44528


title: EAC_030

tag: Patient #42745


title: EAC_031-2


title: EAC_039

tag: Patient #50046


title: EAC_033

tag: Patient #48174


title: EAC_040

tag: Patient #50079


title: Kc167Cells_HSFIP_RT_rep2

tag: treatment

tag: sample type

value: Anti-HSF immunoprecipitated chromosomal DNA was subjected to two rounds of amplification by LM-PCR as described by Ren et al. 2000 and Birch-Machin et al. 2005 with amino-allyl modified nucleotides being incorporated into the amplified product in the second round. Fluorescent dye conjugation and probe clean-up and precipitation was performed as described on the CDMC web site (www.flyarrays.com).

tag: antibody

tag: cell line

tag: label


title: EAC_044

tag: Patient #33519


title: EAC_047

tag: Patient #34823


title: EAC_019

tag: Patient #48576


title: EAC_022

tag: Patient #50118


title: EAC_025-1

tag: Patient #37023