title: MGAS315 + vehicle

city: Chicago

first: Michael

middle: J

last: Federle

state: IL

address: 900 S Ashland Ave. MC870

department: Microbiology & Imm. / Cntr Pharm Biotech

institute: University of Illinois at Chicago

description: This sample is of wild-type Streptococcus pyogenes MGAS315 treated with vehicle and consists of total RNA isolated from three separate cultures and pooled in equal mass amounts prior to cDNA synthesis

hyb_protocol: Hybridization to S. pyogenes whole genome microarrays (Nimbelgen) was performed by the W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, in accordance with the Nimbelgen Hyrbidization protocol (www.nimblegen.com)

scan_protocol: Scanning was performed by the W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, using the Nimlescan software according to manufacturer's instructinos (Nimblegen)

data_processing: The raw data was subjected to RMA normalization by the W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, using Partek software. See www.partek.com.

organism: Streptococcus pyogenes MGAS315

source_name: Streptococcus pyogenes MGAS315 + vehicle

label_protocol: cDNA generation and labeling with Cy3 were performed by the W.M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign following NimbleGen protocols as described previously

growth_protocol: Six separate cultures of the MGAS315 wild type were grown at 37°C in CDM after dilution from mid-logarithmic stocks to OD600 0.01.

extract_protocol: Total RNA was extracted using the RiboPure-Bacteria Kit (Ambion) according to manufacturer's instreuctions. RNA quality was determined by agarose gel electrophoresis and concentration was measured using a NanoDrop 1000 spectrophotometer (Thermo Scientifiic)

treatment_protocol: At OD600 0.4, three of the cultures were treated with 200 nM M3 XIP peptide and the other three with the peptide vehicle only (0.04% DMSO). After 60 min. at 37°C, hyaluronidase (10 units/ml) was added to degrade capsule and cells were harvested by centrifugation at 4°C. RNA was extracted using a RiboPure-bacteria kit (Ambion, Austin, TX) according to the manufacturer’s instructions, including the DNase treatment.

tag: genotype/variation

value: Wild-type

tag: agent

value: control


title: APR08-NH20-M-250

status: Public on Jun 01 2012

type: genomic

city: Beaverton

first: Maria

last: Smit

state: OR

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

country: USA

institute: Oregon Health and Science University

description:
a sector of an ElectraSense 4X2K microarray with 2240 features representing 2200 unique probes was hybridized with an aliquot of biotin--labeled Pseudo-nitzschia ITS1 amplicon preparation
*Location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; LP, La Push transect in the coastal ocean at La Push, Washington; GH21 and GHQR, locations near Grays Harbor, Washington; CM10, Cape Meares transect in the coastal ocean at Oceanside, Oregon; SAT03, SAT03 station in the Columbia River estuary near Astoria, Oregon (river mile 5).
total microbial assemblage from environmental water

hyb_protocol: Hybridization of ElectraSense™ microarrays was performed as recommended by the manufacturer. The microarrays were hybridized at 51˚C for 1-2 hours, using biotin-labeled cDNA targets, 1.5-2 mg per sector for the 4X2K format.

scan_protocol: Hybridized microarrays were used for electrochemical signal detection using the ElectraSense Reader (CombiMatrix) with the corresponding kit as described by the manufacturer.

data_processing: Signal quantification was done by the ElectraSense Reader software during scanning. Data were analyzed using the Probe Weaver software from CombiMatrix, and HybAnalysis software from CustomArray Inc. Data QC was done with scatter plot analysis of duplicate hybridizations, and calculation of pair-wise correlation coefficients among samples using NCI-supported software BRB-ArrayTools (http://linus.nci.nih.gov/pilot/index.html). Then the duplicate samples were used to calculate average normalized signal intensities for each probe in each sample. Detection of ribotype presence was done by using HybAnalysis software to combine multiple probe hybridization signals into ‘sumscores’ for each ITS1 sequence represented on microarrays. The first step was normalization of microarray hybridization signals at the level of individual probes by conversion into Z-values (standard values). Z-value for a probe in a particular hybridization was calculated as the difference between the probe signal intensity and the mean intensity of all signals in this hybridization divided by the standard deviation of all signals. Thus, hybridization signals are transformed into deviations from the population mean, with a standard deviation of 1.0. To include a measurement of probe specificity into the sumscore calculations, the probes were assigned with statistical weights, probe weight values (PWV) that were inversely correlated with the number of calculated non-cognate target hits. A probe produced a calcultaed hit to a target ribotype if the Tm of the probe:target hybridization was at least 55°C. In this case, the corresponding PWV for the probe hybridization to the target ribotype was expressed as 1.0 (number of hits to self) divided by the number of calculated hits to all other targets sequences. Finally, for each target ribotype, the sum of all PWV was normalized to 1.0 (the weighed average approach). PWV were used as multipliers for analysis of each microarray hybridization to transform the probe-level Z-values into sumscores at the ribotype level. A sumscore value was generated for a target ribotype in a given microarray hybridization as the sum of Z-values of each probe multiplied by the corresponding PWV.

label: biotin

molecule: genomic DNA

organism: environmental samples

source_name: filtered environmental water sample

label_protocol: The DNA targets corresponding to the internal transcribed spacer 1 sequences (ITS1) of the diatom genus Pseudo-nitzschia, were amplified from total genomic DNA samples using PCR with the following specific primers: PnAIIF, 5'-TCTTCATTGTGAATCTGA-3', and PnAIIR, 5'-CTTTAGGTCATTTGGTT-3' (Hubbard, Rocap et al. 2008). PCR was done with 10 ng of total genomic DNA, 0.2 uM of each primer, and AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA, USA). The reaction consisted of an initial denaturation at 94˚C for 2 min, followed by 30 cycles of 94˚C for 30 s, 50˚C for 30 s, and 72˚C for 2 min. PCR products were analyzed by gel electrophoresis using the FlashGel® System (Lonza), and then purified with the QIAquick PCR purification kit (Qiagen, Valencia, CA). Biotin labeling was done using LabelIT uArray Biotin Kit (Mirus Bio, Madison, WI) as described by the manufacturer. Finally, the biotin-labeled DNA targets were purified using Illustra ProbeQuant G-50 Micro Columns (GE Healthcare, Piscataway, NJ), and applied for microarray hybridization.

extract_protocol: Total genomic DNA was isolated using FastDNA® SPIN Kit for Soil (MP Biomedicals, Solon, OH) as described by the manufacturer. The resultant genomic DNA was analyzed using rapid gel electrophoresis with FlashGel® System (Lonza, Allendale, NJ).

treatment_protocol: After filtration, samples were preserved in RNAlater and stored at -80oC

tag: sample collection

value: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms

tag: location*

tag: longitude

tag: latitude

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)

value: M

tag: sampling depth (m)

tag: t(oc)


title: APR08-CR7-M-281


title: MGAS315 + XIP

type: RNA

description: This sample is of wild-type Streptococcus pyogenes MGAS315 treated with XIP peptide and consists of total RNA isolated from three separate cultures and pooled in equal mass amounts prior to cDNA synthesis

molecule: total RNA

source_name: Streptococcus pyogenes MGAS315 + XIP peptide

value: XIP peptide


title: OE33_Mock_biologicalreplicate2

city: Baltimore

first: Mirte

middle: Mayke

last: Streppel

state: Maryland

address: 1550 Orleans street, CRBII rm341

department: Pathology

institute: Johns Hopkins Hospital

hyb_protocol: The samples were ice quenched and combined with the hybridization cocktail (5 μl oligonucleotide B2 control, 15 μl 20X eukaryotic hybridization controls, 150 μl 2X hybridization buffer, 30 μl 100% DMSO and 70 μl water).  After 10 minutes of pre-hybridizing Human PrimeView array at 45ºC, 60 rpm, 200 μl of cocktail was loaded onto each array and the arrays were hybridized for 16 hours at 45ºC, 60 rpm. The cocktail was removed and the arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_001 fluidics script.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) Affymetrix software.

data_processing: Data were extracted from the  CEL files, RMA normalized and converted to Log2 notation with Partek Genomics Suite (Partek, Missouri, USA).  These values were labeled as to ARID1A knockdown status and the groups compared with a standard 1-way ANOVA, Student's t-test.

label: Biotin

organism: Homo sapiens

source_name: OE33 cells (esophageal adenocarcinoma cells)

label_protocol: One μg total RNA was combined with 2 μl T7 oligo(dT) primer and 2 μl Poly-A controls and brought to a volume of 12 μl. The samples were incubated at 70ºC for 10 minutes to label as per standard Affymetrix protocol.

growth_protocol: Cells were cultured in 1640 RPMI supplemented with 15% Fetal Bovine Serum

extract_protocol: Total RNA was extracted using the Rneasy kit (Qiagen, Germantown, MD, USA) according to the manufacturer's manual.

treatment_protocol: Cells were plated in wells in a 6 well-plate (0.2 million cells/well). 24 hours after plating, the cells were transfected using lipofectamin 2000 (Life Technologies, Grand Island, NY, USA) and siRNA (final concentration 50nM). The following siRNAs were used: MS_1 and MS_3 were transfected with ON-TARGETplus SMARTpool ARID1A (Thermo Fisher Scientific, Lafayette, CO, USA), whereas MS_2 and MS_4 were transfected with ON-TARGETplus Non-targeting Pool  (Thermo Fisher Scientific). The cells were washed, harvested, and pelleted 48 hours after transfection.

tag: cell line

tag: sirna transfection

value: ON-TARGETplus Non-targeting Pool


title: OE33_Mock_biologicalreplicate1


title: OE33_ARID1Aknockdown_biologicalreplicate2

value: ON-TARGETplus SMARTpool ARID1A


title: POF RIP FA

status: Public on May 31 2012

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

description: nuclear RNA for test and input

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: Affymetrix

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only.
The resulting CHP files are generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only.

organism: Drosophila melanogaster

growth_protocol: For each sample treatment condition we used 300ml D. melanogaster Schneider’s line 2 cells (ATCC CRL-1963) grown at 25°C in an Erlenmeyer flasks at a density of 1×10^7 cells/ml in Drosophila SFM medium (Invitrogen) supplemented with 100U/ml Penicillin G, 100µg/ml Streptomycin sulfate and 2mM of L-glutamine.

extract_protocol: For immunoprecipitation, 1-2 mg nuclear or whole cell extracts were incubated with 8 µl anti-POF for 45 minutes at 4°C with agitation. The antibody complex were precipitated by incubation with 75 µl of Dynabeads conjugated to protein-A (Invitrogen) for 30 minutes at 4°C with agitation. The supernatant was removed and the beads were washed twice with PBS (150 mM NaCl), 0.1% Triton X-100, 32 U/ml RNasin, 0.5 × Protease inhibitor cocktail and twice in PBS (300 mM NaCl), 0.1% Triton X-100, 32 U/ml RNasin, 0.5 × Protease inhibitor cocktail. The crosslinks in sample FA and WCFA were reversed by adding 200 µl 0.45 M LiCl to the beads and incubate 3-4 hours at 65°C. RNA were isolated using TRI-reagent (Ambion) followed by a purification using RNeasy kit (Qiagen) according to the instruction by the suppliers. The RNA samples were concentrated and reverse transcribed into cDNA using random primers with the ImPromII first strand synthesis kit (Promega). The single stranded cDNA was purified with QIAquick PCR purification Kit (Qiagen). The purified cDNA samples were amplified using WGA2 GenomePlex Complete whole genome amplification kit (Sigma) according to the recommendations by the supplier.

treatment_protocol: The cells were pelleted, washed twice in 100 ml 10 mM HEPES pH 7.4, 140 mM NaCl and resuspended in 50 ml of lysis buffer (20 mM HEPES pH 7.4, 3 mM MgCl2, 0.1% Triton X-100, 1 mM dithiothreitol, 0.5 mM PMSF, 10 U/ml RNasin and 0.5 × Protease inhibitor cocktail, Roche).The cells were allowed to swell on ice for 10 minutes and then homogenized on ice with 30 strokes of a Dounce homogenizer. The nuclei were pelleted at 2,000 × g for 5 minutes and used either as native (non-crosslinked) or after formaldehyde crosslinking. For the crosslinked sample (FA) the pelleted nuclei were resuspended in 50 ml lysis buffer and cross-linked by adding formaldehyde to a final concentration of 0.5% and incubated for 10 minutes in room temperature. The crosslinking was stopped by adding glycine (final concentration 0.125 M), the nuclei were washed once in lysis buffer and resuspended in 2 ml of sonication buffer (20 mM HEPES pH 7.4, 10% glycerol, 0.1 M NaCl, 1 mM MgCl2, 0.1% Triton X-100, 1 mM dithiothreitol, 0.5 mM PMSF, 10 U/ml RNasin and 0.5 × Protease inhibitor cocktail) and sonicated using a Bioruptor (Diagenode) for 4 minutes, setting high (30 sec ON, 30 sec OFF). For the native samples (N1, N3, N6) the pelleted nuclei were resuspended in 2 ml sonication buffer and sonicated for 1, 3 or 6 minutes (N1, N3 and N6, respectively). Cellular debris were removed by centrifugation for 25 minutes, 4°C at 14,000 × g and the supernatants were used for immunoprecipitations. For the whole cell sample (WCFA) we used 40 ml D. melanogaster Schneider’s line 2 cells grown as described above. The cells were cross-linked by adding formaldehyde to a final concentration of 0.5% and incubated for 10 minutes in room temperature. The crosslinking was stopped by adding glycine (final concentration 0.125 M) and incubated for 5 minutes on ice. The fixed cells were pelleted, resuspended in 5 ml PBS, washed for 10 minutes in wash A solution (10 mM HEPES pH 7.6, 10 mM EDTA pH 8.0, 0.25% Triton X-100) for 10 minutes at 4°C, and once with wash B solution (10 mM HEPES pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.01% Triton X-100) for 10 minutes. The cells were resuspended in 5 ml TEN140 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 140 mM NaCl), PMSF were added to a final concentration of 1 mM and the samples were sonicated using a Bioruptor (Diagenode), 4 minutes, setting high (30 sec ON, 30 sec OFF). To the resuspended cell extract 50 µl 10% SDS, 500 µl 1% Sodium-deoxycholate, 500 µl 10% Triton X-100, 140 µl 5M NaCl were sequentially added. The extract was then incubated for 10 minutes at 4°C, and centrifuged for 5 minutes, 4°C at 14,000 × g and the supernatants were used for immunoprecipitation.

value: S2 cells (ATCC CRL-1963)

tag: antibody

value: POF

tag: fraction

value: nuclear RNA

tag: treatment

value: cross-linked


title: OE33_ARID1Aknockdown_biologicalreplicate1


title: POF RIP N6

description: nuclear RNA for test and input

label_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

value: 6 min sonication


title: wild type 2

scan_protocol: Standard Affymetrix protocol

data_processing: The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only. The resulting CHP file is generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only.

growth_protocol: Flies were cultivated in vials with potato mash-yeast-agar medium.

extract_protocol: Total RNA was prepared from three biological replicates for both wildtype and PofD119. For each replicate, RNA was isolated from 20 adult female flies using TRI-reagent (Ambion) followed by a purification using RNeasy kit (Qiagen) according to the instruction by the suppliers. The six labeled cDNA probes were hybridized to Affymetrix Drosophila Genome 2.0 tiling array.

tag: age

value: adult

tag: gender

value: female

tag: genotype

value: wild type

tag: genetic background

tag: tissue

value: whole organism


title: wild type 3


title: Pof mutant 3


title: Pof mutant 2


title: wild type 1


title: POF RIP N3

description: nuclear RNA for test and input

value: 3 min sonication


title: POF RIP WCFA

description: total RNA for test and input

value: whole cell


title: fetalcellsinlung_1

city: Boston

first: Stephanie

last: Pritchard

state: MA

address: 800 Washington St, Box 396

department: Genetics

institute: Tufts University

description: Gene expression data from fetal cells collected from the maternal lung in the late stages of pregnancy

hyb_protocol: The arrays were hybridized in an Affymetrix oven at 45°C and 60rpm for 18-40 hours. Arrays were washed using a GeneChip Fluidics Station 450 and stained with streptavidin–phycoerythrin according to the protocol supplied by NuGEN Technologies, Inc. with their Encore Biotin Module.

scan_protocol: Arrays were scanned with the GeneArray Scanner (Affymetrix).

data_processing: The arrays were analyzed using the GeneChip Microarray Suite 5.0 (Affymetrix) and normalized in R using quantile-normalization, with ideal mismatch background correction and Tukey biweight summarization.

organism: Mus musculus

source_name: Fetal cells flow sorted from the maternal lung

label_protocol: Twenty-five μg cDNA were fragmented and biotinylated using the Encore Biotin Module (NuGEN Techonologies, Inc.)

growth_protocol: Male mice homozygous for the enhanced green fluorescent protein (Egfp) transgene (C57BL/6-Tg(CAG-EGFP)C14-Y01-FM131Osb [stock number 267, Riken BioResource Center, Japan, originally provided by Dr. Masaru Okabe, bred in-house]) were mated to 10-12 week-old wild type C57BL/6J females (stock no. 664, Jackson Labs, Bar Harbor, Maine).  With the homozygous male, all pups inherit one copy of the Egfp transgene. Egfp expression was used as a marker for all fetal cells independent of gender.

extract_protocol: GFP+, PI- fetal cells from each set of maternal lungs were sorted directly into the lysis buffer provided with the WT-Ovation One-Direct Amplification system (NuGEN Technologies, Inc., San Carlos, California) at a dilution of 10-40 cells/µl. Cell lysates from each female were pipetted repeatedly and stored at -80°C for 1-8 days following sorting.  cDNA was converted and amplified from the RNA in the cell lysates using the WT-Ovation One Direct Amplification system following the manufacturer’s protocol with the exception of using up to 80 cells as input material.

tag: strain

tag: gestational age of pups


title: fetalcellsinlung_2


title: fetalcellsinlung_5


title: fetalcellsinlung_4


title: fetalcellsinlung_7


title: fetalcellsinlung_6


title: fetalcellsinlung_3


title: POF RIP N1

description: nuclear RNA for test and input

value: 1 min sonication


title: Pof mutant 1


title: PBMC_RNA_Control_18

status: Public on Mar 26 2012

city: Rochester

first: Iftikhar

last: Kullo

state: Minnesota

address: 200, First Street Southwest

department: Division of Cardiovascular Diseases

institute: Mayo Clinic

description: Validation set

hyb_protocol: After fragmentation, 15µg of cRNA was hybridized to HG U133 Plus 2.0 microarray (for 16 hours at 45oC). The microarrays were washed and stained at Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned and data extracted using the GeneChip scanner® 3000 (Affymetrix, Santa Clara, CA)

data_processing: The raw data file formats were generated using Affymetrix GeneChip operating software® (GCOS). Raw gene expression data were analyzed using the GeneSpringGx 11.0 software (Agilent® Technologies). Samples were normalized using RMA method.

source_name: Peripheral Blood Mononuclear Cells (PBMC) - Controls

label_protocol: Biotin labeled cRNA was labeled according to the recommended procedures for Affymetrix Two - Cycle synthesis kit (Affymetrix, Santa Clara, CA). The starting total RNA concentration was 100ng

growth_protocol: PBMC isloated from whole blood were suspended in RPMI - 10 medium for counting the cells (the cell mixture was kept at room temperature).

extract_protocol: The extractions were performed through RNEasy plus minikit and through TRIzol, as per manufacturer instructions.

treatment_protocol: PBMC were introduced on hemocytometer and counted. The cells were washed and pelleted with FBS, resuspended in RPMI - 10 and processed for RNA isolation through RNEasy plus minikit (Qiagen, Valencia, CA) and TRIzol (Invitrogen, Carlsbad, CA).

tag: cell type

tag: disease state

value: normal


title: H2B-WT

status: Public on May 29 2012

city: Stanford

first: Grace

last: Zheng

address: CCSR 2140, 269 Campus Dr

institute: Stanford University

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: Peak calling using standard NimbleGen protocol

organism: Caenorhabditis elegans

source_name: H2B ChIP DNA from WT L4/Young Adults

label_protocol: NimbleGen service was used for fluorescent labeling of samples and hybridization to tiling array (Cat. Number: C4533-02-01) with 50mer probes at 86bp spacing that included full C. elegans chromosome IV sequence as well as chromosome M and parts of chromosomes III and V. Dual labeling was performed for Input and ChIP samples.

extract_protocol: Synchronized populations of worms were grown on agarose plates seeded with OP50 bacteria. Worms were collected at L4/young adult stages not containing eggs and washed extensively with M9 buffer and fixed with 2% paraformaldehyde in M9 buffer for 30 minutes at room temperature. Fixation was followed by washes with 0.1M Tris-HCl and M9 buffers and freezing fixed worms at -80°. Thawed worms were washed in lysis buffer (50mM Hepes-KOH pH 7.6,1mM EDTA, 140mM KCl, 0.5% NP-40, 10% glycerol, 5mM DTT, protease inhibitor) and sonicated with 30 sec pulses 10 times using Branson microtip sonicator at 19% power in the cold room. Protein extracts were span at 5,000g, 4°C for 20 minutes and supernatants were sonicated again (20-30 sec pulses, 6 times at 19% power). Resulting extracts were span at 20,000g, 4°C for 20 minutes and pre-cleared by incubation with DNA-agarose A beads (Upstate) for 90 minutes. 1/20 fraction of the supernatants was taken for the input DNA extraction. For ChIP-chip 20μl of anti-H3 antibody per 1ml of theextract or 10μg of anti-GFP antibody were used. Nonspecific aggregates were cleared by centrifugation at 16,000g for 10 minutes and antibodyantigen complexes were captured on DNA-agarose A beads. The beads were washed with TSE 150mM NaCl, two times with TSE 500mM NaCl, buffer III and two times with TE according to the Upstate protocol. Immunoprecipitated material was eluted with freshly prepared elution buffer (1%SDS; 0.1M NaHCO3). Elution buffer was added to the input samples as well and they were treated identically thereafter. Crosslinking was reversed by incubating samples at 65°C in the presence of NaCl overnight. Samples were treated with proteinase K for 1 hour at 45°C and DNA was extracted by phenol/chloroform and precipitated with ethanol. Blunting, ligation of linkers to DNA and PCR amplification was done exactly as described in (Li et al., 2003). The size of DNA fragments in samples was around 200-300bp. Each DNA sample was provided to NimbleGen at concentration 250-350ng/μl and final amounts ranged from 8 to 15μg DNA per sample.

value: GFP:H2B, AZ212 strain

tag: developmental stage

value: L4/Young Adults (no eggs included)

tag: chip antibody

value: GFP

tag: chip antibody manufacturer

value: Invitrogen

source_name: Input DNA

value: input DNA


title: primary cultured RDEB cSCC fibroblasts RDEB43SCC1F

status: Public on May 16 2012

city: Dundee

first: Andrew

last: South

address: Ninewells Hopsital and Medical School

department: Division of Cancer Research

country: United Kingdom

institute: University of Dundee

description: Primary fibroblast culture

hyb_protocol: standard Agilent Protocol

scan_protocol: standard Agilent Protocol

data_processing: Agilent Feature Extraction Software

source_name: RDEB cSCC fibroblasts

label_protocol: standard Agilent Protocol

extract_protocol: Trizol

tag: body site

value: Hand

value: primary cultured RDEB cSCC fibroblasts

value: recessive dystrophic epidermolysis bullosa, cutaneous squamous cell carcinoma


title: PBMC_RNA_Control_17

description: Validation set

value: Peripheral Blood Mononuclear Cells (PBMC) - Controls


title: GSCs replicate 5

status: Public on Mar 30 2012

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description: GSCs separated by MACS treatment from the gonad of 6.5 days WL embryos.

hyb_protocol: the biotin-labeled IVT-RNA was fragmented and hybridized to the chicken genome GeneChip array at 45°C for 16 h, according to the manufacturer’s instructions.

scan_protocol: After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a non-stringent wash buffer at 25°C, followed by a stringent wash buffer at 50°C. After washing, the arrays were stained with a streptavidin–phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner, controlled by GeneChip Operating Software (GCOS; Affymetrix).

data_processing: The quality of the array image was assessed as described in the GeneChip expression analysis manual (Affymetrix). All arrays were processed to determine the “robust multi-array average” (RMA) using the “affy” software package (Irizarry et al., 2003; Gautier et al., 2004). Expression values were computed in detail from raw CEL files by applying the RMA model of probe-specific correction for perfect-match probes. These corrected probe values were then subjected to quantile normalization, and a median polish was applied to compute one expression measure from all probe values. Resulting RMA expression values were log2 transformed.

organism: Gallus gallus

source_name: GSCs replicate 5

label_protocol: cDNA was synthesized using the One-Cycle cDNA Synthesis Kit (Affymetrix). Single-stranded (ss) cDNA was synthesized using Superscript II reverse transcriptase and T7-oligo (dT) primers at 42°C for 1 h. Double-stranded (ds) cDNA was obtained using DNA ligase, DNA polymerase I, and RNase H at 16°C for 2 h, followed by T4 DNA polymerase at 16°C for 5 min. After cleanup using a Sample Cleanup Module (Affymetrix, Santa Clara, CA), ds cDNA was used for in vitro transcription (IVT). cDNA was transcribed using the GeneChip IVT Labeling Kit (Affymetrix) in the presence of biotin-labeled CTP and UTP.

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions. RNA quality was checked by agarose gel electrophoresis and RNA quantity was determined by spectrophotometry at 260 nm. RNA was then further purified using the RNeasy kit (Qiagen, Valencia,　CA). The total RNA was used for gene expression analysis on an Affymetrix GeneChip Chicken Genome Array (Affymetrix, Santa Clara, CA), containing 38,535 probes.

value: 6.5 days WL embryos

value: gonad

value: GSCs


title: GSCs replicate 3

source_name: GSCs replicate 3


title: GSCs replicate 6

source_name: GSCs replicate 6


title: H3-zfp1

source_name: H3 ChIP DNA from zfp1-/- L4/Young Adults

value: zfp1-/-, ok554 strain

value: whole organism

value: Abcam

tag: chip antibody catalog #


title: PGCs replicate 3

description: PGCs separated by MACS treatment from the gonad of 6.5 days WL embryos.

source_name: PGCs replicate 3

value: PGCs


title: H3-glp4,zfp1

source_name: H3 ChIP DNA from glp4-/-,zfp1-/- L4/Young Adults


title: GSCs replicate 1

source_name: GSCs replicate 1


title: H3-prg1,zfp1

source_name: H3 ChIP DNA from prg1-/-,zfp1-/- L4/Young Adults


title: GSCs replicate 4

source_name: GSCs replicate 4


title: PGCs replicate 2

source_name: PGCs replicate 2


title: PBMC_RNA_Control_15

description: Validation set

value: normal


title: PGCs replicate 1

source_name: PGCs replicate 1


title: GSCs replicate 2

source_name: GSCs replicate 2


title: PBMC_RNA_Control_16

description: Validation set


title: PBMC_RNA_Control_9

description: Discovery set


title: PBMC_RNA_Control_14

description: Validation set


title: PBMC_RNA_Control_5

description: Discovery set


title: PBMC_RNA_Control_12

description: Validation set


title: PBMC_RNA_Control_3

description: Discovery set


title: PBMC_RNA_Control_7

description: Discovery set


title: PBMC_RNA_PAD_18

description: Validation set

source_name: Peripheral Blood Mononuclear Cells (PBMC) - PAD patients

value: peripheral arterial disease (PAD)


title: PBMC_RNA_Control_13

description: Validation set

source_name: Peripheral Blood Mononuclear Cells (PBMC) - Controls


title: PBMC_RNA_Control_8

description: Discovery set


title: PBMC_RNA_Control_11

description: Validation set


title: PBMC_RNA_Control_1

description: Discovery set


title: PBMC_RNA_Control_2

description: Discovery set


title: PBMC_RNA_PAD_19

description: Validation set

value: Peripheral Blood Mononuclear Cells (PBMC) - PAD patients


title: PBMC_RNA_Control_10

description: Validation set


title: PBMC_RNA_Control_4

description: Discovery set


title: PBMC_RNA_PAD_17

description: Validation set


title: PBMC_RNA_PAD_16

description: Validation set


title: PBMC_RNA_Control_6

description: Discovery set


title: PBMC_RNA_PAD_15

description: Validation set


title: PBMC_RNA_PAD_5

description: Discovery set


title: PBMC_RNA_PAD_3

description: Discovery set


title: PBMC_RNA_PAD_14

description: Validation set


title: PBMC_RNA_PAD_12

description: Validation set


title: PBMC_RNA_PAD_8

description: Discovery set


title: PBMC_RNA_PAD_13

description: Validation set


title: PBMC_RNA_PAD_10

description: Validation set


title: PBMC_RNA_PAD_11

description: Validation set


title: PBMC_RNA_PAD_9

description: Discovery set


title: Limited phosphorus 5day Exposure Rep 1

status: Public on Mar 13 2012

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

hyb_protocol: Pre-hybridize Oligonucleotide array in 5X SSC, 0.1% SDS, and 0.4% I-Block at 42 degrees Celcius for 1.5 hrs. Wash array 3X with water (filtered, 0.22um). Centrifuge array at 400 rcf for 2min at RT. Prepare hybridization reaction (27.5 ul of Genisphere 2X formamide hyb buffer, 13.75ul combined labeled aRNA (60pmol/each) and 13.75ul of KREAblock reagent). Incubated at 80 degrees Celcius for 10mins, and then 42 degrees Celcius until ready to use. Add hybridizatoin reaction to Oligonucleotide array in Corning Hybridization Chamber. Incubated in a water bath for 15hrs at 42 degrees Celsius. Post-hybridization washes included 2X SSC/0.2% SDS at 42 degree Celsius for 10min, 2X SSC at RT for 10min, 0.2X SSC at RT (2X) for 10min each with gentle agitation and brief rinse with 0.1X SSC at RT. Centrifuge array slides at 400 rcf for 2min at RT.

scan_protocol: Images were acquired using GenePix Professional 4200A with GenePix Pro software (version 6.0.1.25) at 10 micron resolution.

data_processing:
Signal intensities extracted using GenePix Pro 6.0 and reported as GenePix Result (.GPR) files
log2 CY5 - log2 CY3, no background correction, printtip-loess normalization within arays, scale normalization between arrays

organism: Daphnia pulex

source_name: Total RNA from whole body daphnia, limited phosphorus exposure, 5-days

label_protocol: Labeled 2ug of amplified RNA in 20uL reaction using Kreatech ULS aRNA Cy3/Cy5 Labeling Kit according to manufacture's specifications. Dye removal using KREApure Columns. Degree of labeling assessed using Nanodrop (ND-1000), Microarray assay.

extract_protocol:
Total RNA extraction using TRIZOL reagent and seperation with organics (chloroform). Purification using QIAGEN RNeasy Mini Kit and on-column Dnase digestion. Quanity assessed using Nanodrop (ND-1000), RNA assay. Quality assessed using Agilent Bioanalyzer 2100 and Agilent RNA 6000 Nano Kit, Eukaryote Total RNA assay.
Total RNA (1.5ug) primed with modified Oligo (dT)-T7 primer (100ng) at 65 degrees Celcius for 10mins. First stand cDNA carried out in the presence of SuperScript II RT (200U), 10mM dNTP set (1uL), and RNaseOUT (40U) at 42 degrees Celcius for 2hrs, and then at 65 degrees Celcius for 10mins. Second strand synthesis carried out in the presence of DNA Polymerase I (20U), 10mM dNTP set (1.5uL), and RNase H (2U) for 2hrs at 16 degrees Celsius. ds cDNA purification using Qaigen MiniElute PCR Purification Kit. Invitro transcription with Ambion MEGAscript T7 Kit using 1ug ds cDNA at 1.5X standard reacton size. Incubate for 4hrs at 37 degrees Celsius, followed by Dnase Treatment. Purification using QIAGEN RNeasy Mini Kit with modified washing steps: single wash using Buffer RPE (500uL), centrifuge and discard flow through, followed by 80% ethanol wash (650uL), centrifuge and discard flow through. Quanity assessed using Nanodrop (ND-1000), RNA assay. Quality assessed using Agilent Bioanalyzer 2100 and Agilent RNA 6000 Nano Kit, mRNA Nano assay.

tag: treatment protocol

source_name: Total RNA from whole body daphnia, limited phosphorus exposure control, 5-days


title: PBMC_RNA_PAD_6

description: Discovery set


title: PBMC_RNA_PAD_1

description: Discovery set


title: Limited phosphorus 5day Exposure Rep 2


title: PBMC_RNA_PAD_2

description: Discovery set


title: PBMC_RNA_PAD_7

description: Discovery set


title: Limited phosphorus 5day Exposure Rep 4


title: PBMC_RNA_PAD_4

description: Discovery set


title: Control vs Nosema ceranae (Sample3_chip3)

status: Public on May 23 2012

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybrization master for a given source and biological replicate

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

organism: Apis mellifera

source_name: Total RNA from gut ventriculi infected with Nosema ceranae

label_protocol: Labeled 1 microgram double stranded cDNA with Cy-dye nonamers in triplicate using NimbleGen Dual-Color Labeing kit with recommened user guide. Http://www.nimblegen.com/

extract_protocol: Total RNA extracted using organic solvents from gut ventriculi infected with Nosema ceranae. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

value: gut ventriculi

tag: infection

value: Nosema ceranae

tag: replicate

value: biological

source_name: Control Total RNA from gut ventriculi

extract_protocol: Total RNA extracted using organic solvents from gut ventriculi not infected with Nosema ceranae. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

value: no infection

value: technical


title: Control vs Nosema ceranae (Sample1_chip3)


title: Limited phosphorus 5day Exposure Rep 3


title: WT38 (biological rep 2 of 2)

status: Public on Mar 06 2012

city: Lausanne

first: Andrija

last: Finka

address: Batiment Biophore

department: Department of Plant Molecular Biology

country: Switzerland

institute: University of Lausanne

description: Biological replicate 2 of 2. Control protonemata at 25°C.

hyb_protocol: The sample was placed between the Agilent backing slide and the microarray chip, sealed in the hybridization chamber and set to hybridize for 17 h in a 60°C rotating hybridization oven. Upon completion, the slides were washed sequentially in 6 × SSC (0.9 m NaCl, 90 mm Na-acetate, pH 7.0) buffer at room temperature, then 0.1 × SSC (0.15 m NaCl, 15 mm Na-acetate, pH 7.0) on ice.

scan_protocol: Slides were then dried using nitrogen gas and placed in holders, and scanned using the DNA Microarray Scanner (no. G2565BA, Agilent) with the Agilent Scan Control software.

data_processing:
The raw intensity data then were log2-transformed for normalization. Lowess normalized log2 ratio (test/reference) were used.
A  gene was considered as a significant change in gene expression based on the twofold cutoff with P-values < 0.05.

organism: Physcomitrium patens

source_name: Wild type protonemata [test]

label_protocol: An Agilent-certified microarray service lab (MOgene, LC, St. Louis, MO, USA) was used to perform the microarray experiments.

growth_protocol: Protonemata were  grown for 10 days at minimal medium

extract_protocol: Total RNA was etracted using RNeasy Plant Mini Kit according to manufacturer instructions

treatment_protocol: Moss tisue were transferred in eppendorf tube containing 600 microlioers of liquid minimal media and treated for half an hour at indicated temperatures

tag: genotype/variation

value: Wild type

tag: age

tag: temperature

source_name: Wild type protonemata [control]


title: Control vs Nosema ceranae (Sample3_chip2)


title: Control vs Nosema ceranae (Sample3_chip4)


title: Nosema ceranae vs Control (Sample2_chip2)


title: Control vs Nosema ceranae (Sample1_chip4)


title: CNGCb34 (biological rep 2 of 2)

source_name: CNGCb knockout protonemata [test]

value: CNGCb knockout


title: Control vs Nosema ceranae (Sample3_chip1)


title: CNGCb34 (biological rep 1 of 2)

description: Biological replicate 1 of 2. Control protonemata at 25°C.


title: WT38 (biological rep 1 of 2)


title: WT34 (biological rep 2 of 2)


title: WT34 (biological rep 1 of 2)


title: mycelium wild-type vs. TRA1-deleted mutant rep5

status: Public on Mar 03 2012

city: Kaiserslautern

first: Karsten

last: Andresen

address: Erwin-Schroedinger-Str. 56

country: Germany

institute: IBWF

description:
tra1-wt-rep5
raw data file: mycel-tra1-wt-3.txt

hyb_protocol: Following the manufacturer’s instructions supplied with Aglilent platform.

scan_protocol: Agilent Technologies Scanner System (Scanner Model G2505B) was used with Agilent Scan Control Software Version A.7.0.1

data_processing: Preliminary processing of data was made using the Agilent Feature Extraction Software (9.5.1.1). Prior to normalization all data related to the expression of Oryza sativa genes have been removed. Data normalisation and statistical analyses were performed using Bioconductor R package Limma. Raw signals were background corrected by subtracting local spot background. Two normalization methods were applied: first within arrays using the global loess method and second between the arrays using the Aquantile method. There are two technical replicates of each biological sample (derived from one raw data file indicated in 'Description' and available as Series Supplementary file). The output files from Feature Extraction, where each probe appears twice in the column "ProbeName", were filtered with a script that sorted the first appearance of a probe in the column "ProbeName" to the first replicate and the second appearance to the second replicate.

organism: Pyricularia oryzae

source_name: wt_aerial mycelium

label_protocol: RNA was labelled with Cy3 and Cy5 dyes using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Cat. No. 5184-3523) following the manufacturer’s instructions.

growth_protocol: 10 day old CM (Talbot et al., 1993) agar cultures

extract_protocol: RNA was obtained from the aerial mycelium by grinding in liquid nitrogen and extraction using the Qiagen plant RNA extraction kit.

treatment_protocol: Aerial mycelium was obtained by shaving the surface of 10 day old CM agar cultures of the respective strains with a sterile scalpel.

tag: strain background

value: wild type

source_name: tra1_aerial mycelium

value: tra1 mutant


title: mycelium wild-type vs. TRA1-deleted mutant rep7

description:
tra1-wt-rep7
raw data file: mycel-tra1-wt-4.txt


title: mycelium wild-type vs. TRA1-deleted mutant rep6

description:
tra1-wt-rep6
raw data file: mycel-tra1-wt-3.txt


title: mycelium wild-type vs. TRA1-deleted mutant rep4

description:
tra1-wt-rep4
raw data file: mycel-tra1-wt-2.txt


title: mycelium wild-type vs. TRA1-deleted mutant rep8

description:
tra1-wt-rep8
raw data file: mycel-tra1-wt-4.txt


title: Nosema ceranae vs Control (Sample2_chip1)

tag: tissue


title: CNGCb25 (biological rep 1 of 2)


title: CNGCb25 (biological rep 2 of 2)


title: Nosema ceranae vs Control (Sample2_chip4)


title: Control vs Nosema ceranae (Sample1_chip1)


title: mycelium wild-type vs. TRA1-deleted mutant rep2

description:
tra1-wt-rep2
raw data file: mycel-tra1-wt-1.txt

tag: strain


title: spores wild-type vs. TRA1-deleted mutant rep3

scan_protocol: PerkinElmer Microarray Analysis System was used with ScanArray Express Software Version 3.0.0.0016 (therefore, the header information, usually expected in 'Agilent Feature Extraction' files, is missing in the raw data files).

data_processing: Preliminary processing of data was made using the ArrayInformatics Database Tools (Version 2.1, PerkinElmer Life Sciences). Prior to normalization all data related to the expression of Oryza sativa genes have been removed. Data normalisation and statistical analyses were performed using Bioconductor R package Limma. Raw signals were background corrected by subtracting local spot background. Two normalization methods were applied: first within arrays using the global loess method and second between the arrays using the Aquantile method.

extract_protocol: RNA was obtained from conidia using extraction following spore breakage using FastPrep and extraction using the Qiagen plant RNA extraction kit.

treatment_protocol: Spores were obtained by rubbing the surface of 10 day old CM agar cultures of the respective strains with a sterile spreader and supension in water followed by filtration through 2 layers of Miracloth to remove mycelial fragments


title: B73 endosperm rep1

status: Public on Dec 16 2011

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description:
Sample 1
processed data : fit.B73_endo.05-12-11.txt

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the 2.1M arrays according to the array manufacturer protocol (42°C, 16-20hrs).

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the GenePix4000B Scanner (Axon/Molecular Devices) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files exported from NimbleScan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Sample-dependent MeDIP enrichments were estimated for each probe by fitting a fixed linear model accounting for array, dye, and sample effects to the data using the limma package (Smyth, 2004). The following contrasts were then fit: B73 IP vs B73 input and  Mo17 IP vs (Mo17 input vs B73 input). Moderated t-statistics and the log-odds score for differential MeDIP enrichment was computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05.

organism: Zea mays

source_name: B73 Rep 1 Endosperm input

label_protocol: Amplified input and methylated DNA samples were labeled (3 x 1ug per reaction), hybridized to the 2.1M feature array and washed according to the array manufacturers protocol.  Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5.

extract_protocol: Genomic DNAs were extracted using the Qiagen DNeasy Plant Mini Kit.  10ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps).  Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

treatment_protocol: genomic DNAs were sonicated, amplified, and fluorophore-labeled

tag: genotype

tag: cross date

value: Endosperm

source_name: B73 Rep 1 Endosperm methylated DNA IP

treatment_protocol: genomic DNAs were sonicated, methylated DNAs were isolated, amplified and fluorophore-labeled

tag: ip antibody vendor

tag: ip antibody

value: Zymo Research


title: B73 endosperm rep2

description:
Sample 2
processed data : fit.B73_endo.05-12-11.txt

source_name: B73 Rep 2 Endosperm input

source_name: B73 Rep 2 Endosperm methylated DNA IP


title: B73 endosperm rep3

description:
Sample 3
processed data : fit.B73_endo.05-12-11.txt

source_name: B73 Rep 3 Endosperm input

source_name: B73 Rep 3 Endosperm methylated DNA IP


title: Control vs Nosema ceranae (Sample1_chip2)


title: spores wild-type vs. TRA1-deleted mutant rep1


title: mycelium wild-type vs. TRA1-deleted mutant rep1

description:
tra1-wt-rep1
raw data file: mycel-tra1-wt-1.txt


title: Nosema ceranae vs Control (Sample2_chip3)


title: mycelium wild-type vs. TRA1-deleted mutant rep3

description:
tra1-wt-rep3
raw data file: mycel-tra1-wt-2.txt


title: spores wild-type vs. TRA1-deleted mutant rep2


title: transfected_Neuro2A

status: Public on Feb 29 2012

city: New Delhi

first: Rohini

last: Muthuswami

address: Room# 333, School of Life Sciences, JNU

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

hyb_protocol: Agilent's In situ hybridization kit was used for hybridization

scan_protocol: Agilent Technologies Scanner G2505C US83000164

data_processing: The normalization was done using GeneSpring GX 11.0 software.

source_name: Neuronal cell line

label_protocol: The RNA was labeled using T7 promoter based-linear amplificationn to generate complementary RNA

growth_protocol: Cells were maintained in DMEM media.  Transfected cells were grown in the presence of G418 and pen-strep

extract_protocol: Total RNA was extracted using Trizol (Sigma-Aldrich)

treatment_protocol: Cells were grown to 60% confluency prior to RNA extraction

tag: cell line

value: Mouse neuronal (Neuro2A)

tag: vector


title: breast, pre AF treatment (H7_1349)

status: Public on Dec 20 2011

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
RE1_H7_1349_U133Plus2.0.CEL
Gene expression data from human breast cancer

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing: Expression were estimated using BRB Array Tools software, GCRMA method

source_name: Human breast, pre AF treatment

label_protocol: 3' IVT express

extract_protocol: Trizol extraction

treatment_protocol: After a baseline tumor biopsy, patients were randomized to receive Anastrazole/fulvestrant(AF) or anastrazole/Fulvestrant/Gefitinib (AFG) for 3 weeks, then a second biopsy was obtained. After that all patients received the AFG treatment.

value: AF

value: pre

tag: response

value: PD

value: pos

value: neg

tag: baseline age (years)

tag: baseline tumor size (cm)

tag: patient id (to identify the 2 chips from the same patient)


title: Uvect-UERG Rep 4

status: Public on Oct 19 2011

description:
Total RNA primed with Oligo-dT (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with ChargeSwitch PCR Clean Up Kit (Invitrogen).
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

hyb_protocol: Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

scan_protocol: Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files.

source_name: Immortalized cell line

label_protocol: ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

growth_protocol: RWPE-1 cells were maintained in Keratinocyte Serum Free media with EGF and bovine pituitary extract supplements (Invitrogen)

extract_protocol: Qiagen RNeasy kit with on column DNase digestion

treatment_protocol: Indicated samples were treated with 10 micromolar U0126 for six hours prior to harvesting RNA

tag: sample type

value: RWPE-1 cells expressing Flag-ERG, treated with U0126.

value: Flag-ERG

tag: treatment

value: RWPE-1 cells expressing empty vector, treated with U0126.

value: empty


title: Uvect-UETV1 Rep 4

value: RWPE-1 cells expressing Flag-ETV1, treated with U0126.


title: untransfected_Neuro2A


title: steady-state ammonium limitation biological rep 2 of 3

status: Public on Oct 01 2011

city: Athens

first: Shalabh

last: Sharma

state: GA

address: Department of Marine Science

department: Marine Science

institute: UGA

description: Biological replicate 2 of 3 of the ammonium limitation sample

hyb_protocol: Labeled mRNA samples were hybridized to custom microarray slides manufactured by Combimatrix (Mukilteo, WA, USA) and imaged according to the procedures described in the manufacturer's protocol. Hybridized slides were stripped according to Combimatrix's protocol and re-used up to three times.

scan_protocol: Axon Genpix GenPix 4000B microarray scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at 5 µm resolution.

data_processing: The procedures were modified from Burgmann et al., 2007 (Environmental Microbiology 9: 2742-2755). Each gene was represented by up to two probes and each probe was spotted up to three times on the array (Burgmann et al., 2007). Each hybridized spot was manually examined in GenePix Pro 6.0 Software (Molecular Devices, Sunnyvale, CA) for quality. The fluorescence value for each hybridized spot was subtracted from the five closest empty spots on the array (F635-B635; PRE_VALUE). Spots were flagged as bad with Acuity 4.0 (Molecular Devices) when they were unevenly hybridized (determined manually by checking the hybridization circularity), when the detected fluorescence minus the background fluorescence was less than two standard deviations of the background fluorescence (F635-B635 <2 SD(B635)), or when the signal to noise ratio (SNR635) was <3. Probes were removed when the flagged spots were present in >25% of arrays. For the remaining probes with good hybridization signal, those  targeting 5S rRNA, 16S rRNA, 23S rRNA, mismatch probes, and manufacturer's control probes were removed. These processing steps resulted in 5145 probes across 14 arrays (three biological replicates from glucose, ammonium, phosphate, and sulfate limitations and one technical replicate each for the ammonium and sulfate limitations) whose fluorescence values (PRE_VALUE) were used for global normalization (VALUE).

label: AlexaFluor dye 647 (red emission)

organism: Ruegeria pomeroyi DSS-3

source_name: Steady-state cells limited with 0.26 mM ammonium

label_protocol: This protocol was described by Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755. Amplified mRNA was labeled with AlexaFluor 647 dye (Invitrogen, Carlsbad, CA, USA) according to manufacturer's recommended procedures. Amplified and labeled mRNA was purified with the MEGAclear kit (Applied Biosystems/Ambion, Austin, TX, USA) and concentrated by ethanol precipitation.

growth_protocol: Ruegeria pomeroyi strain DSS-3 was grown in 320 ml custom-made chemostats with a culture volume of 200 ml. Steady-state biomass was limited by nitrogen (ammonium, 0.26 mM) whereas other non-limiting macronutrients were provided in excess. The culture medium was buffered with 10 mM 1,3-bis(tris(hydroxymethyl)methylamino)propane. Vitamins and trace metals were added to the culture medium. The feed medium was added to each chemostat culture at a constant rate, and spent medium and cells were removed at the same rate. During the incubation, cell cultures were mixed by constant stirring. Growth temperature was maintained at 30 degree celsius using a circulating water bath. Salinity was constant at 25. Oxygen was bubbled into the culture at a flow rate of 2 ml per minute through an aquarium air pump, controlled by a flow meter. The pH ranged from 6.6 to 7.0 during all growth regimes. Cell cultures were considered to be at steady-state when the change in OD600 was less than or equal to 10% between two successive measurements.

extract_protocol: Total RNA from steady-state cell culture was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s procedures. DNA was removed by TURBO DNase treatment (Applied Biosystems/Ambion, Austin, TX, USA). Ribosomal RNA was removed with MicrobeExpress (Applied Biosystems/Ambion) according to manufacturer's recommendations. Purified mRNA was amplified with MessageAmp II-Bacteria Kit (Applied Biosystems/Ambion) with procedures as described in manufacturer's manual.

tag: cell growth conditions

value: Chemostat culture with ammonium (0.26 mM) limitation


title: steady-state phosphate limitation biological rep 2 of 3

description: Biological replicate 2 of 3 of the phosphate limitation sample

source_name: Steady-state cells limited with 9.2 µM phosphate

growth_protocol: Ruegeria pomeroyi strain DSS-3 was grown in 320 ml custom-made chemostats with a culture volume of 200 ml. Steady-state biomass was limited by phosphorus (phosphate, 9.2 µM) whereas other non-limiting macronutrients were provided in excess. The culture medium was buffered with 10 mM 1,3-bis(tris(hydroxymethyl)methylamino)propane. Vitamins and trace metals were added to the culture medium. The feed medium was added to each chemostat culture at a constant rate, and spent medium and cells were removed at the same rate. During the incubation, cell cultures were mixed by constant stirring. Growth temperature was maintained at 30 degree celsius using a circulating water bath. Salinity was constant at 25. Oxygen was bubbled into the culture at a flow rate of 2 ml per minute through an aquarium air pump, controlled by a flow meter. The pH ranged from 6.6 to 7.0 during all growth regimes. Cell cultures were considered to be at steady-state when the change in OD600 was less than or equal to 10% between two successive measurements.

value: Chemostat culture with phosphate (9.2 µM) limitation


title: steady-state phosphate limitation biological rep 3 of 3

description: Biological replicate 3 of 3 of the phosphate limitation sample


title: steady-state ammonium limitation biological rep 3 of 3

description: Biological replicate 3 of 3 of the ammonium limitation sample


title: steady-state phosphate limitation biological rep 1 of 3

description: Biological replicate 1 of 3 of the phosphate limitation sample


title: Uvect-UETV1 Rep 2


title: Uvect-Vect Rep 2

value: RWPE-1 cells expressing empty vector


title: Uvect-UERG Rep 1


title: Uvect-Vect Rep 3


title: steady-state ammonium limitation tech rep 1 of 2 from the biological rep 1 of 3

description: Technical replicate 1 of 2 from biological replicate 1 of 3 of the ammonium limitation sample


title: PS2-1 iPSC

status: Public on Sep 10 2011

city: Tokyo

first: Takuya

last: Yagi

address: 35-Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University

hyb_protocol: Following fragmentation, all arrays were hybridized at 45C for 16 hr.

scan_protocol: GeneChips were scanned using an AFX GC3000 G7 scanner.

data_processing: The gene expression raw data were extracted using the AFFX Gene Chip Operation System. Quality control was performed on the basis of Affymetrix quality control metrics. The data were analyzed with the Gene Spring GX 11.0 (Agilent).

source_name: undifferentiated PS2-1 iPSC

label_protocol: Approximately 150 ng of RNA from each sample was labeled using GeneChip 3’IVT Express (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: iPSC were cultured in hES medium containing bFGF.

extract_protocol: Total RNA samples were isolated using RNeasy kit.

treatment_protocol: Cells were washed with PBS and Rneasy kit was used to isolate total RNA.

tag: cell type

value: iPSC from primary fibroblast with presenilin 2 mutation, N141


title: Transient-amplifying matrix cells, rep2

status: Public on Sep 02 2011

city: New York

first: Wen-Hui

last: Lien

state: NY

address: 1230 York Ave Box#300

department: Mammalian cell biology and development

institute: The Rockefeller Unoversity

description:
HF-TAC-2
Gene expression data from transient-amplifying progenitors.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the RMA method using Gene Pattern analysis settings and median scaling as the normalization method.

source_name: Mouse back skins, HF-TACs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: HF-SCs and HF-TACs were FACS-purified from the back skins of mice at the indicated ages.

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

treatment_protocol: No treatment.

value: back skin

value: transient-amplifying matrix cells

tag: gender

value: female

tag: age

tag: sorting markers

value: GFP, integrin α6, ephrinB1


title: Transient-amplifying matrix cells, rep1

description:
HF-TAC-1
Gene expression data from transient-amplifying progenitors.

tag: strain

tag: tissue


title: Activated hair follicle stem cells, rep2

description:
aHF-SC-2
Gene expression data from activated hair follicle stem cells.

source_name: Mouse back skins, aHF-SCs

value: activated hair follicle stem cells

value: GFP, integrin α6, CD34


title: steady-state ammonium limitation tech rep 2 of 2 from the biological rep 1 of 3

description: Technical replicate 2 of 2 from biological replicate 1 of 3 of the ammonium limitation sample


title: PS2-2 iPSC

source_name: undifferentiated PS2-2 iPSC


title: Uvect-UETV1 Rep 1


title: Uvect-UETV1 Rep 3


title: Activated hair follicle stem cells, rep1

description:
aHF-SC-1
Gene expression data from activated hair follicle stem cells.


title: Uvect-Vect Rep 1


title: Uvect-UERG Rep 2


title: Uvect-Vect Rep 4


title: 13H

status: Public on Aug 28 2011

city: Toronto

first: Kolja

last: Eppert

state: Ontario

address: 101 College St., rm 8-301

country: Canada

institute: University Health Network

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Affymetrix HT_HG-U133A microarrays (Affymetrix, Santa Clara, CA)

scan_protocol: standard Affymetrix protocol

data_processing: Data was normalized by robust multichip average using GeneSpring GX (Agilent).

source_name: 13 - unsorted

label_protocol: RNA was amplified using the Ovation Biotin RNA Amplification and Labeling System (NuGEN, San Carlos, CA). Biotinylated cRNA were prepared according to the standard Affymetrix protocol from Nugen amplified RNA.

growth_protocol: Standard protocol for primary human tissue

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

tag: sample #

tag: cell source

value: AML

tag: leukemia stem cells (lsc)

tag: sorted fraction

value: Unsorted


title: Quiescent hair follicle stem cells, rep2

description:
qHF-SC-2
Gene expression data from quiescent hair follicle stem cells.

source_name: Mouse back skins, qHF-SCs

value: quiescent hair follicle stem cells

value: integrin α6, CD34


title: Bark_glutamine+glucose_replicate 3_72h

status: Public on Jul 01 2011

city: college park

first: rongshuang

last: lin

state: MD

address: Plant Sci building

department: Plant sci

institute: Univ Maryland

description: Expression data for bark tissues from excised stems treated with glutamine+glucose

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed using RMA function  in the affy package in R.

organism: Populus trichocarpa

source_name: Barks from glutamine+glucose treatment for 72h for replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT expression kit manual).

growth_protocol: Poplar plants were grown in greenhouse under long-day photoperiod.

extract_protocol: Extraction of total RNA was performed using Qiangen RNeasy plant mini kit with Qiancube with modifications.

treatment_protocol: Excised stems from the LD-grown plants were trimmed off the basal leaves and kept 5 apical leaves; the basal end was immediately placed in water for pre-incubation for 24 h in growth chamber under 16-h light/8-h dark photoperiod. After 24 h, the stems were then transferred to aqueous solutions of 25 mM glutamine, glucose, sucrose, glycine, glutamine+glucose, glutamine+sucrose, for 48 or 72 h at the same condition.

value: Bark

tag: genotype

value: Nisqually

value: glutamine+glucose

tag: time

tag: replicate


title: Uvect-UERG Rep 3

value: RWPE-1 cells expressing Flag-ERG, treated with U0126.

tag: cell line

tag: vector

value: Flag-ERG

value: RWPE-1 cells expressing empty vector, treated with U0126.

value: empty


title: Bark_glutamine+glucose_replicate 3_48h

source_name: Barks from glutamine+glucose treatment for 48h for replicate 3

tag: treatment


title: Bark_H2O_replicate 3_72h

description: Expression data for bark tissues from excised stems treated with H2O

source_name: Barks from H2O treatment for 72h for replicate 3


title: Bark_glucose_replicate 3_48h

description: Expression data for bark tissues from excised stems treated with glucose

source_name: Barks from glucose treatment for 48h for replicate 3

value: glucose


title: Bark_glutamine_replicate 3_48h

description: Expression data for bark tissues from excised stems treated with glutamine

source_name: Barks from glutamine treatment for 48h for replicate 3

value: glutamine


title: Bark_pre2_replicate 3_preincubate 24h

description: Expression data for bark tissues from excised stems preincubated in water for 24h

source_name: Barks after 24h preincubation for replcate 3

value: preincubate 24h:pre2


title: Bark_pre2_replicate 2_preincubate 24h

source_name: Barks after 24h preincubation for replcate 2


title: Bark_glucose_replicate 1_48h

source_name: Barks from glucose treatment for 48h for replicate 1


title: Bark_glutamine_replicate 1_48h

source_name: Barks from glutamine treatment for 48h for replicate 1


title: Bark_H2O_replicate 3_48h

source_name: Barks from H2O treatment for 48h for replicate 3


title: Bark_glucose_replicate 3_72h

source_name: Barks from glucose treatment for 72h for replicate 3


title: Bark_pre1_replicate 3_immediately after excising from plants

description: Expression data for bark tissues from excised stems right after excisng from whole plants

source_name: Barks right after excising from plants for replicate 3

value: No treatment:pre1


title: Bark_pre1_replicate 2_immediately after excising from plants

source_name: Barks right after excising from plants for replicate 2


title: Bark_glutamine_replicate 2_72h

source_name: Barks from glutamine treatment for 72h for replicate 2


title: Bark_H2O_replicate 2_72h

source_name: Barks from H2O treatment for 72h for replicate 2


title: Bark_glutamine+glucose_replicate 2_72h

source_name: Barks from glutamine+glucose treatment for 72h for replicate 2


title: Bark_glucose_replicate 2_72h

source_name: Barks from glucose treatment for 72h for replicate 2


title: Bark_H2O_replicate 1_48h

source_name: Barks from H2O treatment for 48h for replicate 1


title: Bark_glutamine_replicate 3_72h

source_name: Barks from glutamine treatment for 72h for replicate 3


title: Bark_pre2_replicate 1_preincubate 24h

source_name: Barks after 24h preincubation for replcate 1


title: Bark_glutamine+glucose_replicate 1_48h

source_name: Barks from glutamine+glucose treatment for 48h for replicate 1


title: Quiescent hair follicle stem cells, rep1

description:
qHF-SC-1
Gene expression data from quiescent hair follicle stem cells.

source_name: Mouse back skins, qHF-SCs

value: back skin

value: female


title: Bark_H2O_replicate 1_72h

source_name: Barks from H2O treatment for 72h for replicate 1


title: Bark_glucose_replicate 1_72h

source_name: Barks from gluocse treatment for 72h for replicate 1


title: Bark_glutamine+glucose_replicate 1_72h

source_name: Barks from glutamine+glucose treatment for 72h for replicate 1


title: Bark_glutamine+glucose_replicate 2_48h

source_name: Barks from glutamine+glucose treatment for 48h for replicate 2


title: Bark_glutamine_replicate 1_72h

source_name: Barks from glutamine treatment for 72h for replicate 1


title: PTEN inducible MEFs at T0, biological rep1

status: Public on May 03 2011

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: Gene expression from MEFs carrying a tet-inducible Pten transgene

hyb_protocol: standard Affymetrix protocol

scan_protocol: Flourescence was measured by confocal scanner (Agilent, Palo Alto, CA)

data_processing: Signal intensity data was generated with Affymetrix Microarray Suite version 5.0 software with default parameters. Expression values were estimated with robust multi-array average (RMA) using standard background correction. RMA-normalized expression data is provided in log base 2 scale.

label_protocol: standard Affymetrix protocol

growth_protocol: tet-free FBS (5%)/MEF media

extract_protocol: Total RNA was extracted by using Trizol (Invitrogen) per manufacturer's protocol

treatment_protocol: 2 ug/ml doxycycline

tag: genotype/variation

value: Pten-null (Ptenloxp/loxp), with doxycycline-inducible PTEN transgene

value: embryonic fibroblasts

tag: transgene

value: tet-inducible Pten transgene

value: 0 h

tag: genetic background


title: PTEN inducible MEFs at T2 = 48hr, biological rep1

description: Gene expression from MEFs carrying a tet-inducible Pten transgene at 48 hrs after inducing PTEN

source_name: MEFs carrying a tet-inducible Pten transgene, 48 hrs after inducing PTEN

tag: cell type


title: Bark_glutamine_replicate 2_48h

source_name: Barks from glutamine treatemnt for 48h for replicate 2

value: Bark


title: Bark_H2O_replicate 2_48h

source_name: Barks from H2O treatment for 48h for replicate 2

value: Nisqually


title: PTEN inducible MEFs at T1 = 24hr, biological rep1

description: Gene expression from MEFs carrying a tet-inducible Pten transgene at 24 hrs after inducing PTEN

source_name: MEFs carrying a tet-inducible Pten transgene, 24 hrs after inducing PTEN


title: WT MEFs, biological rep2

description: Gene expression from MEFs

source_name: Mouse embryonic fibroblasts (MEFs)

value: PtenL/L (isogenic wildtype)

value: control


title: Bark_glucose_replicate 2_48h

source_name: Barks from glucose treatment for 48h for replicate 2


title: PTEN inducible MEFs at T2 = 48hr, biological rep2


title: PTEN inducible MEFs at T1 = 24hr, biological rep2


title: PTEN inducible MEFs at T0, biological rep2

source_name: MEFs carrying a tet-inducible Pten transgene


title: Bark_pre1_replicate 1_immediately after excising from plants

description: Expression data for bark tissues right after excisng from whole plants

source_name: Barks right after excising from plants for replicate 1


title: glioblastoma cell line_LN018_1

status: Public on Mar 18 2011

city: Basel

first: Michal

last: Grzmil

address: Maulbeerstrasse 66

department: Growth control

institute: Friedrich Miescher Institute for Biomedical Research

hyb_protocol: Samples were hybridized to Affymetrix U133v2.0 GeneChips and scanned as per manufacturer’s instructions.

scan_protocol: Chips were scanned using an Affymetrix GeneChip scanner.

data_processing: Expression values were estimated using the GC-RMA implementation found in Genedata’s Refiner 4.1 (Genedata) package. Data-mining and visualization was performed using Genedata’s Analyst 4.1 package.  Only median fold ratio values with P < 0.05 using t test were used for subsequent analysis. All samples were quintile normalized and median scaled to correct for minor variations in their expression distributions.

source_name: brain tumor cells

label_protocol: RNA was then amplified and labelled using the Affymetrix 2-cycle amplification protocol as per manufacturer’s instructions (Affymetrix).

growth_protocol: Human glioblastoma cells were cultured in DMEM supplemented with 10% FCS and standard antibiotics in an incubator at 37°C and 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was extracted from the primary tumor samples using Trizol reagent, according to manufacturer’s instructions, and resuspended in diethylpyrocarbonate (DEPC) treated water.  Total RNA was further purified using the RNeasy kit (Qiagen) and following the protocol for Total RNA cleanup.  Cultured cells were collected when plates were 70-80% confluent and RNA was extracted using RNeasy Mini kit (Qiagen).

value: glioblastoma


title: glioblastoma cell line_LN215_1


title: glioblastoma cell line_LN229_2


title: glioblastoma cell line_LN319_2


title: glioblastoma cell line_BS149_2


title: WT MEFs, biological rep1

description: Gene expression from MEFs


title: glioblastoma cell line_LN018_2


title: secondary glioblastoma_3

source_name: brain tumor tissue

value: secondary brain tumor

tag: age

tag: gender

tag: tumor grade

value: IV


title: Oligodendrioglioma_6

tag: tissue

value: primary brain tumor

value: oligodendrioglioma

value: male

value: OGIII


title: glioblastoma cell line_LN229_1


title: glioblastoma cell line_LN319_1


title: normal astrocytes_1

source_name: normal astrocytes

value: brain

value: astrocytes


title: glioblastoma cell line_BS149_1


title: Oligodendrioglioma_7

value: OGII


title: secondary glioblastoma_2


title: glioblastoma cell line_LN215_2


title: Oligodendrioglioma_4


title: normal astrocytes_2


title: Oligodendrioglioma_3


title: normal brain_2

source_name: normal brain tissue


title: secondary glioblastoma_1

value: female


title: normal brain_1


title: Oligodendrioglioma_5


title: normal astrocytes_3


title: Oligodendrioglioma_2

value: OA


title: Astrocytoma_6

value: astrocytoma

value: AII


title: Astrocytoma_2


title: Astrocytoma_1

value: AIII


title: Glioblastoma_11


title: Astrocytoma_3


title: Astrocytoma_7

value: AIII/IV


title: Oligodendrioglioma_1


title: CGH: Noir1-SGC-01 vs. Wm82-ISU-01 rep2

city: Saint Paul

first: Robert

middle: M

last: Stupar

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

organism: Glycine max

source_name: Noir1-SGC-01, Leaf tissue

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

extract_protocol: Qiagen DNeasy

value: single plant leaf tissue

tag: cultivar

source_name: Wm82-ISU-01, Leaf tissue


title: Glioblastoma_10

value: glioblastoma


title: Glioblastoma_9


title: Glioblastoma_12


title: Glioblastoma_7


title: Glioblastoma_1


title: Glioblastoma_6


title: CGH: Noir1-SGC-01 vs. Wm82-ISU-01 rep1


title: Glioblastoma_5


title: Astrocytoma_5


title: Glioblastoma_3


title: mixed embryo XX_WT-N_080307_C

status: Public on Mar 01 2011

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

description:
N/A
re-analysis of GSM365597

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: Arrays were normalized by RMA (Robust Multichip Average) using Affymetrix Expression Consol software (Irizarry et al. 2003).    Data were analyzed by ArrayStar.  Statistical analysis was performed using a moderated t-test with FDR multiple testing correction (Benjamini-Hochberg method). Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. 2003. Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 4: 249-264.

source_name: embryo from worms grown on NG plates

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: N2 worms were grown on NG agar that had been seeded with concentrated HB101 bacteria.

extract_protocol: Gravid adults were bleached and embryos harvested as described (Portman, D.S, Wombook, Profiling C. elegans gene expression with DNA microarrays) and 100 µl aliquots snap frozen in liquid nitrogen and stored at -80∞C.  An aliquot was thawed at 65∞C for 10 minutes, resuspended in 1ml Trizol (Invitrogen, Carlsbad, CA), vortexed vigorously to resuspend, and incubated for 20 minutes at room temperature. The sample was then centrifuged for 15 minutes at 12,000xg at 4∞C.  The aqueous phase was transferred to a new tube and 100 µl of BCP (1-bromo-3-chloropropane) (MRC, Cincinnati, OH) was added, the sample was mixed by vortexing, incubated for 15 minutes at room temperature, and centrifuged for 10 minutes at 12,000xg at 4∞C.  The aqueous phase was transferred to a new tube and nucleic acid was precipitated by addition of 500 µl of isopropanol. The sample was incubated for 10 minutes at room temperature, centrifuged at 12,000xg for 8 minutes, washed in 70% ethanol and air dried for 5 minutes.  Nucleic acid was resuspended in 100 µl nuclease-free water and RNA quantified with a UV spectrophotometer. One hundred micrograms of RNA was then treated with 3 µl RQ1-DNAse (Promega, Madison, WI) and RNA isolated with the RNAeasy kit as per the manufacturer's protocol (Qiagen, Valencia, CA). RNA was again quantified with a UV spectrophotometer and cDNA was prepared from 5 µg RNA using the Protoscript Kit (NEB, Ipswich, MA) and diluted 1:15 in water.

treatment_protocol: Embryos used for microarray analysis were obtained from bleached gravid adults.

value: N2 worms grown on HB101.

tag: developmental stage

value: mixed embryo


title: Astrocytoma_8

value: primary brain tumor


title: Glioblastoma_8

value: IV


title: Glioblastoma_2

value: male


title: mixed embryo XX_WT-N_080307_B

description:
N/A
re-analysis of GSM365596


title: Glioblastoma_4


title: CGH: Minsoy-SGC-01 vs. Wm82-ISU-01 rep2

source_name: Minsoy-SGC-01, Leaf tissue


title: CGH: Archer-SGC-01 vs. Wm82-ISU-01 rep2

source_name: Archer-SGC-01, Leaf tissue


title: CGH: Minsoy-SGC-01 vs. Wm82-ISU-01 rep1


title: HEK293 2

status: Public on Feb 01 2011

description: Biological replicate 2 of 4.

hyb_protocol: Single-color hybridization, post-hybridization washing and scanning were done with NimbleGen reagents and according to the NimbleGen's User's Guide for Expression Analysis.

scan_protocol: Images were acquired using a GenePix 4200A scanner with GenePix 6.0 software.

data_processing: Raw signal intensities were extracted from the TIFF images using NimbleScan version 2.4 (Roche NimbleGen) and output into NimbleScan "PAIR" files. These PAIR file outputs show the PM (perfect match) value for each probe. The PAIR files for each treatment group were then loaded into NimbleScan to create RMA_normalized files, based on NimbleScan's RMA (Robust Multichip Average) analysis.  The RMA value is the normalized value of the PM value for each member of the treatment group.  The RMA-normalized value is then converted to a log2 value, which is the value printed in the sample data tables.

source_name: Immortalized cell line HEK293

label_protocol: To synthesize targets for hybridization, we began with 10.0 µg of total RNA and used Invitrogen's SuperScript Double-Stranded cDNA Synthesis kit using oligo (dT) primer (Promega) followed by DNA labeling using 1 O.D. Cy3-labeled random nonamer primer (TriLink Biotechnologies) and 100U Klenow fragment 3’>5’ exo- (NEB) per 1.0 µg double-stranded cDNA.

growth_protocol: Cells grown in DMEM with 10% FBS and penicillin/streptomycin at 37C with 5% CO2 humified air.

extract_protocol: Total RNA was extracted from cells using TRIzol reagent (Invitrogen) under RNase-free conditions, followed by chloroform treatment (100ul/ml).  After centrifugation, the aqueous phase containing total RNA is then extracted and treated with isopropanol (500uL/mL) for 5-10 mins.  After centrifugation, the RNA pellet was isolated, washed with ethanol (75%; 1ml/1mL of reagent solution), followed by another centrifugation and air-dried.  The RNA pellet was resuspended in RNase-free water.  Total RNA quantity was assessed using NanoDrop ND-1000, and the Bioanalyzer 2100 determined the 28S/18S ratio for quality assessment.

treatment_protocol: No treatments were performed. mRNA levels under basal conditions were measured.

value: normal


title: HEK293 4

description: Biological replicate 4 of 4.


title: HEK293 3

description: Biological replicate 3 of 4.


title: mixed embryo XX_WT-N_080307_A

description:
N/A
re-analysis of GSM365595


title: CGH: Archer-SGC-01 vs. Wm82-ISU-01 rep1

status: Public on May 02 2011


title: Astrocytoma_4


title: HEK293 1

description: Biological replicate 1 of 4.


title: Sample8_K2L2_replicate2

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate.

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

source_name: Total RNA from experiment K2

label_protocol: DNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.

extract_protocol: Tissue was homogenized using Trizol reagent (Invitrogen), and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

tag: Sex

value: whole body

tag: strain

source_name: Total RNA from experiment L2


title: Sample5_J1J2_replicate5

source_name: Total RNA from experiment J1

value: juvenile

source_name: Total RNA from experiment J2


title: Sample6_K1L1_replicate2

source_name: Total RNA from experiment L1

source_name: Total RNA from experiment K1


title: Sample4_K2L2_replicate1


title: Sample5_L1L2_replicate2


title: Sample3_K1K2_replicate1


title: Sample3_J1J2_replicate3


title: Sample1_L1L2_replicate1


title: Sample6_J1J2_replicate6


title: Sample7_K1K2_replicate2


title: Sample2_K1L1_replicate1


title: Sample2_J1J2_replicate2


title: Sample43_I1I2_replicate4

source_name: Total RNA from experiment I1

value: adult

value: 21 days

source_name: Total RNA from experiment I2


title: Sample4_J1J2_replicate4

value: female


title: Sample1_J1J2_replicate1


title: Sample47_O1O2_replicate4

source_name: Total RNA from experiment O1

source_name: Total RNA from experiment O2


title: Sample39_I1I2_replicate3


title: Sample48_P1P2_replicate4

source_name: Total RNA from experiment P1

source_name: Total RNA from experiment P2


title: Sample46_N1N2_replicate4

source_name: Total RNA from experiment N1

source_name: Total RNA from experiment N2


title: Sample45_M1M2_replicate4

source_name: Total RNA from experiment M1

source_name: Total RNA from experiment M2


title: Sample44_H1H2_replicate4

source_name: Total RNA from experiment H1

source_name: Total RNA from experiment H2


title: Sample36_M1M2_replicate3


title: Sample40_H1H2_replicate3


title: Sample38_G1G2_replicate3

source_name: Total RNA from experiment G1

source_name: Total RNA from experiment G2


title: Sample42_G1G2_replicate4


title: Sample41_F1F2_replicate4

source_name: Total RNA from experiment F1

source_name: Total RNA from experiment F2


title: Sample37_F1F2_replicate3


title: Sample35_N1N2_replicate3


title: Sample30_C1C2_replicate4

source_name: Total RNA from experiment C1

source_name: Total RNA from experiment C2


title: Sample34_O1O2_replicate3


title: Sample33_P1P2_replicate3


title: Sample31_E1E2_replicate4

source_name: Total RNA from experiment E2

source_name: Total RNA from experiment E1


title: Sample32_D1D2_replicate4

source_name: Total RNA from experiment D2

source_name: Total RNA from experiment D1


title: Sample29_B1B2_replicate4

source_name: Total RNA from experiment B2

source_name: Total RNA from experiment B1


title: Sample28_D1D2_replicate3


title: Sample26_C1C2_replicate3


title: Sample25_B1B2_replicate3


title: Sample23_O1O2_replicate2

source_name: Total RNA from experiment O2

source_name: Total RNA from experiment O1


title: Sample24_P1P2_replicate2

source_name: Total RNA from experiment P1

source_name: Total RNA from experiment P2


title: Sample16_D1D2_replicate2


title: Sample17_F1F2_replicate2


title: Sample19_I1I2_replicate2

source_name: Total RNA from experiment I1

source_name: Total RNA from experiment I2


title: Sample20_H1H2_replicate2

source_name: Total RNA from experiment H2

source_name: Total RNA from experiment H1


title: Sample14_C1C2_replicate2


title: Sample10_N1N2_replicate1

source_name: Total RNA from experiment N2

source_name: Total RNA from experiment N1


title: Sample13_B1B2_replicate2


title: Sample22_N1N2_replicate2


title: Sample09_M1M2_replicate1

source_name: Total RNA from experiment M1

source_name: Total RNA from experiment M2


title: Sample01_B1B2_replicate1


title: Sample15_E1E2_replicate2

source_name: Total RNA from experiment E2

source_name: Total RNA from experiment E1


title: Sample08_H1H2_replicate1


title: Sample11_O1O2_replicate1


title: Sample07_I1I2_replicate1


title: Sample04_D1D2_replicate1

source_name: Total RNA from experiment D2

source_name: Total RNA from experiment D1


title: Sample02_C1C2_replicate1

source_name: Total RNA from experiment C2

source_name: Total RNA from experiment C1


title: Sample03_E1E2_replicate1


title: Sample12_P1P2_replicate1


title: Sample05_F1F2_replicate1

source_name: Total RNA from experiment F2

source_name: Total RNA from experiment F1


title: Sample1_A1A2_replicate4

source_name: Total RNA from experiment A1

source_name: Total RNA from experiment A2


title: Sample06_G1G2_replicate1

source_name: Total RNA from experiment G1

source_name: Total RNA from experiment G2


title: Sample1_A1A2_replicate3


title: Sample1_A1A2_replicate2


title: Sample1_A1A2_replicate1


title: Sample21_M1M2_replicate2


title: N18 4

description: Biological replicate 4 of 4.

data_processing: The data from these arrays were extracted using the software NimbleScan 2.4 (Roche NimbleGen) and processed into PAIR files. The data was not normalized.

source_name: Immortalized cell line N18


title: Sample27_E1E2_replicate3


title: N18 2

description: Biological replicate 2 of 4.


title: N18 1

description: Biological replicate 1 of 4.


title: BV2 3

description: Biological replicate 3 of 4.

source_name: Immortalized cell line BV2


title: Sample18_G1G2_replicate2


title: N18 3

description: Biological replicate 3 of 4.


title: MDA231-FOXA1_H3K4me2

status: Public on Jan 06 2011

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

description: H3K4me2 ChIP in MDA231-FOXA1 cells

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Scanned at the Nantes microarray core facility

data_processing: Model-based analysis of tiling array (MAT) (chip.dfci.harvard.edu/~wli/MAT/). Bar files provide individual probe signal level after MAT normalization (MAT score) (Johnson WE et al. PNAS 2006)

source_name: H3K4me2 ChIP in MDA231-FOXA1 cells

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were grown in DMEM or RPMI supplemented with 10% FBS.

extract_protocol: Cells were cross-linked with 1% formaldehyde and processed as in (Carroll et al. 2005).

tag: antibody

value: 07-030 from Millipore

source_name: Input from MDA231-FOXA1 cells

value: None (input control)


title: BV2 2

description: Biological replicate 2 of 4.


title: AtT20 3

description: Biological replicate 3 of 4.

source_name: Immortalized cell line AtT20


title: BV2 4

description: Biological replicate 4 of 4.


title: BV2 1

description: Biological replicate 1 of 4.


title: AtT20 1

description: Biological replicate 1 of 4.


title: MDA231-CTRL_H3K4me2

description: H3K4me2 ChIP in MDA231-CTRL cells

source_name: H3K4me2 ChIP in MDA231-CTRL cells

source_name: Input from MDA231-CTRL cells


title: MDA231-FOXA1_FOXA1

description: FOXA1 ChIP in MDA231-FOXA1 cells

source_name: FOXA1 ChIP in MDA231-FOXA1 cells

extract_protocol: Cells were cross-linked with 1% formaldehyde and processed as in Carroll et al. 2005 for ChIP-chip, or genomic DNA was directly prepared for MeDIP-chip  as in Weber et al. 2005.

value: Ab5089 (against FOXA1) from Abcam


title: MDA231-FOXA1_MeDIP

description: 5-methylcytosine immunoprecipitation (MeDIP) in MDA231-FOXA1 cells

value: MAb-5MECYT (against 5-methylcytidine) from Diagenode


title: MDA231-FOXA1_H2AZ

description: Antibodies against H2AZ and acetylated H2AZ (H2AZac) were used in combination for ChIP experiments in MDA231-FOXA1 cells

source_name: H2AZ and acetylated H2AZ (H2AZac) ChIP in MDA231-FOXA1 cells

value: Ab4174 (against H2AZ) and Ab18262 (against acetylated H2AZ) from Abcam


title: AtT20 2

description: Biological replicate 2 of 4.


title: MDA231-CTRL_MeDIP

description: 5-methylcytosine immunoprecipitation (MeDIP) in MDA231-CTRL cells


title: MDA231-CTRL_H2AZ

description: Antibodies against H2AZ and acetylated H2AZ (H2AZac) were used in combination for ChIP experiments in MDA231-CTRL cells

source_name: H2AZ and acetylated H2AZ (H2AZac) ChIP in MDA231-CTRL cells


title: LNCaP_CTCF

description: CTCF ChIP in LNCaP cells

source_name: CTCF ChIP in LNCaP cells

value: 07-729 (against CTCF) from Millipore

source_name: Input from LNCaP cells


title: LNCaP_MeDIP

description: 5-methylcytosine immunoprecipitation (MeDIP) in LNCaP cells


title: LNCaP_H2AZ

description: H2AZ and acetylated H2AZ (H2AZac) ChIP were performed independently in LNCaP cells

source_name: H2AZ and acetylated H2AZ (H2AZac) ChIP in LNCaP cells

value: Ab4174 (against H2AZ) or Ab18262 (against acetylated H2AZ) from Abcam


title: MCF7_MeDIP

description: 5-methylcytosine immunoprecipitation (MeDIP) in MCF7 cells

source_name: Input from MCF7 cells


title: MCF7_CTCF

description: CTCF ChIP in MCF7 cells

source_name: CTCF ChIP in MCF7 cells


title: MCF7_H2AZ

description: H2AZ and acetylated H2AZ (H2AZac) ChIP were performed independently in MCF7 cells

source_name: H2AZ and acetylated H2AZ (H2AZac) ChIP in MCF7 cells


title: AtT20 4

description: Biological replicate 4 of 4.


title: Patient 116, 3 month of REBIF

status: Public on Dec 18 2010

city: Barcelona

first: Ramil

last: Nurtdinov

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

country: Spain

institute: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Chips were processed on an Affymetrix GeneChip Fluidics Station 450. Background adjustment by Robust Multi-Array (RMA) algorithm was applied to probes intensities. Raw probes gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: PBMC

label_protocol: Samples were chemically fragmented and biotinylated using the IVT Labelling Kit (Affymetrix).

extract_protocol: Total RNA was extracted from fresh peripheral blood mononuclear cells using an RNeasy kit (Quiagen, Santa Clarita, USA)

value: Female

value: PBMC

tag: individual

value: Patient 116

value: REBIF

tag: time

value: 3 month of REBIF

tag: disease state

value: multiple sclerosis

tag: nab status

value: NAB-


title: Patient 116, baseline

tag: treatment

value: baseline


title: Patient 113, 24 month of REBIF

value: Patient 113

value: 24 month of REBIF


title: Patient 113, 12 month of REBIF

value: 12 month of REBIF


title: Patient 113, baseline


title: Patient 116, 24 month of REBIF


title: Patient 112, 12 month of REBIF

value: Patient 112


title: Patient 112, baseline


title: Patient 116, 12 month of REBIF


title: Patient 108, 24 month of BETAFERON

value: Patient 108

value: BETAFERON

value: 24 month of BETAFERON


title: Sample1_chip1_experimentC_replicate1

city: Notre Dame

first: Jacqueline

last: Lopez

source_name: Total RNA from adult of experiment C condition X

label_protocol: DNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA in triplicate.

treatment_protocol: CX

value: female

value: adult

value: whole body

value: TCO

source_name: Total RNA from adult of experiment C condition Y

treatment_protocol: CY

value: male


title: Patient 112, 3 month of REBIF

value: Female

value: PBMC

value: REBIF


title: Patient 113, 3 month of REBIF

value: 3 month of REBIF

value: multiple sclerosis

value: NAB-


title: Sample2_chip1_experimentC_replicate2


title: Sample3_chip1_experimentB_replicate3

source_name: Total RNA from juveniles of experiment B condition X

treatment_protocol: BX

value: juvenile

source_name: Total RNA from juveniles of experiment B condition Y

treatment_protocol: BY


title: Patient 108, 3 month of BETAFERON

value: 3 month of BETAFERON


title: Sample2_chip1_experimentB_replicate2


title: Sample3_chip1_experimentA_replicate3

source_name: Total RNA from juveniles of experiment A condition X

treatment_protocol: AX

source_name: Total RNA from juveniles of experiment A condition Y

treatment_protocol: AY


title: Sample3_chip1_experimentC_replicate3


title: Patient 998, 24 month of BETAFERON

value: Patient 998

value: NAB+


title: Patient 998, 12 month of BETAFERON

value: BETAFERON

value: 12 month of BETAFERON


title: Patient 108, 12 month of BETAFERON

value: Patient 108


title: Patient 112, 24 month of REBIF

value: Patient 112

value: 24 month of REBIF


title: Sample2_chip2_experimentA_replicate2

value: female

value: whole body

value: TCO


title: Patient 999, 24 month of BETAFERON

value: Female

value: PBMC

value: Patient 999

value: 24 month of BETAFERON


title: Sample1_chip1_experimentA_replicate1


title: Sample3_chip2_experimentA_replicate3


title: Patient 13, baseline

value: Patient 13

value: baseline

value: multiple sclerosis


title: Sample3_chip2_experimentB_replicate3

value: juvenile


title: Patient 4, 24 month of BETAFERON

value: Patient 4

value: NAB+


title: Patient 999, 12 month of BETAFERON

value: BETAFERON

value: 12 month of BETAFERON


title: Patient 13, 24 month of REBIF

value: REBIF


title: Patient 13, 12 month of REBIF

value: 12 month of REBIF


title: Sample2_chip1_experimentA_replicate2

value: female


title: Sample3_chip2_experimentC_replicate3

value: adult

value: whole body

value: male


title: Patient 999, baseline

value: Female

value: PBMC


title: Patient 998, baseline

value: Patient 998


title: Sample1_chip2_experimentB_replicate1


title: Patient 108, baseline

value: Patient 108

value: NAB-


title: Patient 999, 3 month of BETAFERON

value: Patient 999

value: 3 month of BETAFERON

value: multiple sclerosis


title: Patient 4, 3 month of BETAFERON

value: Patient 4

value: NAB+


title: Patient 4, baseline

value: baseline


title: Patient 4, 12 month of BETAFERON

value: BETAFERON

value: 12 month of BETAFERON


title: Sample1_chip2_experimentC_replicate1

value: female

value: TCO


title: GMP_rep2

status: Public on Aug 15 2010

city: Stanford

first: Jun

last: Seita

address: Lokey Stem Cell Building #G3101, 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036.

data_processing: The data were analyzed with R/Bioconductor.

source_name: bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

tag: progenitor population

value: GMP

value: 2 month


title: Patient 998, 3 month of BETAFERON

value: Female


title: Sample2_chip2_experimentB_replicate2

address: 019 Galvin Life Science Center

institute: University of Notre Dame

value: juvenile

value: whole body


title: MPP_FLpos_rep2

value: MMPFL+

value: male


title: Sample2_chip2_experimentC_replicate2

value: adult


title: GMP_rep1


title: CMP_rep3

value: CMP


title: CG AP1 Replicate3

status: Public on Sep 17 2010

city: La Jolla

first: Dwight

last: Kuo

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Arrays scanned using Genepix 4000A scanner and GenePix 6.0 software

data_processing: Background subtraction and LOESS

organism: Nakaseomyces glabratus

source_name: 200989 IP-enriched

label_protocol: BioPrime Array CGH Genomic Labeling System (Invitrogen #18095011)

growth_protocol: Grow YAP samples at OD600 of 0.2 in SC media. For PDR, grow until OD600 is 0.2.

extract_protocol: Cells were fixed for 20 minutes at room temperature with 1% formaldehyde and subsequently inactivated with glycine for 5 minutes and harvested by centrifugation (3000rcf, for 3 minutes). Cells were washed three times with ice-cold TBS and lysed for 2 hours with acid-washed glass beads in a Vibrax-VXR 2000. Cells were subsequently sonicated for 4 cycles of 20 seconds (+100 seconds rest) at power setting 2 on a Misonex Sonicator 3000 and incubated with Dynabeads M-280 conjugated with anti-TAP antibody (Open Biosystems #CAB1001). Reversal of cross-linking was performed overnight at 65◦C. Enrichment was verified by qPCR comparison of promoter-specific gene enrichment (of a known target) vs. a housekeeping control gene (ScACT1 or CgACT1) and compared to a non-antibody enriched control. The enriched DNA was amplified via the GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich #WGA2X)

treatment_protocol: When OD600 is 0.8, treat with 0.03% MMS for 1hr. Fpr PDRs treat with fluconazole (4ug/mL) for 2.2hrs (Cg) or 3.1hrs (Sc)

value: MMS

source_name: 200989 IP-unenriched


title: CG AP1 Replicate1


title: CMP_rep2


title: Sample1_chip2_experimentA_replicate1


title: CG AP1 Replicate2


title: Sample1_chip1_experimentB_replicate1


title: MPP_FLpos_rep1


title: Patient 13, 3 month of REBIF

value: PBMC

value: Patient 13

value: REBIF

value: 3 month of REBIF

value: multiple sclerosis