title: WT_STI_0Gy_Rep_3

description: Gene expression from G1-phase pre-B cells

hyb_protocol: Ten micrograms of fragmented RNA were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) and using the MAS5 algorithm to generate .CHP files.

source_name: Wild type v-abl-transformed pre-B cell

label_protocol: One microgram of total RNA was amplified as directed in the Affymetrix 3’ IVT Express kit protocol, performing the IVT reaction for 16 hours. Twelve and a half micrograms of amplified biotin-aRNAs were fragmented.

growth_protocol: Cells were maintained in suspension in Dulbecco's modified Eagle Medium (DMEM), high glucose, (Gibco BRL 11960-077) supplemented with 10% fetal bovine serum, 1X Sodium Pyruvate (Gibco BRL 11360-070), 1X Non-Essential Amino Acids (Gibco BRL 11140-050), 1X L-Glutamine (Gibco BRL 25030-081), and 2 μl of beta-mercaptoethanol.

treatment_protocol: Cells treated with STI571 were passaged with 3 μM STI-571 (Imatinib Mesylate) added to the media and incubated for 48 hr.  Cells were irradiated at a rate of 0.72 Gy/min for a final dose of 1 Gy in a Cesium source irradiator and pelleted 2 hr following irradiation.

value: G1-phase pre-B cell line

tag: genotype/variation

value: v-abl-transformed


title: Col0_leaf_floated_0.1%Tween20_0.1%acetone_rep3

status: Public on Mar 13 2013

type: RNA

city: York

first: David

last: Wortley

state: North Yorkshire

address: Wentworth Way

country: United Kingdom

institute: University of York

hyb_protocol: Affymetrix Eukaryotic Sample Processing protocol followed - 16 hours at 45oC in rotating hybridisation oven

scan_protocol: Affymetrix GeneChip Command Console Scan Control 1.1.0.845. Affymetrix 450 Scanner.

data_processing: Affymetrix Expression Console software v1.1. MAS5.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaf tissue, floated on 0.1% Tween 20, 0.1% acetone, 4 hours

label_protocol: Affymetrix Eukaryotic Sample Processing protocol followed - biotin labelling of antisense cRNA

growth_protocol: Seeds were chilled for 72 hours at 4 °C prior to sowing on F2 compost and maintaining in growth rooms set to a 16-hour day length, 20 °C.

extract_protocol: Frozen tissue was ground to a fine powder in liquid nitrogen and total RNA extracted using the commercially available Rneasy mini kit (Qiagen).

treatment_protocol: For each replicate, ten leaves were floated on a solution containing 0.1 % Tween 20 + 0.1 % acetone and maintained for 4 hours in growth room conditions. After 4 hours had elapsed tissue was harvested, flash frozen using liquid nitrogen and stored at -80 °C.

tag: ecotype

tag: transgene

tag: tissue

value: leaf tissue


title: MPZ-Tfam Knockout - rep1

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

country: USA

institute: Washington University in St.Louis

hyb_protocol: 750ng of each aRNA in water (10ul) was suspended in Illumina “HYB” buffer (20ul) and heated to 65C for five minutes, then allowed to cool to room temperature.  The samples were applied to HumanHT12v3 Expression Beadchips and hybridized at 58C for 16-20 hours at high humidity.  Arrays were washed according to Illumina standard protocol.  Immobilized, biotinylated aRNAs were then detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.  Arrays were washed and dried according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.

data_processing: Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Beadstudio software.  On-slide spot replicates were averaged by Beadstudio and individual spot data was reported

organism: Mus musculus

source_name: sciatic nerve

label_protocol: RNA samples were labeled with biotin according to Manufacturer's instructions.

extract_protocol: RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol.

value: sciatic nerve

tag: age

value: 2 months

tag: genotype

value: MPZ-Tfam KO


title: WT_STI_1Gy_Rep_2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from irradiated G1-phase pre-B cells

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

source_name: Irradiated wild type v-abl-transformed pre-B cell

extract_protocol: RNA was isolated using Qiagen RNeasy technology following the manufacturer’s instructions, including the addition of DNase.

tag: cell type


title: undivided_rep1

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.

scan_protocol: Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.

data_processing: Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).

organism: Homo sapiens

source_name: undivided B cells

label_protocol: Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).

growth_protocol: Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.

extract_protocol: Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).

treatment_protocol: CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.

value: peripheral blood

value: undivided B cells

value: low

tag: divided in vitro

value: no


title: Bl6 - Control - rep2

value: Bl6 wild type


title: CD27_low_rep4

source_name: CD27_low_proliferating B cells

value: proliferating B cells

value: yes


title: 6H_IP_I_vs_In_I

type: genomic

city: Paris

first: Fredy

last: BARNECHE

address: Rue d'Ulm

department: IBENS

country: France

institute: CNRS

description: Biological replicate 1.2 of H2Bub epigenome in dark +6H light

hyb_protocol: Co-hybridization was performed using the NimbleGen 3x720K array design and following manufacturer’s instructions

scan_protocol: Data acquisition was performed according to Roche Nimblegen instructions.

data_processing: Hybridization data were normalized using an ANOVA model to remove technical biases. Data were averaged on the dye-swap to remove tile-specific dye biases. A two state hidden Markov model (HMM) implemented in CisGenome (Ji and Wong 2005; Ji et al. 2008) package as TileMap application was used on normalized data to identify genomic regions that were significantly enriched for the H2Bub mark at different time points (IP greater than Input). Such regions, referred to as domains in the study, comprised of at least three probes and represent enriched segments in the genome. These domains were then assigned to the underlying annotation (genes) based on a specific consideration of middle 40% of a gene overlapping the domain to significantly separate noise from the signal.

molecule: genomic DNA

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after ChIP and directly from input DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

growth_protocol: 5-day-old seedlings grown in vitro.

extract_protocol: 6H_IP_I. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: dark-grown +6H light

value: 5 days

tag: developmental stage

value: (Boyes et al. Plant Cell 2001) 0.70

tag: antibody

value: Ab_H2Bub [Medimabs ref. MM-0029, lot 298060417]

extract_protocol: 6H_In_I. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

tag: vendor


title: WT_STI_1Gy_Rep_1


title: Col0_leaf_floated_0.1%Tween20_0.1%acetone_rep2


title: WT_STI_0Gy_Rep_2


title: WT_STI_1Gy_Rep_3


title: MCF7 cells  DMSO treated replicate 1

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description: Gene expression data from MCF7 cells treated with the novel anti-cancer agent NSC 59687

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com)

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner

data_processing: Affymetrix Expression console v1.3

label: Biotin

source_name: MCF7 cells untreated

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA).  Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com)

growth_protocol: MCF7 cells grown in RPMI 1640 media + 10% FBS

extract_protocol: Total RNA isolated using Rneasy (Qiagen)

treatment_protocol: Cells were treated with 10microM NSC 59687 for 24 hours

tag: cell line

tag: treatment

value: DMSO


title: MCF7 cells  DMSO treated replicate 2


title: MCF7 cells 59687 treated replicate 1

source_name: MCF7 cells treated


title: HC Pooled sample #2

status: Public on Mar 12 2013

city: Tokyo

first: Hidekata

last: Yasuoka

address: 35 Shinanomachi, Shinjuku

department: Internal Medicine

country: Japan

institute: Keio University School of Med

description: OligoGEArray for Human ECM & Adhesion molecules

hyb_protocol: We followed the Oligo GEArray HybTube Protocol which is supplied.

scan_protocol: Visualized with chemiluminescence and the signal was detected by ChemiDoc XRS with several exposure time.

data_processing: Quantified using GEArray Expression Analysis Suite, and data was normalized with signal intensity of GAPDH, and then compared between SSc and healthy controls

source_name: CD14+ monocytes

extract_protocol: CD14+ monocytes were purified from peripheral blood mononuclear cells. And then total RNA was extracted and reverse transcribed. Each pooled sample was composed of 5 patients with SSc or 5 healthy control. 2 different sets were prepared and compared.

value: CD14+ monocytes

tag: disease state

value: control


title: SSc Pooled sample #2

value: Systemic sclerosis


title: WT_STI_0Gy_Rep_1

value: G1-phase pre-B cell line

value: v-abl-transformed


title: SSc Pooled sample #1


title: HC Pooled sample #1


title: Bl6 - Control - rep1

value: sciatic nerve

value: 2 months


title: MCF7 cells 59687 treated replicate 2


title: HCT 116  siChe-1 rep3

city: rome

first: maurizio

last: fanciulli

address: via e chianesi 53

department: molecular medicine

country: Italy

institute: regina elena cancer institute

description: HCT 116  siChe-1 rep3

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45 °C on Human Gene 1. ST Array. GeneChips were whashed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console™ software (v.1.1) (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HCT 116 cells transfected with siChe-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affimetrix protocol from 6 micrograms of total RNA (Gene Chip Whole Transcript Assay Technical Manual, 2007, Affimetrix)

growth_protocol: HCT 116 cells were cultured in DMEM medium with 10% FBS.

extract_protocol: Trizol extraction of total RNA was performed according manufacturer's instruction

treatment_protocol: HCT116 cells were transiently transfected with  siGFP (siControl) or siChe-1 RNA double strand oligos and analyzed 48 hours later.

value: HCT 116


title: HuT78 DpVp35

city: Bethesda

first: Robert

last: Robey

address: 37 Convent Drive Rm 2112

institute: NCI

description: Test

data_processing: Processing performed as suggested by manufacturer

label: SYBR green

source_name: resistant cell line

extract_protocol: total RNA was extracted using Trizol according to the manufacturer's instructions

value: Romidepsin-resistant Sezary syndrome cell line

value: HuT78 DpVp35


title: HuT78

description: Control

source_name: untreated parental cells

value: Sezary syndrome cell line


title: 1H_IP_II_vs_In_II

description: Biological replicate 2.2 of H2Bub epigenome in dark +1H light

extract_protocol: Dark_IP_II. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: dark-grown +1H light

extract_protocol: Dark_In_II. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: mesenchymal stem cells of ITP 3

city: Jinan

first: Ji

last: Ma

state: Shandong

address: West Wen Hua Road 107

department: Department of Hematology

country: China

institute: Qilu Hospital, Shandong University

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min) at room temperature.

scan_protocol: The scanning setting for the Cy3 and Cy5 channels was manually balanced by visual inspection of the external control spots. The data from the obtained images were extracted with SpotData software (CapitalBio Corp.).

data_processing: For individual channel data extract, faint spots were removed for which intensities were below 400 unit after background subtracted in both channels (Cy3 and Cy5). A spot-exclusion method was adopted to filter faint spots in which genes whose signal intensities were in the lowest 50% were excluded from further analysis.Statistical comparisons were done by using the one class method in significance analysis of microarray (SAM) software.

source_name: MSCs

label_protocol: Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20μL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice.  4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5 μL M-MLV (Promega) were subsequently added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5 μL Klenow buffer, dNTP, and  Cy5-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.

growth_protocol: MSCs were maintained in MesenPRO RS™ Medium (GIBCO BRL, Gaithersburg, MD).

extract_protocol: Total RNA samples were prepared from MSCs from patients with ITP using Trizol reagent (Invitrogen) according to the manufacture’s instructions. RNA was further purified with an RNA clean-up kit (Macherey-Nagel, Germany) and quantified by using of spectrophotometer. RNA quality from each sample was assessed by visualization of the 28S/18S ribosomal RNA ratio on 1.2% formamide agarose gel.

treatment_protocol: MSCs were exposed to 0.5 μg/mL of  thalidomide for 12 hours

value: mesenchymal stem cells of ITP

tag: passage

tag: gender

value: male

tag: anti-gp iib/iiia & ib/ix

value: double positive

tag: bleeding sympotoms

value: petechia & epistaxis

source_name: THD-MSCs

value: mesenchymal stem cells of ITP treated with thalidomide (0.5 μg/mL) for 14 hours


title: mesenchymal stem cells of ITP 1

value: female

value: petechia


title: HCT 116 control rep3

description: HCT 116 control rep3

source_name: HCT 116 cells transfected with siControl

value: control


title: HuT78 DpP100

description: Test

tag: genotype/variation

value: HuT78 DpP100


title: 1H_In_I_vs_IP_I

description: Biological replicate 1.1 of H2Bub epigenome in dark +1h light

extract_protocol: Dark_In_I. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: dark-grown +1h light

tag: ecotype

value: 5 days

value: (Boyes et al. Plant Cell 2001) 0.70

value: Ab_H2Bub [Medimabs ref. MM-0029, lot 298060417]

extract_protocol: Dark_IP_I. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: HCT 116  siChe-1 rep1

description: HCT 116  siChe-1 rep1


title: HCT 116  siChe-1 rep2

description: HCT 116  siChe-1 rep2


title: OC tissue of C57 at 9m, biological rep2

city: Omaha

last: He

state: Nebraska

address: 2500 California Plaza

department: Department of Biomedical Sciences

institute: Creighton University

description: Gene expression data from OC of C57 mice at the age of 9 month

hyb_protocol: Following fragmentation,250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Affymetrix miRNA OC Tool(2008) using Affymetrix default analysis settings and global scaling as normalization method. Each miRNA probe is assayed for detection based on a Wilcoxon Rank-Sum test of the miRNA probe set signals compared to the distribution of signals from the background. If the resulting p-value for the probes is above 0.06, it was interpreted positively expressed.

source_name: OC tissue of C57 at 9m

label_protocol: Biotinylated cRNA were prepared according to the Geneisphere Flashtag Biotin HSR RNA labeling kit from 250 ng total RNA /each sample

growth_protocol: Both strains were bred in-house and housed according to institutional protocol, with original breeding pairs purchased from Jackson Laboratory (Bar Harbor, ME, USA). Care and use of the animals in this study were approved by grants from the National Institutes of Health and by the Institutional Animal Care and Use Committee of Creighton University. (IACUC #0655.3)

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

treatment_protocol: Cochleae were rapidly dissected out in cold phosphate-buffered saline (PBS; 10mM Na2HPO4, 1.7 mM KH2PO4, 137mM NaCl, 2.7 mM KCl, pH7.4) after the mice were euthanized. The bulla was opened up, and the bony shell of the cochlea was removed carefully. The basilar membrane together with the OC was collected in each strain.

tag: tissue

value: the organ of Corti tissue from inner ear

value: wt

tag: strain

value: 9 month old


title: OC tissue of C57 at 9m, biological rep3

tag: genotype

tag: age


title: mesenchymal stem cells of ITP 2

tag: cell type

value: ecchymosis & epistaxis


title: HCT 116 control rep1

description: HCT 116 control rep1

value: HCT 116


title: HCT 116 control rep2

description: HCT 116 control rep2


title: 1H_IP_I_vs_In_I

description: Biological replicate 1.2 of H2Bub epigenome in dark +1H light

tag: developmental stage


title: OC tissue of C57 at 3m, biological rep3

description: Gene expression data from OC of C57 mice at the age of 3 month

source_name: OC tissue of C57 at 3m

value: 3 month old


title: OC tissue of C57 at 9m, biological rep1


title: 6H_In_I_vs_IP_I

description: Biological replicate 1.1 of H2Bub epigenome in dark +6h light

treatment_protocol: dark-grown +6h light

tag: antibody


title: Dark_IP_I_vs_In_I

description: Biological replicate 1.2 of H2Bub epigenome in dark

extract_protocol: Dark_IP_I_vs_In_I. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: dark-grown

extract_protocol: Dark_In_I_vs_IP_I. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

tag: vendor


title: 6H_IP_II_vs_In_II

description: Biological replicate 2.2 of H2Bub epigenome in dark +6H light

extract_protocol: 6H_IP_II. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

extract_protocol: 6H_In_II. Chromatin extractions, immunoprecipitations, DNA amplification, labelling and hybridizations were performed as described previously in Roudier et al (Embo J 30: 1928-1938). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: Dark_In_II_vs_IP_II

description: Biological replicate 2.1 of H2Bub epigenome in dark


title: 6H_In_II_vs_IP_II

description: Biological replicate 2.1 of H2Bub epigenome in dark +6h light


title: Dark_In_I_vs_IP_I

description: Biological replicate 1.1 of H2Bub epigenome in dark


title: Dark_IP_II_vs_In_II

description: Biological replicate 2.2 of H2Bub epigenome in dark


title: DvH_mid-logarithmic phase_evolved salt-stressed (ES) strain grown in LS4D + 100 mM NaCl

type: mixed

city: Berkeley

first: Adam

middle: P.

last: Arkin

state: CA

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in evolved salt-stressed (ES) strain grown in LS4D + 100 mM NaCl.

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A.P. Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, mid-logarithmic phase

growth_protocol: Inoculate 1 ml of log-phase inoculum culture to 100 ml of defined PIPES buffered medium LS4D + 100 mM NaCl in glass bottles. Grow culture at 37°C till mid-log phase (OD of ~0.4) with three replicates. Harvest the mid-log phase cells via centrifugation at 4oC. Remove the residualliquid by pipetting. Cell pellets were immediately frozen in liquid N2 and stored at -80°C until RNA solation.

tag: genetic background

value: Hildenborough

value: phase evolved salt-stressed (ES) strain

value: grown in LS4D + 100 mM NaCl

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.

tag: sample type

value: reference genomic DNA


title: DvH_mid-logarithmic phase_evolved salt stressed (ES) strain grown in LS4D

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in evolved salt stressed (ES) strain grown in LS4D.

label_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

growth_protocol: Inoculate 1 ml of log-phase inoculum culture to 100 ml of defined PIPES buffered medium LS4D in glass bottles. Grow culture at 37°C till mid-log phase (OD of ~0.4) with three replicates. Harvest the mid-log phase cells via centrifugation at 4oC. Remove the residualliquid by pipetting. Cell pellets were immediately frozen in liquid N2 and stored at -80°C until RNA solation.

value: phase evolved salt stressed (ES) strain

tag: treatment

value: grown in LS4D


title: DvH_mid-logarithmic phase_evolved salt-stressed (ES) strain grown in LS4D + 250 mM NaCl

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in evolved salt-stressed (ES) strain grown in LS4D + 250 mM NaCl.

growth_protocol: Inoculate 1 ml of log-phase inoculum culture to 100 ml of defined PIPES buffered medium LS4D + 250 mM NaCl in glass bottles. Grow culture at 37°C till mid-log phase (OD of ~0.4) with three replicates. Harvest the mid-log phase cells via centrifugation at 4oC. Remove the residualliquid by pipetting. Cell pellets were immediately frozen in liquid N2 and stored at -80°C until RNA solation.

extract_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

value: grown in LS4D + 250 mM NaCl


title: DvH_mid-logarithmic phase_evolved control (EC) strain grown in LS4D + 100 mM NaCl

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in evolved control (EC) strain grown in LS4D + 100 mM NaCl.

value: phase evolved control (EC) strain


title: DvH_mid-logarithmic phase_evolved control (EC) strain grown in LS4D + 250 mM NaCl

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in evolved control (EC) strain grown in LS4D + 250 mM NaCl.


title: DvH_mid-logarithmic phase_ancestor (An) strain grown in LS4D + 250 mM NaCl

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in ancestor DvH strain grown in LS4D + 250 mM NaCl.

value: phase ancestor (An) strain


title: DvH_mid-logarithmic phase_evolved control (EC) strain grown in LS4D

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in evolved control (EC) strain grown in LS4D.


title: DvH_mid-logarithmic phase_ancestor (An) strain grown in LS4D + 100 mM NaCl

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in ancestor DvH strain grown in LS4D + 100 mM NaCl.


title: OC tissue of C57 at 3m, biological rep2


title: DvH_mid-logarithmic phase_ancestor (An) strain grown in LS4D

description: This sample is used to investigate the gene expression patterns at mid-logrithmic phase in ancestor DvH strain grown in LS4D.


title: OC tissue of C57 at P21, biological rep3

description: Gene expression data from OC of C57 mice at the age of P21

source_name: OC tissue of C57 at P21

value: Postnatal 21 days


title: OC tissue of C57 at P21, biological rep1


title: Col0_leaf_floated_0.1%Tween20_0.1%acetone_rep1

source_name: leaf tissue, floated on 0.1% Tween 20, 0.1% acetone, 4 hours

extract_protocol: Frozen tissue was ground to a fine powder in liquid nitrogen and total RNA extracted using the commercially available Rneasy mini kit (Qiagen).

tag: transgene

value: leaf tissue


title: OC tissue of C57 at 3m, biological rep1

description: Gene expression data from OC of C57 mice at the age of 3 month

value: the organ of Corti tissue from inner ear


title: OC tissue of CBA at 16m, biological rep2

description: Gene expression data from OC of CBA mice at the age of 16 month

source_name: OC tissue of CBA at 16m

value: wt

value: CBA/J

value: 16 month old


title: OC tissue of CBA at 16m, biological rep3


title: OC tissue of CBA at 16m, biological rep1


title: High-grade PC8

city: Nankoku

first: Kenji

last: Tamura

state: Kochi

address: Kohasu, Oko-cho

department: Urology

institute: Kochi University

description: High-grade prostate cancer cells that were microdissected from prostate cancer tissue, procured by needle biopsy.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Analysis Technical Manual, 701021 Rev. 5)

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The scanned images were analyzed using the GeneChip operating software version 1.4 (Affymetrix 690036) with Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling was used as normalization method. The trimmed mean target intensity of each array was set to 500. Differentially expressed genes were extracted using DNA microarray viewer (Kurabo, osaka, Japan)

source_name: clinical prostate cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev. 5).

extract_protocol: 100,00-200,000 tumor cells or normal cells were isolated selectively using the EZ cut system with a pulsed ultraviolet narrow beam-focus laser in accordance with the manufacturer’s protocols. RNA for microarray analysis was isolated with TRIzol reagent (Life Technologies, Rockville, MD, USA)  and purified with the RNeasy MiniElute kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: prostate cancer cells

tag: clinical stage

value: clinical T3bN0M0

tag: gleason score

value: GS 9

tag: psa level

value: PSA 275ng/ml


title: High-grade PC10

value: clinical T3aN1M0

value: GS 8

value: PSA 234ng/ml


title: High-grade PC6

value: clinical T4N1M1

value: PSA 311ng/ml


title: High-grade PC7

value: clinical T3bN1M1

value: PSA 1000ng/ml


title: 1H_In_II_vs_IP_II

description: Biological replicate 2.1 of H2Bub epigenome in dark +1h light

value: 5 days

value: (Boyes et al. Plant Cell 2001) 0.70

value: Ab_H2Bub [Medimabs ref. MM-0029, lot 298060417]


title: High-grade PC9

value: clinical T3aN0M0

value: PSA 80ng/ml


title: High-grade PC5

value: clinical T3bN0M1

value: PSA 334ng/ml


title: HC Pooled sample #1

description: OligoGEArray for Human ECM & Adhesion molecules

value: CD14+ monocytes

tag: disease state

value: control


title: SSc Pooled sample #2

value: Systemic sclerosis


title: SSc Pooled sample #1


title: High-grade PC4

value: prostate cancer cells

value: clinical T3aN0M1

value: GS 9

value: PSA 630ng/ml


title: SA137/93G_SA1450/94_Chip ID192

city: Bonn

first: Peter

last: Sass

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

country: Germany

institute: University of Bonn

description: SA137/93G_SA1450/94_Chip ID192

hyb_protocol: Hybridization was done with equal amounts of cDNA probes displaying similar picomoles of incorporated dye. Fluorescence-labeled cDNA probes were mixed in hybridization buffer (Scienion) in a total volume of 55 µl and denatured at 95°C for 2 min and subsequently applied to the microarray slide followed by incubation at 42°C for 72 hours under humidified conditions according to the manufacturer’s instructions. Hybridized microarrays were washed at room temperature in SSC buffer with decreasing salt concentrations (1 x SSC / 0.3% SDS for 5 min, 0.2 x SSC for 5 min, 0.06 x SSC for 30s).

scan_protocol: The intensity of fluorescence of the microarray was scanned with a GenePix 4000B scanner (Axon Instruments/Distribution by Biozyme Scientific GmbH, Hessisch Oldendorf, Germany). TIFF images were captured and analysed with GenePixPro4.1 software (Axon Instruments). The actual signal intensity was calculated by substracting the mean value of the local background intensity from the mean value of the signal intensity of the individual spot.

data_processing: The data sets were normalized by using Acuity 3.1 software (Axon Instruments) and by applying the LOWESS algorithm. Significant changes of gene expression were determined by implementing SAM (significance analysis of microarrays, http://www-stat.stanford.edu/~tibs/SAM/ (Tusher, V. G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc.Natl.Acad.Sci.U.S.A 98:5116-5121.)) using the one class response and a false discovery rate of < 1% with a medium number of falsely called significant genes of <1.

organism: Staphylococcus aureus

source_name: SA137/93G, spontaneous mutant strain of SA137/93A

label_protocol: Total RNA (6 µg) was transcribed into cDNA using the Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany) following the manufacturer’s instructions. For direct fluorescent labeling of the cDNA, the transcription reaction was performed in a total volume of 40 µl in presence of 0.1 mM cyanine-3’ or cyanine-5’ labeled dCTP (Perkin Elmer Life Science, Mechelen, Belgium) in addition to 0.2 mM dCTP, 0.5 mM dATP, 0.5 mM dGTP and 0.5 mM TTP, 75 µg/ml random hexamer primers (Amersham, Bioscience, Freiburg, Germany) and 25 U/ml RNase-Out (Invitrogen). RNA was degraded by alkaline hydrolysis at 65°C and cDNA was purified using the MinElute PCR Purification Kit (QIAGEN).

growth_protocol: S. aureus was cultured in brain heart infusion (BHI) medium (Becton Dickinson GmbH, Heidelberg, Germany) at 37°C with aeration. An overnight culture was diluted 100fold in fresh BHI broth and further incubated to an OD600 of 0.8-1.0 to ensure exponential growth conditions.

extract_protocol: Culture aliquots of 10 ml were stabilized by incubation with two volumes RNAprotect Bacteria Reagent (QIAGEN, Hilden, Germany) for 5 minutes at room temperature. Subsequently, cells were harvested by centrifugation, lysed in presence of 400 µg/ml lysostaphin (Sigma-Aldrich, Taufkirchen, Germany) and total RNA was isolated using the RNeasy Midi Kit (QIAGEN) following the manufacturer’s instructions. RNA concentration and integrity was determined by photometric measurement (Nanodrop, Nanodrop Technologies Inc., Wilmington, USA) and agarose gel electrophoresis.

tag: Subculturing of the clinical methicillin-resistant S. aureus (MRSA) SA137/93A displaying heterogeneous intermediate vancomycin resistance (MIC

value: 8 mg/L in BHI) in presence of 6 mg/L vancomycin generated a mutant with homogeneous intermediate vancomycin resistance, that showed an MIC value of 16 mg/L in BHI and was designated SA137/93G.  Source:Reipert, A., K. Ehlert, T. Kast, and G. Bierbaum. 2003. Morphological and genetic differences in two isogenic Staphylococcus aureus strains with decreased susceptibilities to vancomycin. Antimicrob.Agents Chemother. 47:568-576.

source_name: SA1450/94, vancomycin susceptible MRSA/VSSA strain

tag: The MRSA SA1450/94 is a member of the Iberian clone (ST 247).  Source

value: German reference centre for staphylococci, Wernigerode


title: SA137/93G_SA1450/94_Chip ID200

description: SA137/93G_SA1450/94_Chip ID200

label_protocol: Total RNA (10 µg) was transcribed into cDNA using the Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany) following the manufacturer’s instructions. For direct fluorescent labeling of the cDNA, the transcription reaction was performed in a total volume of 40 µl in presence of 0.1 mM cyanine-3’ or cyanine-5’ labeled dCTP (Perkin Elmer Life Science, Mechelen, Belgium) in addition to 0.2 mM dCTP, 0.5 mM dATP, 0.5 mM dGTP and 0.5 mM TTP, 75 µg/ml random hexamer primers (Amersham, Bioscience, Freiburg, Germany) and 25 U/ml RNase-Out (Invitrogen). RNA was degraded by alkaline hydrolysis at 65°C and cDNA was purified using the MinElute PCR Purification Kit (QIAGEN).


title: SA1450/94_SA137/93G_Chip ID197

description: SA1450/94_SA137/93G_Chip ID197


title: High-grade PC1

tag: tissue

value: clinical T4N0M1

value: PSA 5477ng/ml


title: HC Pooled sample #2

source_name: CD14+ monocytes

extract_protocol: CD14+ monocytes were purified from peripheral blood mononuclear cells. And then total RNA was extracted and reverse transcribed. Each pooled sample was composed of 5 patients with SSc or 5 healthy control. 2 different sets were prepared and compared.


title: High-grade PC2

value: clinical T4N1M1

value: PSA 4427ng/ml


title: OC tissue of CBA at 9m, biological rep2

description: Gene expression data from OC of CBA mice at the age of 9 month

source_name: OC tissue of CBA at 9m

value: the organ of Corti tissue from inner ear

tag: genotype

value: wt

tag: strain

value: CBA/J

value: 9 month old


title: OC tissue of CBA at 9m, biological rep1

tag: age


title: SA137/93A_SA1450/94_Chip ID196

description: SA137/93A_SA1450/94_Chip ID196

source_name: SA137/93A, MRSA strain

tag: SA137/93A was isolated from a tracheal secretion in 1993. The strain is methicillin-resistant (MRSA) and was shown to be a member of the Iberian clone (ST 247). SA137/93A displays heterogeneous intermediate vancomycin resistance (hVISA, MIC

value: 8 mg/L in BHI).  Source:Reipert, A., K. Ehlert, T. Kast, and G. Bierbaum. 2003. Morphological and genetic differences in two isogenic Staphylococcus aureus strains with decreased susceptibilities to vancomycin. Antimicrob.Agents Chemother. 47:568-576.


title: OC tissue of CBA at 9m, biological rep3


title: High-grade PC3

value: clinical T2bN1M1


title: SA1450/94_SA137/93G_Chip ID186

description: SA1450/94_SA137/93G_Chip ID186


title: OC tissue of CBA at P21, biological rep2

description: Gene expression data from OC of CBA mice at the age of P21

source_name: OC tissue of CBA at P21

value: Postnatal 21 days


title: SA1450/94_SA137/93A_Chip ID044

description: SA1450/94_SA137/93A_Chip ID044

label_protocol: Total RNA (9 µg) was transcribed into cDNA using the Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany) following the manufacturer’s instructions. For direct fluorescent labeling of the cDNA, the transcription reaction was performed in a total volume of 40 µl in presence of 0.1 mM cyanine-3’ or cyanine-5’ labeled dCTP (Perkin Elmer Life Science, Mechelen, Belgium) in addition to 0.2 mM dCTP, 0.5 mM dATP, 0.5 mM dGTP and 0.5 mM TTP, 75 µg/ml random hexamer primers (Amersham, Bioscience, Freiburg, Germany) and 25 U/ml RNase-Out (Invitrogen). RNA was degraded by alkaline hydrolysis at 65°C and cDNA was purified using the MinElute PCR Purification Kit (QIAGEN).


title: Clp1 knock-out mouse 2

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description:
RNA from spinal cord of a 15 days old male Clp1 knock-out mouse (CBA/J background).
1084_001_M-2_mE1_MB_200209.CEL

hyb_protocol: Target samples were hybridized to Mouse Exon 1.0 ST v1 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the GCRMA method (option GSB.adjust set to FALSE). For gene probe set definition a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 52 and ASTD 1.1.

source_name: Clp1 knock-out mouse 2

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: All mice were kept under SPF conditions.

extract_protocol: Total RNA was extracted using the TRIZOL protocol according to the manufacturer's protocol, depleted of ribosomal RNA and transcribed into cDNA using T7-promoter-tagged hexamer primers. Antisense RNA was produced by T7-polymerase and transcribed into cDNA using random priming in the presence of dUTP which was used to enzymatically fragment the cDNA.

treatment_protocol: Untreated.

value: Clp1 KO

value: spinal cord

value: 15 days old


title: SSc Pooled sample #1

tag: cell type

value: CD14+ monocytes

value: Systemic sclerosis


title: Clp1 knock-out mouse 3

description:
RNA from spinal cord of a 15 days old male Clp1 knock-out mouse (CBA/J background).
1085_001_M-2_mE1_MB_200209.CEL

source_name: Clp1 knock-out mouse 3


title: Wild type mouse 3

description:
RNA from spinal cord of a 15 days old male wild type mouse (CBA/J background).
1082_001_WT-3_mE1_MB_200209.CEL

source_name: Wild type mouse 3

value: WT


title: Clp1 knock-out mouse 1

description:
RNA from spinal cord of a 15 days old male Clp1 knock-out mouse (CBA/J background).
1083_001_M-1_mE1_MB_200209.CEL

source_name: Clp1 knock-out mouse 1


title: SA137/93A_SA1450/94_Chip ID188

description: SA137/93A_SA1450/94_Chip ID188

value: German reference centre for staphylococci, Wernigerode


title: SA1450/94_SA137/93A_Chip ID043

description: SA1450/94_SA137/93A_Chip ID043


title: OC tissue of CBA at P21, biological rep1


title: Wild type mouse 1

description:
RNA from spinal cord of a 15 days old male wild type mouse (CBA/J background).
1080_001_WT-1_mE1_MB_200209.CEL

source_name: Wild type mouse 1


title: Wild type mouse 2

description:
RNA from spinal cord of a 15 days old male wild type mouse (CBA/J background).
1081_001_WT-2_mE1_MB_200209.CEL

source_name: Wild type mouse 2


title: T84_control

status: Public on Mar 11 2013

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
G052_G05_T1_C.CEL
Pool of 3 cell culture wells.

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument according to the manufacturer's recommendations.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

source_name: T84 human colonic carcinoma epithelial cells, non-treated (control)

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT Expression Kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: T84 human colonic carcinoma epithelial cells were cultured in DMEM F-12 medium (Lonza, the Netherlands) containing 5% fetal calf serum (FCS) and 1% penicillin/streptomycin at 37°C in a humidified incubator of 95% air/5% CO2. Cells were grown till 80-90% confluence before treatment.

extract_protocol: Total RNA was prepared using TRIzol reagent (Invitrogen), whereafter purified total RNA was isolated using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For microarray analysis, RNA samples from 3 wells per treatment were pooled.

treatment_protocol: T84 cells were treated with rosiglitazone (0.1 μM) or butyrate (1 mM or 8 mM) for 24 hrs. Non-treated cells served as the control.

tag: cell line

value: colonic carcinoma epithelial cells

tag: treatment duration

value: 24 hrs


title: T84_butyrate1mM

description:
G052_G07_T2_1B.CEL
Pool of 3 cell culture wells.

source_name: T84 human colonic carcinoma epithelial cells, treated with 1mM butyrate for 24 hrs

value: 1mM butyrate


title: T84_butyrate8mM

description:
G052_H07_T5_8B.CEL
Pool of 3 cell culture wells.

source_name: T84 human colonic carcinoma epithelial cells, treated with 8mM butyrate for 24 hrs

value: 8mM butyrate


title: CgPDR1OE - repeat 4 - mAdbID:56815

first: Jason

middle: A

last: Noble

state: Maryland

address: 10 Center Drive, Building 10, Room 11N228

department: NIAID

institute: National Institutes of Health

description: mAdb experiment ID: 56815

hyb_protocol: Hybridization Protocol The microarrays were prehybridized at 42°C in prehybridization buffer (5× SSC [1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 1% bovine serum albumin [BSA], 0.1% SDS) for 30 to 60 min and then hybridized to the labeled cDNA in 50 ul of hybridization buffer (25% formamide, 5× SSC, 0.2% SDS, 20 ug/ml poly[dA]40-60, 200 ug/ml Cot-1 DNA [Invitrogen], 80 ug/ml yeast tRNA) overnight at 42°C. The microarrays were washed three times in wash buffer A (1× SSC, 0.05% SDS) and washing buffer B (0.1× SSC).

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.08;; 3.08 Temperature: 30.42

data_processing:
CgPDR1OE Data Processing Protocol
Calculation Method: Default Ratio: ChanB/ChanA (Cy5/Cy3); Signal calculation: Median Intensity minus Median Background; Any Features designated Control were excluded; Normalization method: 50th Percentile (Median) using all spot filtered Genes; Spot Filter Options: Include Spots not flagged BAD or Not Found AND Target diameter >= 0 um AND Target diameter <= 300 um AND Both Chan A and Chan B Percentage of Target Pixels Saturated <= 50% AND Both Chan A and Chan B Signal/Background Ratios >= 2.000 AND Both Chan A and Chan B Signal >= 500 Override other Chan A & B criteria and Include if Chan A Signal >= 5000 OR Chan B Signal >= 5000 Signal Values were floored at 100 (ChanA and ChanB); Data was extracted and aligned by the Inventory Well ID; Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B); Note: For all GenePix results from Axon scanned arrays Chan A is CY3 and Chan B is CY5.

organism: Nakaseomyces glabratus

source_name: Cg84 Control_Cy3

label_protocol:
Cy3 Sample Labeling Protocol
Total RNA was reverse transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care, Piscataway, NJ).

extract_protocol:
Trizol Sample Extraction Protocol
Total RNA was isolated by using Trizol (Invitrogen, Carlsbad, CA) and the RNeasy MiniElute cleanup kit (Qiagen, Valencia, CA).

tag: genotype/variation

value: wild type

label_protocol:
Cy5 Sample Labeling Protocol
Total RNA was reverse transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care, Piscataway, NJ).

treatment_protocol: To create pGRB2.2-CgPDR1, the PDR1 gene from Candida glabrata strain 13928 was amplified by PCR with primers PDR2 and PDR4. The Cg13928 PDR1 ORF contains a gain of function mutation that results in constitutively high expression of CDR1. The PCR product was blunt ended with T4 polymerase and ligated into the pCgACU vector, which had been previously digested with Sma1. The pCgACU-CgPDR1 plasmid was transformed into 84u.

tag: strain background

value: Cg84u (uracil auxotroph of Cg84)

value: CgPDR1 overexpression


title: CgPDR1OE - repeat 3 - mAdbID:56814

description: mAdb experiment ID: 56814

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.02;; 3 Temperature: 30.36


title: CgPDR1OE - repeat 5 - reverse fluoro - mAdbID:56816

description: mAdb experiment ID: 56816

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.06;; 3.09 Temperature: 30.54

source_name: Cg84 Control_Cy5


title: CgPDR1OE - repeat 2 - mAdbID:56654

description: mAdb experiment ID: 56654

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.22;; 3.19 Temperature: 29.96


title: CgPDR1OE - repeat 1 - mAdbID:56651

description: mAdb experiment ID: 56651

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.16;; 3.1 Temperature: 29.81


title: mouse lung 4 month after treatment with bleomycin, biological replicate 3

city: Pittsburgh

first: Kazuhisa

last: Konishi

state: PA

address: 1212 Kaufmann Building  3471 Fifth Ave

department: Pulmonry, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

hyb_protocol: Biotin-labelled and fragmented cRNA were hybridized with an individual CodeLink Mouse Uniset 20K BioArray (Amersham Biosciences/GE Healthcare) for 18 hours.  The array slides were then incubated in Cy5-Streptavidin working solution for 30 minutes in order to detect the target with cy5 fluorophore.

scan_protocol: The arrays were scanned using a GenePix 4000B microarray scanner (Axon Instruments, Union City, CA).

data_processing:
Raw Intensity values for each spot were corrected for background by subtracting Median Local Background Intensity using Codelink Expression Analysis Software.  GeneSpring GX and BRB array tools were used for statistical data analysis.
In Platform GPL2894, there are BLANK and MASK probes, which have been omitted in the batch extraction process.

label_protocol: Biotin-labeled cRNA was obtained from 1 ug total RNA by an in vitro transcription reaction.

extract_protocol: Trizol extraction of total RNA and additional clean up in column was performed according to the manufacturer's instructions.

value: lung

tag: agent

value: bleomycin

tag: time

tag: fibrotic response

value: reversion


title: T84_rosiglitazone

description:
G052_G09_T3_0_1R.CEL
Pool of 3 cell culture wells.

source_name: T84 human colonic carcinoma epithelial cells, treated with 0.1 μM rosiglitazone for 24 hrs

tag: treatment

value: 0.1 μM rosiglitazone


title: mouse lung 4 month after treatment with bleomycin, biological replicate 2


title: mouse lung 3 month after treatment with bleomycin, biological replicate 3


title: OC tissue of CBA at P21, biological rep3

first: David

value: the organ of Corti tissue from inner ear

value: wt

value: CBA/J

value: Postnatal 21 days


title: mouse lung 3 month after treatment with bleomycin, biological replicate 2


title: OC tissue of C57 at P21, biological rep2

description: Gene expression data from OC of C57 mice at the age of P21

source_name: OC tissue of C57 at P21


title: mouse lung 2 month after treatment with bleomycin, biological replicate 3

value: fibrotic


title: mouse lung 2 month after treatment with bleomycin, biological replicate 2


title: mouse lung 2 month after treatment with bleomycin, biological replicate 1


title: mouse lung 4 month after treatment with bleomycin, biological replicate 1


title: mouse lung 1 month after treatment with bleomycin, biological replicate 3


title: SNP017XLQ4

city: changsha

first: xiong

last: bo

address: xiangya road

institute: xiangya

description:
Whole genome amplification DNA.
Hybridized to 250K_Nsp SNP array.

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics Stations.

scan_protocol: The arrays were scanned using the GeneChip Scanner 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using the DNAcopy package for R Bioconductor on raw data.

source_name: whole genome amplification product of trophectoderm cells

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.

growth_protocol: None.

extract_protocol: Whole genome amplification of the biopsied trophectoderm cells was performed using a WGA4 GenomePlex Single Cell Whole Genome Amplification kit (Sigma-Aldrich, MO, USA) according to the manufacturer's instructions.

treatment_protocol: Blastocyst cultivation and biopsy reference to clinical standard procedure. The normal/balance embryos detected by SNP-array would been transfer to patients as clinical standard procedure.

value: trophectoderm cells

tag: karyotype of patient donor

tag: karyotype classification

value: reciprocal translocation

tag: analysis result

tag: result classification

value: De novo aneuploidy


title: SNP138LXQ3

value: De novo aneuploidy and segmental abnormality


title: mouse lung 3 month after treatment with bleomycin, biological replicate 1

tag: tissue


title: SNP005XM2

value: Unbalanced translocation and de novo aneuploidy


title: SNP067CY4

value: Robertsonian translocation

value: De novo segmental abnormality


title: SNP097LYM5

value: Unbalanced translocation and de novo segmental abnormality


title: SNP031CXJ2

value: Unbalanced translocation


title: SNP067CY3


title: mouse lung 1 month after treatment with bleomycin, biological replicate 1

tag: strain

value: lung

value: bleomycin


title: SNP011ZJ3


title: mouse lung 1 month after treatment with bleomycin, biological replicate 2


title: SNP059LY8

value: normal female


title: SNP038WXJ9


title: SNP016LLH2

value: complex aneuploid


title: CgSTB5OE - repeat 4 - reverse fluoro - mAdbID:112911

description: mAdb experiment ID: 112911

hyb_protocol: Agilent Hybridization According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45103101

data_processing:
CgSTB5OE Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. Default Ratio: ChanB/ChanA (Cy5/Cy3); Signal calculation: Agilent FE Processed Signals; Any Features designated Control were excluded; Normalization method: None (Using Agilent FE Processed Signals); Spot Filter Options: Both Chan A and Chan B Percentage of Target Pixels Saturated <= 50% AND Both Chan A and Chan B Signal >= 10 Override other Chan A & B criteria and Include if Chan A Signal >= 1000 OR Chan B Signal >= 1000 Signal Values were floored at 50 (ChanA and ChanB); Data was extracted and aligned by the Inventory Well ID Within array multiple occurrences of Well ID were reduced to a single instance by selecting the Median Value.
FeatureExtractor_Version: 10.7.3.1
Protocol_Name: GE2_107_Sep09 (Read Only)

value: wild type

treatment_protocol: The 84u/stb5 mutant (Cgstb5delta) was generated as follows. The S. cerevisiae URA3 gene replaced the CAGL0I02552g ORF in the 84u strain. Transformants were selected on MIN media, and CAGL0I02552g deletion was confirmed by southern blot. Subsequently, CgSTB5 was sequence confirmed, digested with BamH1 and EcoR1 (both New England Biosciences), and ligated (Rapid DNA Ligation Kit , Roche Diagnostics, Germany) into pGRB2.2 (pGRB2.2/STB5) for overexpression in the C. glabrata 84u strain (CgSTB5OE).

value: Cg84u (uracil auxotroph of Cg84)

value: CgSTB5 overexpression


title: SNP054LH5


title: CgSTB5OE - repeat 3 - mAdbID:112910

description: mAdb experiment ID: 112910


title: mouse lung 7 days after treatment with bleomycin, biological replicate 1

value: inflammatory


title: SNP093BLY4

value: trophectoderm cells


title: mouse lung treated with saline, biological replicate 3

value: saline

value: control


title: CgSTB5OE - repeat 2 - mAdbID:112909

description: mAdb experiment ID: 112909


title: mouse lung 7 days after treatment with bleomycin, biological replicate 2


title: mouse lung treated with saline, biological replicate 2


title: SNP036XD5

value: reciprocal translocation


title: SNP059LY3


title: CgSTB5OE - repeat 1 - mAdbID:112908

description: mAdb experiment ID: 112908


title: SNP002CL6


title: mouse lung treated with saline, biological replicate 1


title: SNP036XD7


title: mouse lung 7 days after treatment with bleomycin, biological replicate 3


title: Cgstb5D - repeat 4 - reverse fluoro - mAdbID:112368

description: mAdb experiment ID: 112368

data_processing:
Cgstb5D Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. Default Ratio: ChanB/ChanA (Cy5/Cy3); Signal calculation: Agilent FE Processed Signals; Any Features designated Control were excluded; Normalization method: None (Using Agilent FE Processed Signals); Spot Filter Options: Both Chan A and Chan B Percentage of Target Pixels Saturated <= 50% AND Both Chan A and Chan B Signal >= 10 Override other Chan A & B criteria and Include if Chan A Signal >= 1000 OR Chan B Signal >= 1000 Signal Values were floored at 50 (ChanA and ChanB); Data was extracted and aligned by the Inventory Well ID; Within array multiple occurrences of Well ID were reduced to a single instance by selecting the Median Value.
FeatureExtractor_Version: 10.7.3.1
Protocol_Name: GE2_107_Sep09 (Read Only)

treatment_protocol: The 84u/stb5 mutant (Cgstb5delta) was generated as follows. The S. cerevisiae URA3 gene replaced the CAGL0I02552g ORF in the 84u strain. Transformants were selected on MIN media, and CAGL0I02552g deletion was confirmed by southern blot. Deletion of CAGL0I02552g (CgSTB5) resulted in a null mutant (Cgstb5delta).

value: CgSTB5 null mutant


title: SNP043SYH2


title: SNP027YLQ5


title: SNP027YLQ8


title: SNP036XD8


title: SNP010XHM2


title: SNP049XJ4


title: Cgstb5D - repeat 1 - mAdbID:112365

description: mAdb experiment ID: 112365


title: Cgstb5D - repeat 3 - mAdbID:112367

description: mAdb experiment ID: 112367


title: Cgstb5D - repeat 2 - mAdbID:112366

description: mAdb experiment ID: 112366


title: SNP013TYY5


title: IY28-01064B3215P99ZR1

status: Public on Mar 10 2013

city: Redwood City

first: Anita

last: Lal

address: 595 Penobscot Dr

department: Product Development

institute: Pathwork Diagnostics

hyb_protocol: Affymetrix GeneChip standard protocol

scan_protocol: Affymetrix GeneChip standard protocol

data_processing: Pathwork standardization

label_protocol: Genisphere RampUP Kit

extract_protocol: Agencourt FormaPure Kit

treatment_protocol: FFPE

tag: age

tag: gender

value: male

tag: anatomical site

value: Nasopharynx

tag: morphology

value: Squamous cell carcinoma


title: IY31-26749B6947P99Z

value: lymph node


title: SNP002CL4

tag: cell type


title: Dm_ovary_spn-E1/spn-E03987_rep3

city: Moscow

first: Sergey

last: Lavrov

address: Kurchatov sq. 2

department: DMBC

country: Russia

institute: IMG

description: The data in the table is normalized ratio. The ratio in the Value column was derived from normalized data. Bad or undetected spots has a value = 0.

hyb_protocol: Equal amounts (10 mkg) of Cy3-coupled aRNA from flies of genotype spn-E1/spn-Ehls03987 and Cy5-coupled aRNA from flies spn-E1/+; spn-Ehls03987/+ were mixed together and concentrated on speedvac to app. 10 mkl. For hybridization, 70 mkl of Dig EasyHyb (Roche) solution containing yeast tRNA (0.5 mkg/mkl) and DTT (0.1 mM) was added to aRNA mix and denatured at 65C fo 10'. 80 mkl of hybridization mix was applied to microarray slide (CDMC) pretreated according to manufacturer recommendations. Slides were covered by plastic Hybrislips (Corning) and hybridized overnight at 37C in moist chamber. Washings were: 1xSSC, 0.1%SDS,  0.1 mM DTT at 37C. Remove coverslips. 3x15' in 1xSSC, 0.1%SDS,  0.1 mM DTT at 37С 1xSSC, 0.1 mM DTT   ≤1' at room temperature 0.1xSSC, 0.1 mM DTT for ≤15sec After washing, slides were centrifugated 5' at 500G in swinging rotor to remove drops and scanned.

scan_protocol: Microarray slides were scanned at 10µm resolution in PE ScanArray Express Microarray Scanner, using both green and red lasers (PMT75 for Cy5 and PMT90 for Cy3). The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing:
TIF images were processed in GenePix 6 software. Spots with percent of saturated pixels >3 and damaged or having abnormal appearance were flagged as bad, spots which fall below background threshold criteria:

(([% > B635+1SD] < 50 And [% > B532+1SD] < 50) Or ([SNR 635] < 2 And [SNR 532] < 2) Or (([F635 Median - B635]/[B635] < 1) And ([F532 Median - B532]/[B532] < 1))
flagged as "Not found"
Resulting .gpr files were exported into FlexArray 1.6.1.1 software, where raw data were background-corrected (normexp algorithm, saddle-point approximation to maximum likelihood without offset) and normalized using loess MA normalizaton (by print tip). Tables for submission were prepared in Excel

organism: Drosophila melanogaster

source_name: Drosophila melanogaster ovaries from heterozygotes spn-E/+

label_protocol:
3 mkg of total RNA was reverse-transcribed using SuperScript II (Invirtogen) and 0.4 mkg of T7-oligo(dT)21 primer (5’–GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG –(dT)21–3’) in 20 mkl at 45C for 1 h 40'. Reaction was transferred into ice, then to 16C and 124 mkl cooled second strand synthesis mix (Enzymes from Invitrogen) added:
DEPC-treated water  91 mkl
5X Second-Strand Reaction Buffer 30  mkl
10 mM dNTP mix 3 mkl
E. coli DNA Ligase (10 U/μl) 1 mkl
E. coli DNA Polymerase I (10 U/μl) 4 mkl
E. coli RNase H (2 U/μl) 1 mkl
After incubation for 2 h 20' at 16C, 2 µl (10U) of T4 DNA Polymerase was added and the reaction was additionally incubated 5' at 16C, then placed  on ice and 10 μl of 0.5 M EDTA added.
RNA in second strand synthesis reaction was hydrolyzed by NaOH (10М NaOH was added to 0.2 М, reaction incubated 15' at 70C and neutralized by 50 mkl of 1М Tris-HCl pH 8), ds cDNA then purified on Millipore Microcon 30 columns according to manufacturer instructions.
IVT and aminoallyl incorporation was carried using Ambion T7 MegaScript kit and T7-bearing ds cDNA from previous step. IVT was performed in the presence of aminoallyl-UTP (1:1,16 unmodified UTP)) for 5 h 30', aRNA from reaction mixture was purified using Qiagen RNAeasy MinElute kit according to manufacturer instruction.
Aminoallyl-aRNA (10-25 mkg) was dye-coupled to succinimide ester of either Cy3 or Cy5 in NaHCO3 -buffer at pH 8.7 for 1 h at room temperature, then purified on Millipore Microcon 30.

growth_protocol: Flies were crossed and propagated at 25 degrees Celsius on standard medium. 2-3 days old adult females were picked for ovary dissection.

extract_protocol: Ovaries were dissected from adult females in PBT (phosphate buffer saline + 0.1% Tween-20). Dissection time - 1-2 h at room temperature. Total RNA was extracted from 30-50 pairs of ovaries using Qiagen RNAeasy Mini kit and columns according to manufacturer instructions. Result of extraction - 30-40 mkg of RNA in sterile water. RNA was immediately used in indirect labeling reaction.

treatment_protocol: Females heterozygous for Spn-E over TM3 balancer were selected from the progeny of cross, spn-E1/TM3 x spn-Ehls03987/TM3, used also to produce transheterozygous flies, spn-E1/spn-Ehls03987.

value: mix of spn-E1/TM3 and spn-Ehls03987/TM3 flies

value: 2-3 days old adults

value: female

value: adult ovaries

source_name: Drosophila melanogaster ovaries from trans-heterozygotes spn-E1/spn-E03987

growth_protocol: Flies were crossed and propagated at 25 degrees Celsius on standard medium. 4-5 days old adult females were picked for ovary dissection.

treatment_protocol: Females trans-heterozygotes spn-E1/spn-Ehls03987 were selected from the progeny of cross, spn-E1/TM3 x spn-Ehls03987/TM3.

value: 4-5 days old adults


title: IY31-26752B6953P99Z


title: IY16-07119B3980P99Z

value: Lymph node


title: IY13-03855B4570P99Z

value: Larynx


title: IY19-00318B4792P99Z

value: Lung


title: IY13-26850B7979P99Z

value: Lymph nodes


title: IY13-02955B4583P99ZR1

value: Oral cavity


title: IY13-02871B4576P99ZR1


title: IY19-80938B4742P99Z


title: SNP033ZX1

value: trophectoderm cells

value: normal female


title: Dm_ovary_spn-E1/spn-E03987_rep2

description: The data in the table is normalized ratio. The ratio in the Value column was derived from normalized data. Bad or undetected spots are empty.

treatment_protocol: Females trans-heterozygotes spn-E1/spn-Ehls03987 were selected from the progeny of cross, spn-E1/TM3 x spn-Ehls03987/TM3

treatment_protocol: Females heterozygous for Spn-E over TM3 balancer were selected from the progeny of cross, spn-E1/TM3 x spn-Ehls03987/TM3, used also to produce trans-heterozygous flies, spn-E1/spn-Ehls03987.


title: IY13-03364B4579P99Z


title: IY13-03026B4573P99Z


title: IY19-80143B4722P99Z


title: IY13-02371B4575P99Z


title: SNP003DS3

value: reciprocal translocation


title: IY13-02230B4567P99Z

value: male


title: IY13-02050B4569P99Z


title: IY13-02032B4571P99Z


title: SNP017XLQ7


title: SNP038WXJ2

value: Robertsonian translocation


title: SNP001CLM4


title: IY13-01958B4585P99Z

value: Squamous cell carcinoma


title: IY08-41384B3600P99Z

value: lung


title: IY13-01994B4593P99Z


title: IY13-02011B4582P99Z


title: IY08-23149B3488P99ZR1

value: soft tissue


title: IY08-23159B3458P99Z

value: lymph node


title: IR28-01063B3213P99Z

value: The left side of the tongue


title: SNP027YLQ3

value: normal male


title: IR09-36723B3353P99Z


title: IR16-07115B3940P99Z


title: IY08-23097B3056P99Z

value: Lymph Node


title: IY08-65111B3559P99Z

value: female

value: derma


title: IR09-57729B3323P99Z

value: Larynx


title: IR09-33234B3283P99Z

value: Lung


title: IR09-45709B3303P99Z


title: IR09-39326B3383P99Z


title: IR09-39171B3373P99Z


title: IR08-65133B3553P99Z


title: IR16-07124B4379P99Z

value: Brain


title: IR08-65150B3512P99Z

value: frontal sinus


title: IR19-80023B4716P99Z


title: IR16-07102B4289P99Z

value: Right upper lung


title: SNP018ZXP2

value: trophectoderm cells


title: IR09-32499B3313P99Z


title: IY19-01555B4802P99Z

value: male


title: IR08-23167B3433P99Z


title: IR08-41358B3620P99Z


title: IR09-37572B3413P99Z


title: IR08-23100B3050P99Z


title: IR08-41194B3680P99Z


title: IR08-23156B3472P99Z

value: larynx


title: IR08-41216B3670P99Z

value: Squamous cell carcinoma


title: IQ16-07113B3933P99V

value: Lymph node


title: IR08-23165B3443P99Z


title: IR08-23099B3080P99Z


title: IQ08-41256B3652P99V


title: IQ19-70410B4698P99V


title: IQ16-07117B3963P99V

value: Soft tissue


title: Dm_ovary_spn-E1/spn-E03987_rep1

description: The data in the table is normalized ratio. The ratio in the Value column was derived from normalized data. Bad or undetected spots has a value of 0.

value: mix of spn-E1/TM3 and spn-Ehls03987/TM3 flies

value: 2-3 days old adults

value: adult ovaries

value: 4-5 days old adults


title: IQ19-70865B4708P99V


title: IQ16-07118B3972P99V

value: Tonsil


title: IQ08-23144B3505P99V

value: lymph node


title: IQ16-07116B3952P99V


title: IQ09-29217B3256P99V

value: female

value: Lymph Node


title: IQ08-41402B3586P99V

value: lung


title: IQ16-03502B4272P99V

value: Left Lower lobe


title: IQ08-41433B3576P99V


title: IQ08-41385B3596P99V


title: IQ08-23161B3455P99V


title: IQ08-65136B3545P99V


title: PANC1_BRD7552_3d_rep2

city: Cambridge

first: Yuan

last: Yuan

state: MA

address: 7 Cambridge center

institute: Broad Institute

description: Gene expression data from BRD7552 treated PANC-1 cells at 72-hour

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: PANC1 cells treated with BRD7552 for 72 hours

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

growth_protocol: PANC1 cells were cultured according to ATCC instructions.

extract_protocol: Total RNA extraction was performed using Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: PANC1 cells were treated in 6-well plate with BRD7552 (5uM) and DMSO at a final concentration of 01%.

value: pancreatic carcinoma

tag: cell line


title: PANC1_BRD7552_3d_rep3


title: IQ08-41259B3642P99V


title: PANC1_BRD7552_3d_rep1


title: IQ09-39134B3365P99V

value: Lung


title: PANC1_BRD7552_6h_rep2

description: Gene expression data from BRD7552 treated PANC-1 cells at 6-hour

source_name: PANC1 cells treated with BRD7552 for 6 hours

value: 6 h


title: IQ08-23152B3484P99V

value: male


title: IQ09-50956B3345P99V

value: Tongue

value: Squamous cell carcinoma


title: IR08-65147B3524P99V


title: IQ16-07111B4371P99V

value: Right upper lung


title: PANC1_BRD7552_6h_rep1


title: PANC1_BRD7552_6h_rep3


title: PANC1_DMSO_rep3

description: Gene expression data from DMSO treated PANC-1 cells

source_name: PANC1 cells treated with DMSO

value: DMSO

value: control


title: IQ09-31859B3335P99V


title: PANC1_DMSO_rep1


title: 17 day old larvae

city: Shanghai

first: Yuanshuai

last: Fu

address: Hu-Cheng-Huan Road

institute: Shanghai Ocean University

description: Total RNA of 5 larvae at 17 dph during flounder metamorphosis

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

organism: Paralichthys olivaceus

source_name: whole larvae of 17 dph

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

growth_protocol: To breed Larva of the metamorphosis phase which is from14dph(day post hatching) to 42dph in the Japanese flounder postembryonic development

extract_protocol: To extract total RNA by Trizol reagent

treatment_protocol: Flounder larvae were treated using anesthetic and collected in tube by 5 larvae/tube, and then RNAstore Reagent were added in theae tubes.

value: larvae after hatching

value: 17  days post hatching

tag: developmental stage

value: Pre-metamorphosis larva


title: 29 day old larvae

description: Total RNA of 5 larvae at 29 dph during flounder metamorphosis

source_name: whole larvae of 29 dph

value: 29  days post hatching

value: Mid-metamorphosis larva


title: experiment #3 scr

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description: Gene expression data from leukemia cell line experiments

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: leukemia cell line

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

growth_protocol: K562 cells were cultured under standard conditions in RPMI 1640 medium (Biochrom, Berlin, Germany) containing 10-20% FCS, 2 mM L-glutamine, 100 units/ml penicillin and 100 units/ml streptomycin.

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: In indicated samples K562 cells were transfected with siRNA (RNAi8) and/or scrambled RNA. In brief, 2-3 x 10e6 K562 cells were pelleted, resuspended in 100 µl Cell Line Nucleofector Solution V (Lonza Cologne, Germany), and nucleofected with up to 200 nM siRNA using the program T-016. Following nucleofection cells were mixed with pre-warmed culture medium, transferred into 6 well plates, and incubated at 37°C at 5% CO2 for 24 h. Then, siRNA or scrRNA transfected cells were treated with DMSO control or ATRA at final concentrations of 10e-7 mol/l.

tag: leukemia cell line

tag: RNAi

value: scrRNA

value: ATRA


title: IQ09-39327B3295P99V


title: experiment #3 RNAi


title: PANC1_DMSO_rep2

tag: time


title: IQ09-54642B3265P99V

value: Abdominal wall


title: experiment #2 RNAi

tag: treatment

value: DMSO control


title: IQ08-23143B3092P99V

value: brain


title: experiment #2 scr


title: experiment #1 scr


title: IQ08-21113B3072P99V

value: larynx


title: IQ16-07103B4301P99V

value: male


title: experiment #1 RNAi


title: WT vehicle (7991003028_E)

status: Public on Mar 09 2013

city: Brisbane

first: Steven

last: Lane

address: 300 Herston Rd

country: Australia

institute: QIMR

description: WT vehicle

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene Pattern (Broad Institute) software, Illumina module, Quantile normalization

source_name: HSC

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit according to protocol

growth_protocol: In vivo isolation

extract_protocol: Invitrogen PicoPure extraction kit

treatment_protocol: Interferon 10,000 units per day for 4 weeks or vehicle control

tag: background mouse strain

tag: genotype

value: WT

value: Vehicle


title: Jak2VF Interferon (7991003028_D)

description: Jak2VF Interferon

value: Interferon


title: WT vehicle (7991003040_E)

description: WT vehicle


title: Jak2VF Interferon (7991003028_H)

description: Jak2VF Interferon


title: Jak2VF Interferon (7991003040_D)

description: Jak2VF Interferon


title: WT vehicle (7991003040_A)

description: WT vehicle


title: WT Interferon (7991003040_G)

description: WT Interferon


title: WT Interferon (7991003028_G)

description: WT Interferon


title: WT Interferon (7991003028_C)

description: WT Interferon


title: Jak2VF vehicle (7991003028_B)

description: Jak2VF vehicle


title: Jak2VF vehicle (7991003040_F)

description: Jak2VF vehicle


title: Jak2VF vehicle (7991003040_B)

description: Jak2VF vehicle


title: WT Interferon (7991003040_C)

description: WT Interferon


title: Jak2VF Interferon (7991003040_H)

description: Jak2VF Interferon


title: Jak2VF vehicle (7991003028_F)

description: Jak2VF vehicle


title: BMMCs_coculture_Pla2g3+/+_Rep4

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

description: Gene expression after coculture for 96 h

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with a Laser Scanner GenePix 4000B (Molecular Devices) using a scan resolution of 5µm and appropriate gains on the photomultiplier (PMT) to obtain the highest intensity without saturation.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5.1.1), using default for all parameters. Data were subsequently imported into GeneSpringGX11.5 (Agilent Technologies) for the analysis of gene expression microarray data. Probes were normalized by quantile normalization among all microarray data.

source_name: Pla2g3+/+, cocultured BMMC

label_protocol: 450 ng of total RNA was amplified and labeled using the Agilent Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: Mouse BM cells were cultured in IL-3-containing BMMC-complete medium. After 4–6 weeks of culture, > 97% of the cells were identified as Kit+FcεRIα+ mast cells by flow cytometry.

extract_protocol: Total RNA was extracted from BMMCs derived from Pla2g3–/– and Pla2g3+/+ mice before and after coculture and purified using the RNeasy Mini Kit (Qiagen). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: BMMCs were seeded onto the Swiss 3T3 fibroblast monolayer and cocultured for 4 days in the presence of mouse SCF (100 ng/ml). The cells were trypsinized and reseeded in culture dishes, and nonadherent cells were collected. Purity (> 99%) was confirmed by flow cytometry for Kit and FcεRIα. The maturation of BMMCs into CTMC-like cells was verified by staining of their granules with alcian blue and counterstaining with safranin O.

value: Pla2g3 wild-type

tag: maturation

value: mature


title: EF14_wt_MEF_biological_replicate2

city: Milano

first: Pasquale

last: Laise

address: Via Adamello,16

institute: IEO

hyb_protocol: Hybridization was performed according to Affimetrix guidelines

scan_protocol: Scanning was performed using the Affimetrix scanner

data_processing:
Data was processed using the affy package available on bioconductor (http://www.bioconductor.org) using standard RMA analysis settings
Probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: MEF extracted at E13.6

label_protocol: Labeling was performed according to Affimetrix guidelines

growth_protocol:
Cell culture: iPSC clones were cultured in ESC medium (high glucose DMEM, 15% knockout serum replacement-Invitrogen-, 2mM L-glutamine, 50 units/ml penicillin, 50µg/ml streptomycin, 0,1 mM non-essential amino acids, 1/500 home-made leukaemia inhibitory factor, 0,1 mM 2-β-mercaptoethanol) in feeder-free conditions on gelatin coated dishes
iPSC derivation protocol: MEF at passage 1 to 3 were seeded at a density of 2x105 cells/well in a 6-well tissue culture dish. 24hr later, MEF were transduced in a 1:1 PBS/DMEM/GlutaMAX (Invitrogen) solution with 50 µg/ml of recombinant TAT-Cre recombinase. 16 hour after transduction, medium was replaced, and MEF were infected with the STEMCCA and rtTA lentiviruses. 24 hours following infection with STEMCCA and rtTA, MEF were harvested and seeded at  clonal density on a mytomycin-treated MEF feeder layer. One day after, MEF medium was replaced with ESC medium supplemented with 1 µg/ml doxycycline to induce expression of the reprogramming factors. Doxycycline treatment was replaced every other day for 23 days. Four days after doxycycline withdrawal, iPSC colonies were picked and expanded on a mitomycin-treated MEF feeder layer to establish individual iPSC clones.

extract_protocol: Total RNA was extracted with Trizol reagent and purified using QUIAGEN RNeasy Mini kit following  manufacturer's instructions

tag: genotype/variation

value: wt

value: mouse embryonic fibroblasts (MEFs)


title: wt mESC

source_name: E14tg2a mESC line

value: E14Tg2a embryonic stem cells


title: 36B10_Ezh2 ∆SET/∆SET_iPSC_biological_replicate4

source_name: established iPSC clone

value: Ezh2 ∆SET/∆SET

value: induced pluripotent stem cells (iPSC)


title: JJN3 cells, infected with LV expressing an shRNA vs. XBP1

city: Toronto

first: Rodger

middle: E

last: Tiedemann

state: ON

address: 610 University Avenue

department: Medical Oncology and Hematology

country: Canada

institute: University Health Network, University of Toronto, Princess Margaret Cancer Centre

hyb_protocol: Hybridization to Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix) was performed as recommended by the manufacturer.

scan_protocol: As recommended by the manufacturer

data_processing: The data were analyzed with RMA using GenSpringGX default settings including quantile normalization and baseline transformation to the median of all samples.A filter for expressed genes was implemented per cell line and arbitrarily set at >20%-ile expression in at least one sample per cell line. Separate XBP1 transcription factor and IRE1 signatures were derived as all expressed genes will >2-fold decline in expression in at least one cell line with either shXBP1 or shIRE1 treatment versus control NT shRNA treatment.

label_protocol: cDNA synthesis and cRNA preparation was performed as recommended by Affymetrix.

growth_protocol: Cells were cultured in IMDM 10%FBS supplmented with glutamine at 37oC in 5%CO2

extract_protocol: Total RNA was purified by RNAeasy according to the manufacturer's instructions, and was column purified with RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Lentivirus transductions were performed with lentivirus-containing supernatant diluted to 30-50% in IMDM/10% FCS over 16 hrs at 37˚C/5%CO2, using 8 μg/mL of polybrene (Sigma) . Cells were harvested at 96hours

value: multiple myeloma cell


title: BMMCs_coculture_Pla2g3–/–_Rep3

source_name: Pla2g3–/–, cocultured BMMC

value: Pla2g3 knockout


title: EF12_wt_MEF_biological_replicate1

source_name: MEF extracted at E13.5


title: BMMCs_coculture_Pla2g3–/–_Rep2


title: EF16_wt_MEF_biological_replicate3

source_name: MEF extracted at E13.7


title: WT vehicle (7991003028_A)

description: WT vehicle


title: BMMCs_coculture_Pla2g3–/–_Rep1


title: BMMCs_coculture_Pla2g3+/+_Rep3


title: JJN3 cells, infected with LV expressing an shRNA vs. IRE1


title: RPMI-8226 cells, infected with LV expressing an shRNA vs. IRE1


title: JJN3 cells, infected with LV expressing a non-targeted (NT) shRNA


title: RPMI-8226 cells, without LV infection

source_name: RPMI-8226 cells, without LV infection


title: RPMI-8226 cells, infected with LV expressing an shRNA vs. XBP1


title: BMMCs_coculture_Pla2g3+/+_Rep1


title: RPMI-8226 cells, infected with LV expressing a non-targeted (NT) shRNA


title: JJN3 cells, without LV infection

source_name: JJN3 cells, without LV infection


title: 48B4_Ezh2 ∆SET/∆SET_iPSC_biological_replicate2


title: BMMCs_coculture_Pla2g3+/+_Rep2


title: prim.Melanocytes/HOM1=Pat1

city: Cologne

first: Kerstin

last: Brinkmann

address: Joseph-Stelzmann-Str. 9

department: IMMIH2, Geb. 37

institute: University Hospital Cologne

description: Schmidt, P., Kopecky, C., Hombach, A., Zigrino, P., Mauch, C., and Abken, H. (2011). Eradication of melanomas by targeted elimination of a minor subset of tumor cells. Proceedings of the National Academy of Sciences of the United States of America 108, 2474-2479.

hyb_protocol: Samples were hybridized overnight to topic-defined PIQORTM Ubiquitin-PS Microarrays Human Antisense using a-Hyb HybridizationTM Station.

scan_protocol: Fluorescence signals were detected using a laser scanner from Agilent

data_processing: Mean signal and mean local background intensities were obtained for each spot of the microarray images using the ImaGena software (Biosiscovery). Low-quality spots were flagged and excluded from data analysis. Unflagged spots were analysed with the PIQOR Analyzer software. The PIQOR analyzer allows automated data processing of the raw data text files derived from the ImaGene software. This inclides background substraction to obtain the net signal intensity, data normalization, and calculation of the Cy5/Cy3 ratios. As an additional quality filtering step, only spots/genes are taken into account for the calculation that have at least in one channel a signal intensity that is at least 2-fold higher than the mean background. The linked PIQOR_Analysis.xls file includes normalized mean ratios (Cy5/Cy3) representing test/reference with the respective coefficient of variation (cv, in%) of four replicates per gene; blank values indicate that only one out of four spots could evaluated. Genes that are 1.7 fold up- or down-regulated represent putative candidate genes and are highlighted by red and green color.

source_name: Epidermal Melanocytes adult (primary cells from CellSystems Biotech)

label_protocol: Sample labeling was performed according to the PIQOR User manual

growth_protocol: Cells were grown under standard cell culture conditions

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin RNAII; Macherey-Nagel)

treatment_protocol: Cells were not treated prior analyses

value: n/a (primary)

value: primary epidermal melanocytes

source_name: primary cells from melanoma patients (HOM-Cy5)

value: primary melanoma


title: Skmel23/Colo38

description:
Zigrino, P., Mauch, C., Fox, J.W., and Nischt, R. (2005). Adam-9 expression and regulation in human skin melanoma and melanoma cell lines. International journal of cancer Journal international du cancer 116, 853-859.
Giacomini, P., Aguzzi, A., and Ferrone, S. (1986). Differential susceptibility to modulation by recombinant immune interferon of HLA-DR and -DQ antigens synthesized by melanoma COLO 38 cells. Hybridoma 5, 277-288.
SKmel23 cell line is comparable to non-malignant cells for the specific feature being investigated

source_name: melanoma cell line

value: melanoma


title: Shoot_non_sterile_rep3

city: Saint Lucia

first: Lilia

last: Costa Carvalhais

state: QLD

address: The University of Queensland John Hines Blg 5th floor room 517A

institute: The University of Queensland

description: Biological replicate 3 of 3. Shoots collected from Arabidopsis thaliana Col-0 cultivated in sterile and unsterile soil

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. M values are normalized log ratio (Cy5/Cy3) representing test/reference.

source_name: Shoots, non-sterile

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript III RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Seeds of Arabidopsis thaliana ecotype Col-0 were surface-sterilised using the vapour-phase sterilisation method. Briefly, seeds were exposed to chlorine fumes in a desiccator jar for four hours. Chlorine fumes were generated by adding concentrated hydrochloric acid to commercial bleach (minimum 10.5% available chlorine) up to a final concentration of 1%. Seeds were then sown onto a half-strength Murashige and Skoog (MS) medium (pH 5.7) containing 0.8% agarose and incubated at 4°C in the dark for 72 hours to break the dormancy. Plates with seeds were then transferred to a tissue culture room with a photoperiod of 16 h of light/8 h darkness and light intensity of 60–100 μmol m2 sec-1 at 22°C for 14 days. Five seedlings were then transplanted into a 15 cm-diameter clear transparent vessel which contained 50 g of a 1:1 mixture of University of California mix and commercial compost soil.

extract_protocol: Total RNA from roots and shoots was extracted independently with the SV Total RNA Isolation System (Promega, Madison, WI).

treatment_protocol: Treatment and control consisted of three biological replicates containing 10 vessels each. Vessels were autoclaved twice at 121oC for 30 min. Sterile soils were tested for microbial contamination by incubating autoclaved soil samples in Luria-Bertani and Potato Dextrose broth for a week at 30oC. The treatment consisted of applying non-sterile compost soil extract prepared by adding compost soil to sterile water up to a final concentration of 3.3%, which constituted a source of soil microbial communities. Large particles were removed from this extract before treatment application by filtering through Whatman grade 1 filter paper (11 µm). The control received sterile compost soil extract, in which microbes were removed by further filtration at 0.22 µm. Four weeks after germination, plants were evaluated for phenotypic differences before harvesting. Fresh weights of roots and shoots were quickly measured, snap-frozen in liquid nitrogen, and stored at -80°C.

tag: ecotype

tag: tissue

value: Shoot

source_name: Shoots, sterile


title: 42B10_Ezh2 +/+ _iPSC_biological_replicate3

value: Ezh2 fl/fl


title: prim.Melanocytes/MOO1=Pat3

source_name: primary cells from melanoma patients (MOO1=Pat3)


title: 36B7_Ezh2 ∆SET/∆SET_iPSC_biological_replicate1


title: prim.Melanocytes/HM1=Pat2

source_name: primary cells from melanoma patients (HM1=Pat2)


title: SKOV3 control 1

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with MAS5 by Affymetrix Expression Console Version 1.1

source_name: SKOV3 cell,without rhSTIP1 treatment

label_protocol: Standard Affymetrix protocol

extract_protocol: cellular RNA extraction with TRIZOL

value: control


title: 48B7_Ezh2 ∆SET/∆SET_iPSC_biological_replicate3


title: SKOV3 +rhSTIP1 2

source_name: SKOV3 cell treated with rhSTIP1


title: 40A8_Ezh2 +/+ _iPSC_biological_replicate4


title: BMMCs_Pla2g3–/–_Rep3

description: Gene expression before coculture

source_name: Pla2g3–/–, BMMC

tag: strain

value: immature


title: BMMCs_Pla2g3–/–_Rep4

description: Gene expression before coculture


title: BMMCs_Pla2g3–/–_Rep1

description: Gene expression before coculture


title: Shoot_non_sterile_rep2

description: Biological replicate 2 of 3. Shoots collected from Arabidopsis thaliana Col-0 cultivated in sterile and unsterile soil


title: 40A7_Ezh2 +/+_ iPSC_biological_replicate1


title: BMMCs_Pla2g3–/–_Rep2

description: Gene expression before coculture


title: BMMCs_Pla2g3+/+_Rep3

description: Gene expression before coculture

source_name: Pla2g3+/+, BMMC

value: Pla2g3 wild-type


title: SKOV3 control 2


title: Shoot_non_sterile_rep1

description: Biological replicate 1 of 3. Shoots collected from Arabidopsis thaliana Col-0 cultivated in sterile and unsterile soil


title: L1309/L591

description: Kashkar, H., Kronke, M., and Jurgensmeier, J.M. (2002). Defective Bax activation in Hodgkin B-cell lines confers resistance to staurosporine-induced apoptosis. Cell death and differentiation 9, 750-757.

source_name: control B-bell line

value: B-bell

source_name: Hodgkin Lymphoma cell line

value: Hodgkin lymphoma


title: Root_non_sterile

description: One sample, no replication. Roots collected from Arabidopsis thaliana Col-0 cultivated in sterile and unsterile soil

source_name: Roots, non-sterile

value: Root

source_name: Roots, sterile


title: Blood_2wk

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

institute: Ehime University

description: Gene expression after 2 weeks of lithium medication in human blood.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1-v5_10_April08 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were global intra-array normalized on to the 75.0 percentile using GeneSpring GX 12.1.

source_name: Peripheral blood, 2 weeks after medication

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent One-Color Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Freshly drawn peripheral blood from healthy volunteers was collected in the PAXgene Blood RNA tube (Qiagen, Tokyo, Japan) according to the manufacturer's recommendations.

extract_protocol: RNA was prepared using the PAXgene Blood RNA tube (Qiagen, Tokyo, Japan) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample type

value: pool from 8 subjects

value: whole blood

tag: gender

value: male

tag: mean age

tag: disease status

value: healthy

value: lithium

tag: time point

value: 2 weeks after medication


title: L1309/L428

tag: cell line

tag: cell type


title: Blood_after2wk

description: Gene expression 2 weeks after stopping lithium medication in human blood.

source_name: Peripheral blood, 2 weeks after stopping medication

value: 2 weeks after stopping medication