title: Control2 other strain

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

description:
Sv129_0_2
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control

hyb_protocol: Fifteen µg of each cRNA sample was hybridized for 16 h at 45°C to an Affymetrix mouse genome 430 2.0 GeneChip containing 45.000 probe sets and covering the complete transcribed mouse genome. Chips were washed and stained with streptavidin-phycoerythrin using a fluidics station according to the protocols recommended by the manufacturer.

scan_protocol: Finally, arrays were scanned at 1.56-µm resolution using the Affymetrix GeneChip System confocal scanner 3000.

data_processing: Microarray data analysis was performed using bioconductor available in the statistical package R using package affy. Expression values were calculated using the Robust Multichip Average (RMA) method. Note that the two mice strains were normalised separatly. Absent/present calls were calculated using mas5 package

label_protocol: The amplification and labeling of RNA samples were conducted according to the manufacturer's instructions (Affymetrix). One µg from each sample was transcribed to cDNA using an oligo(dT)24 primer containing a T7 RNA polymerase promoter. After RNAse H-mediated second strand cDNA synthesis, the product was purified and served as a template in the subsequent in vitro transcription reaction. Biotin-labeled cRNA was prepared from double-stranded cDNA by in vitro transcription using the GeneChip RNA transcript labeling kit (Affymetrix). After cleanup, biotin-labeled cRNA was fragmented by alkaline treatment [40 mmol/l Tris-acetate (pH 8.2), 100 mmol/l potassium acetate, and 50 mmol/l magnesium acetate] at 94°C for 35 minutes.

extract_protocol: For RNA isolation hippocampi were dissected from fresh brains, flash frozen and stored at -80 °C. Total RNA was isolated using TRItidy-reagent (Applichem), followed by an additional purification step using RNEasy columns (Qiagen), quantified by UV-spectroscopy and its quality verified using a LabChip BioAnalyzer (AGILENT Technologies).

treatment_protocol: 3 month old male mice were injected with kainic acid or isotonic saline solution according to institutional guidelines. Kainic acid (16 mg/kg, Ascent scientific) or similar amounts of isotonic saline were administered by i.p. injection. Animals were sacrificed by cervical luxation 1, 2, 4, 8, or 24 h after onset of the first seizure (each time point, n = 3), control animals were sacrificed after saline injection (0h, n = 6).

tag: mouse strain

tag: age

value: 3 months

value: male

tag: injected with

value: isotonic saline

tag: time point

value: hippocampal region


title: Control3 other strain

status: Public on Oct 23 2013

type: RNA

city: Berlin

country: Germany

description:
Sv129_0_3
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control

label: biotin

molecule: total RNA

organism: Mus musculus

tag: gender

tag: tissue


title: 4118698426

status: Public on Oct 24 2013

type: genomic

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Genotyping BeadChips (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.

scan_protocol: After allele-specific staining BeadChip arrays were scanned on a BeadArray Reader

data_processing: Data processing was carried out with BeadStudio software v3.1.0 provided by Illumina

molecule: genomic DNA

organism: Homo sapiens

source_name: Urinary bladder carcinoma

label_protocol: 400ng of genomic DNA was whole-genome amplified, fragmented , precipitated and resuspended in hybridization buffer

extract_protocol: Extraction of genomic DNA from fresh frozen tissue using the DNAeasy blood and tissue kit (Qiagen)

value: bladder

tag: disease state

value: carcinoma


title: 4118698433

value: M


title: Control1 other strain

description:
Sv129_0_1
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control


title: SB380202

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Duo Genotyping BeadChips (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays (Human 1M Genotyping BeadChips (Illumina)). After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.


title: H24243-DC

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

country: USA

institute: Washington University in St.Louis

description: Differentiated chondrocytes, replicate 9

data_processing: The non-normalized_data.txt file contains the CT values exported from the OpenArray ® Real-Time qPCR Analysis . Data were analyzed with the Applied Biosystems DataAssist ™ Software.CT values normalized to RNU44 using the Applied Biosystems DataAssist ™ Software. Series supplementary file GSE49152_non-normalized.txt reports raw CT values. Series supplementary file GSE49152_fold-change_data.txt reports test/control ratios.

label: FAMTP

source_name: human embryonic limb tissue

label_protocol: Megaplex ™ RT Primers were used to label the cDNA. Protocol specified  in TaqMan(R) OpenArray(R) MicroRNA Panels User Guide June 2011.

growth_protocol: Frozen blocks of human embryonic limb tissue were sectioned (20um) onto RNAse-free polyethylene naphthalate (PEN)-coated glass slides (Leica Microsystems) that are specifically designed for laser capture microdissection (LCM).Frozen sections were stored at minus 80oC for up to 48 h before being processed for LCM.

extract_protocol: Total RNA including small RNAs was isolated using either the Total RNA Purification Micro Kit (Norgen Biotek Corp.) or the mirVanaTM miRNA Isollation kit in accordance with the manufacturer’s protocol.

treatment_protocol: Upon removal from cold storage, the tissue sections were exposed to 30 s incubations in cold 75% ethanol followed by 50% ethanol, 20% ethanol, dH2O, 0.02% Toluidine Blue (prepared in RNAse free H2O), two dH20 washes, 75% ethanol, 95% ethanol and 100% ethanol. Finally, sections were transferred to xylene for 3 min and air-dried.LCM was immediately carried out using the LMD7000 system (Leica Microsystems). The three cartilage regions of interest in each tissue section were selected using the system software resulting in a contact and contamination-free collection of tissue directly into one of the three sterile 0.5 mL Eppendorf caps containing 60 ul of lysis buffer from the RNA isolation kit of choice.

value: Differentiated chondrocytes


title: Kainic acid 4hrs 2 other strain

description:
Sv129_4_2
Gene expression profile of hippocampus 4 hours after kainic actid injection

source_name: Kainic acid 4hrs_alternative strain

value: kainic acid


title: Kainic acid 4hrs 3 other strain

description:
Sv129_4_3
Gene expression profile of hippocampus 4 hours after kainic actid injection


title: Kainic acid 4hrs 1 other strain

description:
Sv129_4_1
Gene expression profile of hippocampus 4 hours after kainic actid injection


title: SB380224


title: SB380201


title: Kainic acid 8hrs 3

description:
BL6_8_3
Gene expression profile of hippocampus 8 hours after kainic actid injection

source_name: Kainic acid 8hrs


title: Control4

description:
BL6_0_4
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control

source_name: isotonic saline_control


title: Kainic acid 1hr 1

description:
BL6_1_1
Gene expression profile of hippocampus 1 hour after kainic actid injection

source_name: Kainic acid 1hr


title: Kainic acid 24hrs 2

description:
BL6_24_2
Gene expression profile of hippocampus 24 hours after kainic actid injection

source_name: Kainic acid 24hrs


title: Control5

description:
BL6_0_5
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control


title: Kainic acid 1hr 3

description:
BL6_1_3
Gene expression profile of hippocampus 1 hour after kainic actid injection


title: Kainic acid 4hrs 3

description:
BL6_4_3
Gene expression profile of hippocampus 4 hours after kainic actid injection

source_name: Kainic acid 4hrs


title: Kainic acid 8hrs 2

description:
BL6_8_2
Gene expression profile of hippocampus 8 hours after kainic actid injection


title: Kainic acid 1hr 2

description:
BL6_1_2
Gene expression profile of hippocampus 1 hour after kainic actid injection


title: 4118698416


title: Kainic acid 8hrs 1

description:
BL6_8_1
Gene expression profile of hippocampus 8 hours after kainic actid injection


title: Control6

description:
BL6_0_6
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control


title: Kainic acid 4hrs 1

description:
BL6_4_1
Gene expression profile of hippocampus 4 hours after kainic actid injection


title: SB380225

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Duo Genotyping BeadChips (Illumina).


title: Kainic acid 4hrs 2

description:
BL6_4_2
Gene expression profile of hippocampus 4 hours after kainic actid injection


title: Control2

description:
BL6_0_2
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control


title: Control3

description:
BL6_0_3
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control


title: Control1

description:
BL6_0_1
Gene expression profile of hippocampus 1 hour after isotonic saline injection, serves as control


title: 4118698428

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Genotyping BeadChips (Illumina).


title: day 3 of ES cell differentiation, dox-induced Snail Flk1- cells

city: Saint Louis

first: Jennifer

last: Gill

address: 660 South Euclid Ave.

department: Pathology/Immunology

institute: Washington University School of Medicine

description: Gene expression data from day 3 of differentiation of Flk1- ES cells inducibly expressing Snail in DKK1

hyb_protocol: The Affymetrix operating system (Command Console) was used to manage the washing and hybridization steps.

scan_protocol: The Affymetrix operating system (Command Console) was used for scanning.  Affymetrix analysis software (Genotyping Console) was used to derive Quality Control metrics, create .cel files and scaled expression data from the scanned Expresison array image files

data_processing: The data were analyzed with dChip 2008 using default analysis settings.  All samples were normalized to a single baseline array of median intensity.

source_name: A2.snail, DKK+dox treatment, Flk1- sort, day 3

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

growth_protocol: ES cells were differentiated as embryoid bodies in petri dishes at a density of 50,000 cells/mL in differentiation media consisting of 10% FCS and DKK1.

extract_protocol: RNA was isolated using Qiagen RNeasy kit per the manufacture's instructions.

treatment_protocol: In DKKdox conditions, doxycycline was added for a final concentration of 250ng/mL on day 2

tag: cell type

value: mouse embryonic stem cells

tag: cell line

tag: day of differentiation

value: day 3

tag: dox treatment

value: 250 ng/mL


title: day 3 of ES cell differentiation, untreated Flk1- cells

description: Gene expression data from day 3 of differentiation of ES cells in DKK1

source_name: A2.snail, DKK treatment, day 3

value: 0 ng/mL


title: Caecum del(1-4i) ds cDNA

type: mixed

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

description: ds cDNA normalized with gDNA

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
cDNA array data were normalized with ds cDNA array replicates for ss cDNA, to genomic DNA array replicates for ds cDNA, and scaled to feature intensity of 10 using TAS software (Affymetrix). PM-MM pairs mapping within a sliding window of 75 bp was used.
bar files of normalized signals

source_name: Caecum

label_protocol: standard Affymetrix protocol

extract_protocol: Caeca were dissected from E13.5 embryos and and stored in RNAlater reagent (QIAGEN) until genotyped. After disruption with PT1200E Polytron (Kinematica), RNA was isolated using the RNeasy minikit (QIAGEN).

treatment_protocol: RNA was depleted of rRNA 18S and 28S using RiboMinus Human/Mouse Transcriptome Isolation kit (Affymetrix). Using T7-(N)6 primers, RiboMinus-enriched RNA was stepwise reverse transcribed to cRNA (SuperScript II) and to double-stranded (ds) cDNA (DNA Polymerase I). cDNA was further amplifed by in vitro transcription to cRNA and reverse transcribed again to single-stranded (ss) cDNA (Superscript II) with incorporation of deoxyuridine using the GeneChip Whole Transcript Amplified Double-Stranded Target Assay kit (Affymetrix). For ss cDNA tiling array, cDNA was treated with NaOH 1M and blocked with HCl 1M. For ds cDNA tiling array, cDNA was reverse transcribed to ds cDNA (DNA Polymerase I) with incorporation of deoxyuridine. Both ss and ds cDNAs were fragmented with apurinic / apyrimidinic endonucleases and uracil DNA glycosylases and labeled with terminal deoxynucleotidyl transferase using GeneChip WT Double- Stranded DNA Terminal Labeling Kit (Affymetrix). The profile of all different steps was analysed with a Bioanalyser. cDNAs were hybridized to custom-made tiling arrays (Soshnikova and Duboule, 2009). Tiling arrays were processed according to manufacturer instructions. Transcript profiling experiment was repeated once for each sample, except for del(1-4i) and del(9-11) caeca.

tag: genotype

tag: sample type

value: ds cDNA

tag: strain

value: Caecum

source_name: gDNA


title: Caecum del(9-11) ds cDNA

description: ds cDNA normalized with gDNA


title: BUTANTAN 117.rma-gene-default-Signal

city: Sao Paulo

first: Marcelo

last: De Franco

state: Sao Paulo

address: Avenida Vital Brasil 1500

department: Imunogenetica

country: Brazil

institute: Instituto Butantan

description: 117- AIRmin exp male

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST 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: AIRmin exp male

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

extract_protocol: Total RNA from the footpads of mice on days 0 and 160 after the second pristane injections were isolated using the RNAspin mini kit (GE Healthcare, Buckinghamshire, UK). The concentrations of the extracted RNA were checked using Nano-Drop (Thermo scientific), and their integrity was tested using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice received two intraperitoneal injections with 0.5 ml of the non-immunogenic mineral oil pristine (2,6,10,14-tetramethylpentadecane, Sigma Chemical Co., San Diego, USA) at 60-day intervals. Arthritis development was examined twice weekly for 160 days, by recording arthritis incidence and maximum severity scores for each paw

value: 2 to 4 months

tag: genotype/variation

value: outbred stock

tag: sample group

value: pristane-induced

value: footpad

tag: inflammation level

value: low


title: BUTANTAN 119.rma-gene-default-Signal

description: 119- AIRmin exp female

source_name: AIRmin exp female

value: female


title: BUTANTAN 114.rma-gene-default-Signal

description: 114- AIRmin control male

source_name: AIRmin control male

value: male

value: control


title: BUTANTAN 110.rma-gene-default-Signal

description: 110- AIRmax exp male

source_name: AIRmax exp male

value: high


title: 4118698403

value: bladder

value: carcinoma


title: BUTANTAN 115.rma-gene-default-Signal

description: 115- AIRmin control female

source_name: AIRmin control female


title: BUTANTAN 111.rma-gene-default-Signal

description: 111- AIRmax exp female

source_name: AIRmax exp female


title: BUTANTAN 116.rma-gene-default-Signal

description: 116- AIRmin control female


title: BUTANTAN 118.rma-gene-default-Signal

description: 118- AIRmin exp male


title: BUTANTAN 106.rma-gene-default-Signal

description: 106- AIRmax control male

source_name: AIRmax control male


title: BE2C_BIX01294_rep2

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO). Gene annotation enrichment analysis was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 and Ingenuity Pathways Analysis (IPA Ingenuity® Systems) for all significantly changed genes (≥ ±1.5 fold, P < 0.01).

label: TdT

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: BE(2)-C cells were cultured in DMEM (HyClone SH30022, Thermo Scientific) supplemented with 10% dialyzed FBS (Gibco 26400-036).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: BE(2)-C cells were treated either with 0.05% DMSO or with 5 µM BIX01294 (B9311, Sigma-Aldrich) for 24 hours.

tag: tumor cell line

tag: treatment

value: 5 µM BIX01294 for 24 hr


title: BUTANTAN 108.rma-gene-default-Signal

description: 108- AIRmax control female

source_name: AIRmax control female

tag: age


title: BUTANTAN 112.rma-gene-default-Signal

description: 112- AIRmax exp female


title: BUTANTAN 120.rma-gene-default-Signal

description: 120- AIRmin exp female


title: BUTANTAN 113.rma-gene-default-Signal

description: 113- AIRmin control male


title: Caecum inv ss cDNA

description: ds cDNA normalized with ss cDNA

value: ss cDNA


title: Caecum inv ds cDNA

description: ds cDNA normalized with gDNA


title: BUTANTAN 105.rma-gene-default-Signal

description: 105- AIRmax control male


title: BE2C_BIX01294_rep3

description: RNA expression value


title: BE2C_BIX01294_rep1

description: RNA expression value


title: BUTANTAN 107.rma-gene-default-Signal

description: 107- AIRmax control female


title: BUTANTAN 109.rma-gene-default-Signal

description: 109- AIRmax exp male


title: Kainic acid 24hrs 3

description:
BL6_24_3
Gene expression profile of hippocampus 24 hours after kainic actid injection

tag: mouse strain

value: 3 months

tag: injected with

value: kainic acid

tag: time point

value: hippocampal region


title: Caecum flox ds cDNA

description: ds cDNA normalized with gDNA

value: ds cDNA

tag: tissue

value: Caecum


title: Caecum flox ss cDNA

description: ds cDNA normalized with ss cDNA


title: BE2C_DMSO_rep2

description: RNA expression value

value: 0.05% DMSO for 24 hr


title: Caecum ss cDNA

description: ds cDNA normalized with ss cDNA

value: wild-type


title: Caecum ds cDNA

description: ds cDNA normalized with gDNA


title: Caecum H3K27me3

data_processing:
Array data were normalized with input replicates and scaled to feature intensity of 100 using TAS software (Affymetrix). PM-MM pairs mapping within a sliding window of 250 bp was used.
bar files of normalized signals

extract_protocol: Trizol

treatment_protocol: ChIP was performed according to (Lee et al., 2006). Caeca were dissected from E13.5 embryos, fixed in formaldehyde 1% for 15 min at RT and washed three times with cold phosphate buffer solution (PBS). Pools of fifty caecum were sonicated with Bioruptor Next Gen (Diagenode), precleared with either EZview Red protein G/A Affinity Gel (Sigma) or Dynabeads M280 Sheep anti-Mouse IgG (Invitrogen) to avoid unspecific binding and immunoprecipitated with 2-6 ug of RNAPII (8WG16, Covance), H3K4me1 (ab8895, Abcam), anti-H3K4me3 (07-473, Millipore) or H3K27me3 (17-622, Millipore) antibodies and EZview Red protein G/A Affinity Gel (Sigma) / Dynabeads M280 Sheep anti-Mouse IgG (Invitrogen). After several washing steps, chromatin was eluted, decrosslinked and digested with RNAseA and Proteinase K. Immunoprecipitated chromatin and whole cell extract DNA (input) was blunted with T4 DNA Polymerase, and linker adaptors of oligos 1; 5’-GCGGTGACCCGGGAGATCTGAATTC-3’ and 2; 5’-GAATTCAGATC-3’ were ligated to blunt ends. This allowed amplification using ligation-mediated PCR (Lee et al., 2006). PCR was fragmented with apurinic / apyrimidinic endonucleases and uracil DNA glycosylases and labeled with terminal deoxynucleotidyl transferase using GeneChip WT Double- Stranded DNA Terminal Labeling Kit (Affymetrix). The profile of all different steps was analysed with a Bioanalyser. DNAs were hybridized to custom-made tiling arrays (Soshnikova and Duboule, 2009). Tiling arrays were processed according to manufacturer instructions. For each sample and antibody, ChIP-chip was repeated once.

tag: chip antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

value: input


title: BE2C_DMSO_rep1

description: RNA expression value


title: CaecumH3K4me3


title: SB380200

source_name: Urinary bladder carcinoma

tag: gender

value: M

tag: disease state


title: Caecum 4C d4

treatment_protocol: Chromosome conformation capture on chip (4C) technique was performed as described (Hagège et al., 2007; Simonis et al., 2006). Caeca were dissected from E13.5 embryos, dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed in formaldehyde 2% for 10 min at room temperature and reaction was quenched on ice with glycine. Cells were further lysated with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, PIC 1x to isolate nuclei. Nuclei from pools of fifty caecum or two brains were digested with DpnII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were amplified using previously described inversed PCR primers (Montavon et al., 2011) and AmpliTaq DNA polymerase (Applied Biosystems). 4C PCR was fragmented with apurinic / apyrimidinic endonucleases and uracil DNA glycosylases and labeled with terminal deoxynucleotidyl transferase using GeneChip WT Double- Stranded DNA Terminal Labeling Kit (Affymetrix). The profile of all different steps was analysed with a Bioanalyser. DNAs were hybridized to custom-made tiling arrays (Soshnikova and Duboule, 2009). Tiling arrays were processed according to manufacturer instructions.

tag: sample type

value: chromatin


title: 4F human iPS cell-derived Hematopoietic Progenitor Cells

city: Iowa City

first: Eunmi

last: Kim

state: IA

address: 601 HWY 6 w

institute: University of Iowa

description: Gene expression data from CD34+ cells sorted following coculture of 4F iPS cells with OP9 stromal cells

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer, placed onto Affymetrix Human Gene 1.0 ST arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin, signal amplified with antistreptavidin antibody using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing: The data were analyzed with Heatmap.2 package using the default settings for Affymetrix analysis and normalization through global scaling.

source_name: HPCs derived in vitro through OP9 co-culture from iPS cells reprogrammed from fibroblasts

label_protocol: 50ng total RNA was converted to SPIA amplified cDNA using using the WT-Ovation Pico RNA Amplification System v2 according to the manyfacturer's recommended protocol. Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module per the manufacturer’s recommended protocol.

growth_protocol: Confluent human iPS cells were cocultured for 8-12 days on top of (70-80% confluent) OP9 stromal feeder cells in alpha MEM media supplemented with 20%FBS, 10uM ascorbic acid and 10uM MTG. The CD34+ cells were then sorted using Miltenyi CD34 beads and MACS columns according to the manufacturer's instructions.

extract_protocol: Total RNA was performed according to the manufacturer's instructions (Qiagen's RNAeasy isolation kit).

treatment_protocol: CD34 enriched cells were prepared for RNA extraction according to manufacturer's instructions (Qiagen's RNAeasy isolation kit).

tag: cell origin

value: iPS cells retrovirally reprogrammed from human fibroblasts using the 4 Yamanaka transcription factors (Oct-4, Klf-4, c-Myc, Sox2)

tag: disease

value: iPS cells from MRC5 fetal fibroblasts


title: BE2C_DMSO_rep3

description: RNA expression value


title: Caecum H3K4me

value: Abcam

tag: strain


title: Kainic acid 24hrs 1

description:
BL6_24_1
Gene expression profile of hippocampus 24 hours after kainic actid injection

value: male


title: Caecum RNA PolII

value: RNA Pol III

value: Covance


title: Brain 4C d4

source_name: Brain

value: Brain


title: Caecum 4C d13


title: day 3 of ES cell differentiation, dox-induced Snail Flk1+ cells

description: Gene expression data from day 3 of differentiation of Flk1+ ES cells inducibly expressing Snail in DKK1

source_name: A2.snail, DKK+dox treatment, Flk1+ sort, day 3

tag: cell type

value: mouse embryonic stem cells

tag: cell line

tag: day of differentiation

value: day 3

tag: dox treatment

value: 250 ng/mL


title: Umblical Cord Blood-CD34+ Cells

description: Gene expression data from CD34+ cells sorted from UCB

source_name: cord blood cells

value: naturally found cord blood


title: Brain 4C d13

tag: age


title: WT human iPS cell-derived Hematopoietic Progenitor Cells

description: Gene expression data from CD34+ cells sorted following coculture of WT iPS cells with OP9 stromal cells

value: iPS cells reprogrammed from human fibroblasts using the STEMCAA lentiviral cassette (Oct-4, Klf-4, c-Myc, Sox2).

value: iPS cells from fibroblasts of apparently healthy non-fetal tissue


title: pink human iPS cell-derived Hematopoietic Progenitor Cells

description: Gene expression data from CD34+ cells sorted following coculture of pink iPS cells with OP9 stromal cells

value: iPS cells from fibroblasts from a patient with Muscular Dystrophy


title: Bl-04-Cellobiose technical replicate 2

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

hyb_protocol: Performed as described: Broadbent et al. J. Bacteriol. 2010, 192(9):2445 (DOI: 10.1128/JB.01618-09)

scan_protocol: All scanning were done accordingly to the Affymetrix guidelines: GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 3)

data_processing: All data (CEL files) were imported into SAS JMP Genomics (SAS institute Inc, Cary, NC) for all 24 samples described in study. The data was quantile normalized and ANOVA was performed using Bonferroni correction (α=0.05) to identified statistically significant and differentially up-regulated genes to each carbohydrate growth condition.

label: Biotin

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on cellobiose

label_protocol: All labeling were done accordingly to the Affymetrix guidelines: GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 3)

growth_protocol: B. lactis Bl-04 was grown in fresh 1% (w/v) carbohydrate supplemented semidefined media with a 1% inoculum from an overnight culture for a total of five subcultured passages.

extract_protocol: Total RNA isolation, DNase-treatment and RNA purification were performed essentially as described previously (Goh et al., 2006 Appl. Environ. Microbiol. 72:7518-30).

tag: carbohydrate

value: cellobiose

tag: technical replicate


title: Bl-04-Panose technical replicate 1

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on panose

value: panose


title: Bl-04-Cellobiose technical replicate 1

organism: Bifidobacterium animalis subsp. lactis Bl-04


title: Bl-04-Raffinose technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on raffinose

value: raffinose


title: CHOP human iPS cell-derived Hematopoietic Progenitor Cells

description: Gene expression data from CD34+ cells sorted following coculture of CHOP iPS cells with OP9 stromal cells

value: iPS cells from fibroblasts of a patient with mucopolysaccharidosis type VI


title: Bl-04-XOS technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on XOS

value: XOS


title: Bl-04-Raffinose technical replicate 1


title: Bl-04-Melibiose technical replicate 1

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on melibiose

value: melibiose


title: Bl-04-GOS technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on GOS

value: GOS


title: Bl-04-Melibiose technical replicate 2


title: Bl-04-GOS technical replicate 1


title: Bl-04-Xylobiose technical replicate 1

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on xylobiose

value: xylobiose


title: Bl-04-Xylobiose technical replicate 2


title: Bl-04-Glucose technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on glucose

value: glucose


title: Bl-04-XOS technical replicate 1


title: Bl-04-Maltotriose technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on maltotriose

value: maltotriose


title: Smoke_testis rep 1

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

state: NSW

address: University Drive

department: Science and IT

country: Australia

institute: University of Newcastle Australia

description: Smoke 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using BioConductor (v.2.12.)'s lumi package in R statistical software

source_name: Adult testis from cigarette smoke exposed mouse

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

growth_protocol: All experimental procedures involving the use of animals were performed with the approval of the University of Newcastle’s Animal Care and Ethics Committee (ACEC). Specific pathogen-free adult female (6-week-old) C57BL/6 mice were obtained from the animal services unit and maintained according to the recommendations prescribed by the ACEC. Mice were housed under a controlled lighting regime (16L:8D) at 21–22°C and supplied with food and water ad libitum.

extract_protocol: Total RNA (approximately 3 µg) was isolated from adult ovaries using a QIAGEN RNeasy Mini Kit (Hilden, Germany) in accordance with the manufacturer’s recommendations.

treatment_protocol: C57BL/6 5 week-old female mice were exposed via the nose-only to cigarette smoke [twelve 3R4F reference cigarettes (University of Kentucky, USA) twice/day, five times per week, for 12-18 weeks]. Each exposure lasted 60 minutes. Control mice received room air. In total, 27 mice underwent cigarette smoke exposure. Eleven week-old female mice exposed to cigarette smoke for 6 weeks were separated into groups of three and housed with a single control stud male aged 7-8 weeks with proven fertility for a maximum of 12 weeks. Females were monitored every second day for post-coital plugs and pregnancy. Pregnant females were separated into single cages and litter sizes/pup weights recorded. Smoke exposure via dams continued throughout mating/pregnancy/lactation until weaning of pups at 21days post birth.

value: adult

tag: exposed to

value: cigarette smoke in utero

tag: tissue

value: testis


title: Smoke_testis rep 2

description: Smoke 2


title: Bl-04-Maltotriose technical replicate 1


title: Smoke_testis rep 3

description: Smoke 3


title: Control_testis rep 2

description: Control 2

source_name: Adult testis from room air exposed mouse

value: room air in utero (control)


title: CCRCC#5-C

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

country: United Kingdom

institute: University of Oxford

data_processing:
miRNA QC tool normalised- intensity reverse logged
analysed in Genespring (no added normalisation)

extract_protocol: extracted with recoverall kit from FFPE blocks

value: CCRCC

value: tumor


title: Control_testis rep 3

description: Control 3


title: CCRCC#5-B


title: CCRCC#1


title: Bl-04-Gentiobiose technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on gentiobiose

value: gentiobiose


title: Bl-04-Gentiobiose technical replicate 1


title: CCRCC#5-A


title: Control_testis rep 1

description: Control 1


title: CCRCC#2


title: siTCTP 3

city: Oslo

first: Margrethe

last: Storm

address: Blindernveien 31

country: Norway

institute: University of Oslo

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with standard Illumina BeadStudio.

source_name: LNCaP cells transfected with siRNA against TCTP, 72 h

label_protocol: Illumina TotalPrep RNA Amplification Kit.

growth_protocol: LNCaP cells were grown in RPMI 1640 supplemented with 10% FBS.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen). 500 ng of total RNA was used in the amplification and labeling reaction. 1.5 ug of biotin-labeled cRNA was used to hybridise onto Illumina HumanWG-6 v3 Expression BeadChips.

treatment_protocol: Cells were transfected with 100 nM of respective siRNAs for 72 h and then harvested.

value: LNCaP

tag: sirna

value: TCTP


title: Bl-04-Isomaltose technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on isomaltose

value: isomaltose


title: CCPRCC#4-B

value: CCPRCC


title: Bl-04-Isomaltose technical replicate 1


title: siTCTP 2


title: CCPRCC#4-A


title: Ext1 MO 2

city: Houston

first: Amy

middle: of

last: Sater

state: TX

address: 4800 Calhoun Rd

department: Biology and Biochemistry

institute: University of Houston

description: Gene expression data from embryos at st. 10.5

hyb_protocol: Performed by the Baylor College of Medicine Genomic and RNA profiling Core

scan_protocol: Genechip scanner 3000 (Affymetrix) was used by the Baylor College of Medicine Genomic and RNA profiling Core

data_processing: Raw CEL and DAT files were generated using Affymetrix Microarray Suite 5.0 (MAS 5). The intensity of the control and experimental array was normalized (Quackenbush 2001), and the fold change of each gene between mismatch and Ext1 MO was calculated.

organism: Xenopus laevis

source_name: Xenopus laevis embryos at St 10.5

growth_protocol: Xenopus laevis embryos were obtained by in vitro fertilization and kept in sixteen degree incubator

extract_protocol: mRNA was extracted immediately after the embryos were lysed. The RNA was purified using RNAeasy easy kit (Qiagen). The vitelline envelope of embryos was manually removed prior to the extraction. Five embryos (St 10.5) were lysed by pipetting in 1 ml RLT buffer with 10 μl β-mercaptoethanol.

treatment_protocol: Embryos were obtained and microinjected using standard protocol. And the embryo stages were determined by Nieuwkoop and Faber, 1994). Two-cell stage embryos were injected with either mismatch MO or Ext1 MO (20ng each). Five embryos from each treatment were combined for individual RNA sample preparation.

tag: developmental stage

value: gastula

tag: treatment

value: embryos injected with ext1 MO


title: Ext1 MO 3


title: siTCTP 1


title: Sample 244-09

first: Gard

middle: Olav

last: Thomassen

address: Radiumhospitalet, Rikshospitalet HF

department: Institute for Cancer Research

institute: Rikshospitalet

description: Low grade fibromyxoid sarcoma

hyb_protocol: Hybridized for 16-20 hours using Hybridization kit form Roche NimbleGen

scan_protocol: Scanned using an Agilent microarray skanner

data_processing: According to related manuscript; in short, raw data was log2 transformed and normalised by subtracting the average probe value across all samples from each probe value. See also GPL 11054 and related manuscript

source_name: Patient 244-09

label_protocol: Double stranded  cDNA was labeled with Cy3 using One-colour labelling kit from Roche NimbleGen

growth_protocol: Standard conditions

extract_protocol: TRIzol

value: Low grade fibromyxoid sarcoma


title: CCPRCC#1-B

tag: disease state


title: Sample 2430-90 vol 2011

description: Synovial sarcoma

value: Synovial sarcoma

tag: sample type


title: Sample 9972

description: Synovial sarcoma

source_name: Patient 9972


title: Bl-04-Stachyose technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on stachyose

value: stachyose


title: siLuc 1

source_name: LNCaP cells transfected with siRNA against Luc, 72 h

value: luciferase


title: siLuc 3


title: Bl-04-Stachyose technical replicate 1


title: CCPRCC#3-A


title: Bl-04-Panose technical replicate 2

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on panose

value: panose


title: Mispair MO 2

value: embryos injected with mismatch MO


title: Mispair MO 3


title: Ext1 MO 1


title: Sample 14319

description: Alveolar rhabdomysarcoma

source_name: Patient 14319

value: Alveolar rhabdomysarcoma


title: Sample 10908

description: Ewing sarcoma

source_name: Patient 10908

value: Ewing sarcoma


title: Sample 885-89

description: Myxoid liposarcoma

source_name: Patient 885-89

value: Myxoid liposarcoma


title: CCPRCC#3-B

value: tumor


title: CRCC#3

value: CRCC


title: Sample 4640

description: Ewing sarcoma

source_name: Patient 4640


title: Bl-04-Glucose technical replicate 1

source_name: Bifidobacterium animalis subsp. lactis Bl-04 grown on glucose

value: glucose


title: Sample 3214 vol 2009

description: Myxoid liposarcoma

source_name: Patient 3214 vol 2009


title: siLuc 2

value: LNCaP


title: Sample 3490-00

description: Low grade fibromyxoid sarcoma

source_name: Patient 3490-00


title: Sample 6499

description: Synovial sarcoma

source_name: Patient 6499


title: Sample 14476

description: Ewing sarcoma

source_name: Patient 14476


title: Sample 2492-08

description: Ewing sarcoma

source_name: Patient 2492-08


title: Sample 3214 vol 2011

description: Myxoid liposarcoma

source_name: Patient 3214 vol 2011


title: Mispair MO 1

source_name: Xenopus laevis embryos at St 10.5


title: WT-PRC-2

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

description: WT in pyruvate plus choline and propargylcholine, replicate 2

hyb_protocol: Following fragmentation, 2.4 ug of cRNA were hybridized on the Pseudomonas aeruginosa PAO1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe intensities were first generated using the AGCC program (Affymetrix). Probe-level intensities were background-corrected, normalized, and summarized, and Robust Multichip Average (RMA) statistics were calculated for each probe set and sample as is implemented in Partek Genomic Suites®, version 6.6

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa WT in MOPS pyruvate plus choline and propargylcholine

label_protocol: Biotinylated cDNA was prepared from 50 ng of whole RNA using the NuGen Ovation Pico system and the Encore Biotin Module according to manufacturer's instructions.

growth_protocol: Cells were pregrown for 18 h in MOPS with 25 mM pyruvate and 5 mM glucose and then resuspended in MOPS pyruvate or MOPS pyruvate + 250 µM of choline or analogue for four hours

extract_protocol: RNA was extracted from RNA Protect-treated pellets using the Qiagen RNeasy kit using lysozyme-aided lysis. RNA from the first round of columns was treated with DNase I and another round of RNeasy conducted including the on-column DNase step.

treatment_protocol: Cell suspension was treated with two volumes of RNA Protect Bacterial Reagent (Qiagen) and processed to a wet pellet as per manufacturer's instructions

tag: genotype

value: PAO1 wild type

value: choline + propargylcholine


title: PRCC#2

value: PRCC


title: Sample 7757

description: Synovial sarcoma

source_name: Patient 7757


title: dgcA-CHO-1

description: dgcA mutant in pyruvate plus choline, replicate 1

source_name: Pseudomonas aeruginosa dgcA mutant in MOPS pyruvate plus choline

value: PAO1 dgcA deletion

value: choline


title: dgcA-CHO-2

description: dgcA mutant in pyruvate plus choline, replicate 2


title: Sample 2430-90 vol 2009

description: Synovial sarcoma

value: Synovial sarcoma


title: WT-ETC-1

description: WT in pyruvate plus ethylcholine, replicate 1

source_name: Pseudomonas aeruginosa WT in MOPS pyruvate plus ethylcholine

value: ethylcholine


title: WT-ETC-2

description: WT in pyruvate plus ethylcholine, replicate 2


title: PRCC#4


title: WT-PRC-1

description: WT in pyruvate plus choline and propargylcholine, replicate 1


title: CCPRCC#2-B

value: CCPRCC


title: CCRCC#4-A

value: CCRCC


title: Sample 168-97

description: Extraskeletal myxoid chondrosarcoma

source_name: Patient 168-97

value: Extraskeletal myxoid chondrosarcoma


title: CCRCC#4-C


title: Sample 3065

description: Synovial sarcoma

source_name: Patient 3065


title: organoid_ ER_b

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

description: Sample 12

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 1.1 ST Arrays according to manufacturer’s protocol.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: The expression data extracted from the raw celfiles were normalized with the RMA-sketch algorithm from Affymetrix Power Tools. Data was analyzed using the R2 web application, which is freely available at http://r2.amc.nl.

source_name: Troy positive chief cell derived organoid in ER medium

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 100-300ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol.

growth_protocol: Two different experiments were performed. For the first experiment (Sample 1-7), sorted cells of intestines from Troy-EGFP-ires-CreERT2 mice were used. Two differrent populations of Troy positive cells can be found in the gastric corpus: chief cells and parietal cells. For each array, whole gastric corpus glands from 10 mice were first isolated by incubation with EDTA, followed by trypsinization to single cells. The two different popualtions of Troy positive cells can be seperately isolated by FACS. For each array, around 100,000 sorted cells were used. As a reference, whole gastric corpus glands were directly processed. For the second experiment (samples 8-13), single Troy positive chief cell derived organoids were used and exposed to two different media: EGFNWR and ER medium.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

tag: culture

value: organoid derived from single sorted Troy positive chief cells

tag: culture medium

value: ER medium


title: organoid_ EGFNWR_b

description: Sample 9

source_name: Troy positive chief cell derived organoid in EGFNWR medium

value: EGFNWR medium


title: CCRCC#4-B

value: tumor


title: organoid_ EGFNWR_a

description: Sample 8


title: organoid_ ER_a

description: Sample 11


title: organoid_ EGFNWR_c

description: Sample 10


title: organoid_ ER_c

description: Sample 13


title: PRCC#3


title: whole_corpus_glands_b

description: Sample 7

source_name: Isolated whole gastric corpus glands

value: gastric corpus

tag: cell type

value: whole gland


title: WT-DTC-2

description: WT in pyruvate plus diethylcholine, replicate 2

source_name: Pseudomonas aeruginosa WT in MOPS pyruvate plus diethylcholine

value: diethylcholine


title: whole_corpus_glands_a

description: Sample 6


title: CCPRCC#2-A


title: WT-DTC-1

description: WT in pyruvate plus diethylcholine, replicate 1

value: PAO1 wild type


title: WT-CHO-2

description: WT in pyruvate plus choline, replicate 2

source_name: Pseudomonas aeruginosa WT in MOPS pyruvate plus choline


title: WT-CHO-1

description: WT in pyruvate plus choline, replicate 1


title: Troy_corpus_parietal_a

description: Sample 4

source_name: FACS sorted Troy positive parietal cell from gastric corpus from Troy-EGFP-ihres-CreERT2 mice

value: Troy positive parietal cell


title: WT-PYR-2

description: WT in pyruvate, replicate 2

source_name: Pseudomonas aeruginosa WT in MOPS pyruvate

value: pyruvate control


title: csn5 vs WT replicate 2

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Biological replicate 2 of 2

hyb_protocol: cDNA Microarray Yeast 6.4k ver. 7 purchased from UHN Microarray Centre were pre-hybridized at 42 °C for at least 45 min in a solution containing, 5× saline sodium citrate buffer (SSC), 0.1% SDS and 0.1% BSA. The labeled cDNAs (Cy3 sample and HyPer5 sample mixed) were added to an equal volume of hybridization buffer containing 50% formamide, 10× SSC, 0.2% SDS pre-heated at 70°C for 3 min. Hybridization was carried out for 16 h at 42 °C and unbound DNA was washed off using 3 steps with solutions containing: 1) 1XSSC 0.2% SDS pre-heated at 42 °C; 2) 0.1X SSC 0.2 % SDS at room temperature; 3) two times 0.1X SSC at room temperature

scan_protocol: Scanned on an PerkinElmer ScanArray Lite scanner. Images were quantified using ScanArray Express and GenePix Pro 6.1 software

data_processing: LOWESS normalized, median background intensity subtraction, with Goulphar script running on R software. We filtered the data to exclude artifacts, saturated spots, and low signal spots

organism: Saccharomyces cerevisiae

source_name: csn5/rri1 mutant

label_protocol: 20 μg of total RNA extracted from cell culture as described above was mixed with 2 μg of 16mers oligo dT and incubated at 70 °C for 10 min. cDNA was synthesized in a final volume of 40 μl with 25 mM each of dATP, dCTP and dGTP, 15 mM of dTTP, 10 mM of aminoallyl-dUTP, 10 mM DTT and 400U of SuperScript III reverse transcriptase (Life Technologies, Carlsbad, California) in 1× reaction buffer. The samples were incubated for 2 hours at 42°C. cDNA was labeled with Cy3 and HyPer5 Post-Labeling Reactive Dye (GE Healthcare cod. 28-9224-19, Little Chalfont, United Kingdom) according to manufacturer’s protocol.

growth_protocol: strains were grown in YPD medium at 30°C

extract_protocol: Total RNA was extracted from S. cerevisiae cell cultures at 1 OD600/mL with hot acid phenol extraction method

tag: strain

value: csn5/rri1 deleted strain

tag: genetic background

source_name: WT strain W303

value: wild type


title: csn5 vs WT replicate 1

description: Biological replicate 1 of 2


title: CCPRCC#5-B


title: PRCC#5

value: PRCC


title: WT-PYR-1

description: WT in pyruvate, replicate 1


title: Sample 10408

description: Negative

source_name: Patient 10408

value: Fibrosarcoma

value: Negative


title: Troy_corpus_chief_c

description: Sample 3

source_name: FACS sorted Troy positive chief cell from gastric corpus from Troy-EGFP-ihres-CreERT2 mice

value: Troy positive chief cell


title: PRCC#1


title: aTSLPR 2007 week 2 8h-post-challenge

status: Public on Oct 22 2013

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure.  Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release.  As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis.  A total of 13,115 out of 54,675 probesets passed the QC and curation processes, corresponding to 11,629 unique genes.

organism: Macaca fascicularis

source_name: BAL fluid sample from animal 2007 at 8h-postChallenge timept (Week2)

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).

extract_protocol: Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

tag: agent

value: aTSLPR

tag: session

tag: time

value: bronchoalveolar lavage

tag: challenge

value: A. suum

tag: subject

value: animal 2007


title: Troy_corpus_parietal_b

description: Sample 5

tag: tissue


title: Troy_corpus_chief_a

description: Sample 1


title: Troy_corpus_chief_b

description: Sample 2


title: aTSLPR 2007 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 2007 at 24h-postChallenge timept (Screening)

value: Screening


title: aTSLPR 2007 week 6 24 hr post

source_name: BAL fluid sample from animal 2007 at 24 hr post timept (Week6)

value: 24 hr post


title: aTSLPR 2007 week 2 24 hr post

source_name: BAL fluid sample from animal 2007 at 24 hr post timept (Week2)


title: aTSLPR 2007 week 2 pre-challenge

source_name: BAL fluid sample from animal 2007 at preChallenge timept (Week2)

value: pre-challenge

value: baseline


title: vehicle 1101 Screening pre-challenge

source_name: BAL fluid sample from animal 1101 at preChallenge timept (Screening)

value: vehicle

value: animal 1101


title: aTSLPR 2007 week 6 pre-challenge

source_name: BAL fluid sample from animal 2007 at preChallenge timept (Week6)


title: vehicle 1101 week 2 24 hr post

source_name: BAL fluid sample from animal 1101 at 24 hr post timept (Week2)


title: CCPRCC#5-A

value: CCPRCC

value: tumor


title: aTSLPR 2007 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 2007 at 8h-postChallenge timept (Week6)


title: aTSLPR 2007 Screening 8 hr

source_name: BAL fluid sample from animal 2007 at 8 hr timept (Screening)

value: 8 hr


title: vehicle 1101 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 1101 at 8h-postChallenge timept (Week2)


title: vehicle 1007 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 1007 at 24h-postChallenge timept (Screening)

value: animal 1007


title: vehicle 1101 week 2 pre-challenge

source_name: BAL fluid sample from animal 1101 at preChallenge timept (Week2)


title: CCPRCC#1-A


title: aTSLPR 2007 Screening pre-challenge

source_name: BAL fluid sample from animal 2007 at preChallenge timept (Screening)


title: vehicle 1101 week 6 pre-challenge

source_name: BAL fluid sample from animal 1101 at preChallenge timept (Week6)


title: vehicle 1101 Screening 8 hr

source_name: BAL fluid sample from animal 1101 at 8 hr timept (Screening)


title: vehicle 1101 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 1101 at 8h-postChallenge timept (Week6)


title: vehicle 1101 week 6 24 hr post

source_name: BAL fluid sample from animal 1101 at 24 hr post timept (Week6)


title: vehicle 1007 Screening pre-challenge

source_name: BAL fluid sample from animal 1007 at preChallenge timept (Screening)


title: aTSLPR 2005 Screening pre-challenge

source_name: BAL fluid sample from animal 2005 at preChallenge timept (Screening)

value: animal 2005


title: aTSLPR 2006 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 2006 at 24h-postChallenge timept (Screening)

value: animal 2006


title: aTSLPR 2006 Screening pre-challenge

source_name: BAL fluid sample from animal 2006 at preChallenge timept (Screening)


title: vehicle 1007 Screening 8 hr

source_name: BAL fluid sample from animal 1007 at 8 hr timept (Screening)


title: aTSLPR 2006 week 2 pre-challenge

source_name: BAL fluid sample from animal 2006 at preChallenge timept (Week2)


title: aTSLPR 2006 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 2006 at 8h-postChallenge timept (Week2)


title: aTSLPR 2006 week 2 24 hr post

source_name: BAL fluid sample from animal 2006 at 24 hr post timept (Week2)


title: vehicle 1101 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 1101 at 24h-postChallenge timept (Screening)


title: aTSLPR 2005 Screening 8 hr

source_name: BAL fluid sample from animal 2005 at 8 hr timept (Screening)


title: aTSLPR 2006 week 6 24 hr post

source_name: BAL fluid sample from animal 2006 at 24 hr post timept (Week6)


title: vehicle 1006 week 2 pre-challenge

source_name: BAL fluid sample from animal 1006 at preChallenge timept (Week2)

value: animal 1006


title: vehicle 1006 week 6 pre-challenge

source_name: BAL fluid sample from animal 1006 at preChallenge timept (Week6)


title: vehicle 1006 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 1006 at 8h-postChallenge timept (Week2)


title: vehicle 1007 week 6 24 hr post

source_name: BAL fluid sample from animal 1007 at 24 hr post timept (Week6)


title: aTSLPR 2006 Screening 8 hr

source_name: BAL fluid sample from animal 2006 at 8 hr timept (Screening)

value: aTSLPR


title: vehicle 1007 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 1007 at 8h-postChallenge timept (Week6)

value: bronchoalveolar lavage


title: vehicle 1006 week 2 24 hr post

source_name: BAL fluid sample from animal 1006 at 24 hr post timept (Week2)

value: A. suum


title: aTSLPR 2006 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 2006 at 8h-postChallenge timept (Week6)


title: vehicle 1007 week 2 pre-challenge

source_name: BAL fluid sample from animal 1007 at preChallenge timept (Week2)


title: vehicle 1007 week 2 24 hr post

source_name: BAL fluid sample from animal 1007 at 24 hr post timept (Week2)


title: aTSLPR 2006 week 6 pre-challenge

source_name: BAL fluid sample from animal 2006 at preChallenge timept (Week6)


title: aTSLPR 2005 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 2005 at 24h-postChallenge timept (Screening)


title: vehicle 1007 week 6 pre-challenge

source_name: BAL fluid sample from animal 1007 at preChallenge timept (Week6)


title: aTSLPR 2005 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 2005 at 8h-postChallenge timept (Week6)


title: vehicle 1006 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 1006 at 8h-postChallenge timept (Week6)


title: aTSLPR 2005 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 2005 at 8h-postChallenge timept (Week2)


title: vehicle 1006 week 6 24 hr post

source_name: BAL fluid sample from animal 1006 at 24 hr post timept (Week6)


title: aTSLPR 2004 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 2004 at 8h-postChallenge timept (Week6)

value: animal 2004


title: aTSLPR 2004 week 6 24 hr post

source_name: BAL fluid sample from animal 2004 at 24 hr post timept (Week6)


title: aTSLPR 2005 week 2 24 hr post

source_name: BAL fluid sample from animal 2005 at 24 hr post timept (Week2)


title: aTSLPR 2004 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 2004 at 8h-postChallenge timept (Week2)


title: aTSLPR 2005 week 2 pre-challenge

source_name: BAL fluid sample from animal 2005 at preChallenge timept (Week2)


title: aTSLPR 2004 week 2 pre-challenge

source_name: BAL fluid sample from animal 2004 at preChallenge timept (Week2)


title: aTSLPR 2005 week 6 pre-challenge

source_name: BAL fluid sample from animal 2005 at preChallenge timept (Week6)


title: vehicle 1005 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 1005 at 8h-postChallenge timept (Week2)

value: animal 1005


title: aTSLPR 2005 week 6 24 hr post

source_name: BAL fluid sample from animal 2005 at 24 hr post timept (Week6)

value: 24 hr post


title: vehicle 1006 Screening pre-challenge

source_name: BAL fluid sample from animal 1006 at preChallenge timept (Screening)

value: Screening

value: pre-challenge


title: aTSLPR 2004 week 2 24 hr post

source_name: BAL fluid sample from animal 2004 at 24 hr post timept (Week2)


title: vehicle 1006 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 1006 at 24h-postChallenge timept (Screening)

value: vehicle


title: vehicle 1005 week 6 24 hr post

source_name: BAL fluid sample from animal 1005 at 24 hr post timept (Week6)


title: aTSLPR 2003 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 2003 at 8h-postChallenge timept (Week2)

value: animal 2003


title: aTSLPR 2004 week 6 pre-challenge

source_name: BAL fluid sample from animal 2004 at preChallenge timept (Week6)

value: baseline


title: aTSLPR 2003 week 2 pre-challenge

source_name: BAL fluid sample from animal 2003 at preChallenge timept (Week2)


title: aTSLPR 2003 week 6 24 hr post

source_name: BAL fluid sample from animal 2003 at 24 hr post timept (Week6)


title: aTSLPR 2003 week 6 pre-challenge

source_name: BAL fluid sample from animal 2003 at preChallenge timept (Week6)


title: vehicle 1006 Screening 8 hr

source_name: BAL fluid sample from animal 1006 at 8 hr timept (Screening)


title: vehicle 1005 week 6 pre-challenge

source_name: BAL fluid sample from animal 1005 at preChallenge timept (Week6)


title: vehicle 1005 week 2 24 hr post

source_name: BAL fluid sample from animal 1005 at 24 hr post timept (Week2)


title: vehicle 1005 Screening pre-challenge

source_name: BAL fluid sample from animal 1005 at preChallenge timept (Screening)


title: aTSLPR 2003 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 2003 at 8h-postChallenge timept (Week6)


title: vehicle 1004 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 1004 at 8h-postChallenge timept (Week6)

value: animal 1004


title: vehicle 1005 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 1005 at 8h-postChallenge timept (Week6)


title: vehicle 1005 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 1005 at 24h-postChallenge timept (Screening)


title: vehicle 1004 week 2 24 hr post

source_name: BAL fluid sample from animal 1004 at 24 hr post timept (Week2)


title: vehicle 1003 week 2 pre-challenge

source_name: BAL fluid sample from animal 1003 at preChallenge timept (Week2)

value: animal 1003


title: vehicle 1005 week 2 pre-challenge

source_name: BAL fluid sample from animal 1005 at preChallenge timept (Week2)


title: vehicle 1003 week 6 pre-challenge

source_name: BAL fluid sample from animal 1003 at preChallenge timept (Week6)


title: vehicle 1005 Screening 8 hr

source_name: BAL fluid sample from animal 1005 at 8 hr timept (Screening)

value: 8 hr


title: vehicle 1004 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 1004 at 8h-postChallenge timept (Week2)


title: vehicle 1003 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 1003 at 8h-postChallenge timept (Week6)


title: vehicle 1004 week 2 pre-challenge

source_name: BAL fluid sample from animal 1004 at preChallenge timept (Week2)


title: aTSLPR 2002 week 6 pre-challenge

source_name: BAL fluid sample from animal 2002 at preChallenge timept (Week6)

value: animal 2002


title: vehicle 1004 week 6 pre-challenge

source_name: BAL fluid sample from animal 1004 at preChallenge timept (Week6)


title: aTSLPR 2004 Screening 8 hr

source_name: BAL fluid sample from animal 2004 at 8 hr timept (Screening)


title: vehicle 1003 week 6 24 hr post

source_name: BAL fluid sample from animal 1003 at 24 hr post timept (Week6)


title: vehicle 1004 week 6 24 hr post

source_name: BAL fluid sample from animal 1004 at 24 hr post timept (Week6)


title: aTSLPR 2004 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 2004 at 24h-postChallenge timept (Screening)


title: aTSLPR 2003 Screening 8 hr

source_name: BAL fluid sample from animal 2003 at 8 hr timept (Screening)


title: aTSLPR 2003 Screening pre-challenge

source_name: BAL fluid sample from animal 2003 at preChallenge timept (Screening)


title: aTSLPR 2003 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 2003 at 24h-postChallenge timept (Screening)


title: vehicle 1003 week 2 24 hr post

source_name: BAL fluid sample from animal 1003 at 24 hr post timept (Week2)


title: aTSLPR 2002 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 2002 at 8h-postChallenge timept (Week2)


title: aTSLPR 2002 week 6 24 hr post

source_name: BAL fluid sample from animal 2002 at 24 hr post timept (Week6)


title: vehicle 1002 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 1002 at 8h-postChallenge timept (Week6)

value: animal 1002


title: vehicle 1003 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 1003 at 8h-postChallenge timept (Week2)


title: aTSLPR 2002 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 2002 at 8h-postChallenge timept (Week6)


title: vehicle 1003 Screening pre-challenge

source_name: BAL fluid sample from animal 1003 at preChallenge timept (Screening)


title: vehicle 1002 week 2 pre-challenge

source_name: BAL fluid sample from animal 1002 at preChallenge timept (Week2)


title: vehicle 1004 Screening 8 hr

source_name: BAL fluid sample from animal 1004 at 8 hr timept (Screening)


title: vehicle 1002 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 1002 at 8h-postChallenge timept (Week2)


title: vehicle 1003 Screening 8 hr

source_name: BAL fluid sample from animal 1003 at 8 hr timept (Screening)


title: vehicle 1004 Screening pre-challenge

source_name: BAL fluid sample from animal 1004 at preChallenge timept (Screening)


title: aTSLPR 2002 week 2 pre-challenge

source_name: BAL fluid sample from animal 2002 at preChallenge timept (Week2)


title: vehicle 1002 week 2 24 hr post

source_name: BAL fluid sample from animal 1002 at 24 hr post timept (Week2)


title: vehicle 1003 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 1003 at 24h-postChallenge timept (Screening)


title: vehicle 1002 week 6 pre-challenge

source_name: BAL fluid sample from animal 1002 at preChallenge timept (Week6)


title: aTSLPR 2001 Screening pre-challenge

source_name: BAL fluid sample from animal 2001 at preChallenge timept (Screening)

value: animal 2001


title: aTSLPR 2001 Screening 8 hr

source_name: BAL fluid sample from animal 2001 at 8 hr timept (Screening)

value: aTSLPR


title: aTSLPR 2002 Screening 8 hr

source_name: BAL fluid sample from animal 2002 at 8 hr timept (Screening)

value: bronchoalveolar lavage


title: vehicle 1004 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 1004 at 24h-postChallenge timept (Screening)

value: A. suum


title: aTSLPR 2001 week 2 24 hr post

source_name: BAL fluid sample from animal 2001 at 24 hr post timept (Week2)


title: vehicle 1002 week 6 24 hr post

source_name: BAL fluid sample from animal 1002 at 24 hr post timept (Week6)


title: vehicle 1001 week 2 24 hr post

source_name: BAL fluid sample from animal 1001 at 24 hr post timept (Week2)

value: animal 1001


title: aTSLPR 2001 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 2001 at 8h-postChallenge timept (Week2)


title: aTSLPR 2002 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 2002 at 24h-postChallenge timept (Screening)


title: aTSLPR 2001 week 6 pre-challenge

source_name: BAL fluid sample from animal 2001 at preChallenge timept (Week6)


title: aTSLPR 2001 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 2001 at 24h-postChallenge timept (Screening)


title: aTSLPR 2001 week 2 pre-challenge

source_name: BAL fluid sample from animal 2001 at preChallenge timept (Week2)


title: vehicle 1001 week 2 8h-post-challenge

source_name: BAL fluid sample from animal 1001 at 8h-postChallenge timept (Week2)


title: vehicle 1002 Screening 8 hr

source_name: BAL fluid sample from animal 1002 at 8 hr timept (Screening)


title: aTSLPR 2001 week 6 8h-post-challenge

source_name: BAL fluid sample from animal 2001 at 8h-postChallenge timept (Week6)


title: aTSLPR 2001 week 6 24 hr post

source_name: BAL fluid sample from animal 2001 at 24 hr post timept (Week6)


title: vehicle 1001 week 6 pre-challenge

source_name: BAL fluid sample from animal 1001 at preChallenge timept (Week6)


title: vehicle 1001 week 2 pre-challenge

source_name: BAL fluid sample from animal 1001 at preChallenge timept (Week2)


title: vehicle 1001 Screening 8 hr

source_name: BAL fluid sample from animal 1001 at 8 hr timept (Screening)


title: vehicle 1002 Screening 24h-post-challenge

source_name: BAL fluid sample from animal 1002 at 24h-postChallenge timept (Screening)


title: vehicle 1001 week 6 24 hr post

source_name: BAL fluid sample from animal 1001 at 24 hr post timept (Week6)


title: PBMCs rep15

city: Cullowhee

first: Heather

middle: B

last: Coan

address: 132 Natural Science Building

department: Biology Department

institute: Western Carolina University

hyb_protocol: Hybridization was performed according to manufacturer's instructions.

scan_protocol: Samples were scanned on the Illumina BeadArray 500GX Reader using Illumina BeadScan image data acquisition software (version 2.3.0.13).

data_processing: Raw data were uploaded to Genome Studio (Illumina Inc., San Diego, CA), quantile normalized, and background corrected. Differential gene expression was analyzed using Genome Studio to compare expression of genes between the two tissues and reported as a Diff Score.

organism: Papio hamadryas

source_name: Baboon Peripheral blood mononuclear cells

label_protocol: Isolated total RNA was then used to generate anti-sense RNA using the Ambion MessageAmp II Amplification Kit (Ambion, Austin, TX) followed by RNA biotinylation and amplification with the Illumina Total Prep RNA Amplification kit (Illumina Inc., San Diego, CA).

extract_protocol: RNA was isolated from the resulting powdered bone using the QIAGEN RNeasy Lipid Tissue Kit (Qiagen Corp. Inc., Valencia, CA) according to manufacturer’s instructions. PBMC RNA was obtained using the QIAGEN RNeasy Kit. All RNA was treated using the Qiagen RNase-free DNase set.

treatment_protocol: Blood was placed in an 8-mL BD Vacutainer® CPT™ Tube system for collection of PBMCs. After centrifugation, the cell layer was collected and cells were washed according to the manufacturer’s protocol. The cells were then resuspended in RPMI-C medium (10% DMSO, 90% RPMI 1640, Fisher Scientific, Pittsburgh, PA) and stored at -80°C. PBMC RNA was obtained using the QIAGEN RNeasy Kit.

tag: gender

value: female

tag: age (yrs)


title: T98G stably transfected with retroviral vector carying WWOX cDNA, replicate 1, 2

city: Lodz

first: Karolina

last: Pospiech

address: Zeligowskiego 7/9

department: Department of Molecular Carcinogenesis

country: Poland

institute: Medical University of Lodz

hyb_protocol: Before pre-hybridization microarrays were pre-heated at 60˚C for 10 min., followed by 99% ethanol wash. Residual ethanol was removed by thorough rinse in deionized water. Hybridization was carried out in a humidity chamber filled with 2X SSPE buffer at 42°C for 16 – 18 h. Post-hybridization washings comprised 1 X SSPE / 0.03% SDS for 2 min. at 42°C, then in 1 X SSPE for 2 min. RT, and  0.1 X SSPE, RT.

scan_protocol: Microarray scanning was done by means of ProScanArray (Perkin Elmer, USA).

data_processing:
Preliminary analysis using ScanArrayExpress software (Perkin Elmer, USA). Further analysis procedures were carried out on freeware TM4 software suite, which is provided by The Institute for Genomic Research on http://www.tm4.org/ site. Normalization and transformation was performed using MIDAS (v2.22). Data from dye-swap experiments were merged,lowess normalized with a smoothing parameter of 0.33  and then standard deviation regularized. Pairs of flip-dye data were then subjected to a flip-dye consistency check.
Statystical analysys were performed in MeV software (v.4.6.1; MultiExperiment Viewer, TM4 software suite)

label: Cy3, Cy5

source_name: glioma cell line

label_protocol: Labeling with Cy3 and Cy5 was performed according to the ULS™ Labelling Kit manufacturer's instructions (Kreatech Diagnostics, Netherlands)

growth_protocol: T98G cells, derived from a human glioblastoma, were obtained from the ECACC (European Collection of Cell Cultures). The cells were grown according to the manufacturer’s protocol in minimum essential medium (MEM, Gibco) supplemented with 2 mM L-glutamine (Gibco), 0.1 mM NEAA (Gibco), 10% heat inactivated FBS (Gibco), 0.05 mg/ml penicillin (Gibco), 0.05 mg/ml streptomycin (Gibco) and 0.1 mg/ml neomycin (Gibco) in a humified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated using TRIzol reagent (Life Technologies). The cDNA synthesis was performed from 10 µg of total RNA  using ImProm RT-IITM reverse transcriptase (Promega)

treatment_protocol: The WWOX gene cDNA was introduced into T98G glioblastoma cells by a retroviral transfection. The pLNCX2 retroviral vector with cloned WWOX was produced in the PT67 packaging line. Target cells were grown to 30% confluence and infected with the viruses (approximately 106 CFU/ml) suspended in culture medium with Polybrene as vehicle (8 μg/ml, Sigma Aldrich). After 24 h, medium was replaced, and stable transfectants were selected with 400 μg/ml G418 (Sigma Aldrich) for 3 weeks. Pool of stable transfectants was used for a microarray study of global gene expression and biological experiments. Transfection efficiency was confirmed by real-time RT-PCR and Western Blot.

tag: treatment

value: WWOX transfection

tag: cell line

label: Cy5, Cy3

source_name: Universal Human Reference RNA (Stratagene)

value: Universal Human Reference RNA composed of total RNA from 10 human cell lines


title: PBMCs rep11

value: Baboon Peripheral blood mononuclear cells


title: whl006

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: cell line

hyb_protocol: GeneChips were hybridizd, washed and stained with the highthroughput Titan protocol.

scan_protocol: GeneChips were scanned using the Titan high-throughput scanner.

data_processing: The data were RMA summarized with Partek Genomics Suite version 6.3

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

growth_protocol: 0.5M cells of each cell line (in 2ml DMEM+10%FBS+PS) were seeded onto 6 well-plate in the presence of DMSO (control) or 56µM of spironolactone.

extract_protocol: The cells were collected by trypsinization (TrypLE Express, Invitrogen). Total RNA were extracted using TRIzol reagent (Invitrogen). 4. 2.5µg of the isolated RNA were used to prepare cDNA using SuperScript VILO cDNA synthesis kit (Invitrogen).

treatment_protocol: SPIR: Cell lines treated with 56uM spironloactone for 3 days, DMSO: Control (vehicle)

value: SPIR


title: PBMCs rep13


title: whl013

description: cell line

value: DMSO


title: PBMCs rep14


title: whl012

description: cell line


title: PBMCs rep12


title: whl014

description: cell line


title: PBMCs rep5


title: PBMCs rep9


title: PBMCs rep7


title: T98G stably transfected with retroviral vector carying WWOX cDNA, replicate 3, 4

tag: sample type


title: Control T98G cells transfected with an empty vector, replicate 3, 4

value: control empty vector transfection


title: Control T98G cells transfected with an empty vector, replicate 1, 2


title: whl004

description: cell line


title: PBMCs rep4


title: PBMCs rep8

value: male


title: whl005

description: cell line


title: whl003

description: cell line


title: whl011

description: cell line


title: PBMCs rep3


title: PBMCs rep6


title: PBMCs rep10


title: PBMCs rep2


title: aTSLPR 2002 Screening pre-challenge

source_name: BAL fluid sample from animal 2002 at preChallenge timept (Screening)

value: Screening

value: pre-challenge

value: baseline


title: Cortical Bone rep13

source_name: Baboon cortical bone

treatment_protocol: Cortical bone samples were collected from the midshaft of the left femur and frozen using liquid nitrogen. The bone tissue was pulverized using a BioPulverizer ™ (BioSpec Products Inc., Bartlesville, OK) cooled with liquid nitrogen. RNA was isolated from the resulting powdered bone using the QIAGEN RNeasy Lipid Tissue Kit (Qiagen Corp. Inc., Valencia, CA) according to manufacturer’s instructions.

value: Baboon cortical bone


title: Exvivo bone marrow derived M2 macrophage_4

city: Nagoya

first: Kazumi

last: Taguchi

address: Kawasumi-1, Mizuho-cho, Mizuho-ku

department: Nephro-urology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description: Gene expression after IL-4/M-CSF stimulated

hyb_protocol: Cy3 labbeled cRNA was hybridyzed for 17 hours on SurePrint G3 Mouse GE Microarray ( 8×60K ) slides using Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Softwarev.10.7.3.1 (Agilent) using default parameters.

source_name: Bone marrow derived M2 macrophage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the SureTag DNA Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Micro kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. Then cDNA was synthesized using Ovation® PicoSL WTA System V2 (NuGEN, San Carlos, CA) .RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: B6C3Fe a/a-Csf1op/J wild type/homozygous mice were admistered 80mg/kg gyyoxylate (GOX) for 6days, then The Kidneys were extracted and sorted CD11b+/CD11c+ macrophages using autoMACS.

value: B6C3Fe a/a-Csf1op/J

value: bone marrow


title: Exvivo bone marrow derived M2 macrophage_2


title: PBMCs rep1


title: Cortical Bone rep14


title: Exvivo bone marrow derived M1 macrophage_4

description: Gene expression after LPS/GM-CSF stimulated

source_name: Bone marrow derived M1 macrophage


title: Cortical Bone rep12


title: Exvivo bone marrow derived M2 macrophage_3


title: Cortical Bone rep15


title: Cortical Bone rep4


title: Exvivo bone marrow derived M1 macrophage_3


title: Cortical Bone rep8


title: Cortical Bone rep11


title: Cortical Bone rep5


title: Cortical Bone rep7


title: Wild type renal macrophage for 6days GOX injection_4

description: Gene expression after GOX treated for 6 days

source_name: Wild type renal macrophage

value: kidney


title: Exvivo bone marrow derived M1 macrophage_2


title: Cortical Bone rep9


title: op/op renal macrophage for 6days GOX injection_1

source_name: op/op renal macrophage


title: Δrse2-Δrse3 s mat - Replicate 2

city: Gif-sur-Yvette

first: Annie

last: Sainsard-Chanet

address: Allée de la Terrasse

department: Régulation et Compartimentation des Fonctions Cellulaires

country: France

institute: Centre de Génétique Moléculaire du CNRS UPR 3404

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

source_name: Δrse2-Δrse3 s

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: P. anserina strains used in this study are the wild type s mat- , rse2Y326D mat-, rse3G642V mat-, rse2Y326D-rse3G642V mat-, Δrse2 mat-, Δrse3 mat- and Δrse2-Δrse3 mat-. Growth was carried out on a minimal synthetic medium at 27°C (http://podospora.igmors.u-psud.fr/methods.php)

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) placed on square Petri-dishes (10 cm wide). In order to collect sufficient amounts of biological materials (20 to 100 mg), 4 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

value: Δrse2-Δrse3 s

tag: mating type

value: mat -

tag: growth condition

value: harvested after 48 hours of growth in darkness, on M2 media covered with a sheet of cellophane

source_name: Common reference (pool of four condition M48h, M96h, C48h and C96h)

tag: biosource 1 growth conditon

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane

tag: name biosource 1

tag: biosource 2 growth conditon

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3 growth conditon

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

tag: biosource 4 growth conditon

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name biosource 4


title: Δrse2-Δrse3 s mat - Replicate 1

description: pool of four condition M48h, M96h, C48h and C96h

tag: strain


title: op/op renal macrophage for 6days GOX injection_2

tag: tissue


title: op/op renal macrophage for 6days GOX injection_4


title: Cortical Bone rep10

tag: gender

value: female


title: Wild type renal macrophage for 6days GOX injection_1


title: Δrse2-Δrse3 s mat - Replicate 4


title: Wild type renal macrophage for 6days GOX injection_2


title: Cortical Bone rep6

tag: age (yrs)


title: Δrse2-Δrse3 s mat - Replicate 3


title: Cortical Bone rep3


title: Δrse3 s mat - Replicate 3

source_name: Δrse3 s

value: Δrse3 s


title: Δrse3 s mat - Replicate 4


title: Cortical Bone rep2


title: CLL-1 24h capped 2

city: Gent

first: Valerie

last: Pede

address: De Pintelaan 185

country: Belgium

institute: Ghent University

data_processing: The data were normalized using quantile normalization from the ‘affy’ package using Rgui statistical language

source_name: Enriched CD19+ B-cells

label_protocol: Standard Illumina labeling protocol

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from blood drawn in EDTA tubes on a Lymphoprep. Cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with penicillin (100 U ml-1), streptomycin (100 mug ml-1) and 10% heat-inactivated fetal calf serum at a humidified atmosphere of 37 °C containing 7% (v/v) CO2  layer

extract_protocol: Total cellular RNA was extracted using the miRNeasy kit

treatment_protocol: CD19-selection, electroporation with 40 ug ZAP-70 capped or uncapped mRNA, BCR stimulation (16h post electroporation) using anti-IgM immunobeads

tag: patient nr

tag: time

tag: treatment

value: electoporated with capped ZAP-70 mRNA


title: Δrse3 s mat - Replicate 2

tag: mating type


title: Δrse2 s mat - Replicate 1

source_name: Δrse2 s

value: Δrse2 s

tag: growth condition


title: rse2Y326D-rse3G642V s mat - Replicate 4

source_name: rse2Y326D-rse3G642V s

value: rse2Y326D-rse3G642V s

tag: biosource 1 growth conditon


title: Δrse2 s mat - Replicate 3

tag: name biosource 1


title: CLL-2 24h capped


title: Δrse2 s mat - Replicate 4

tag: biosource 2 growth conditon


title: Δrse3 s mat - Replicate 1

tag: name biosource 2


title: CLL-3 24h capped


title: VV000861_up

city: Seoul

first: Jin Hwan

last: Park

address: Gwanak-ro 599

country: South Korea

institute: Seoul National University

description: Identification of c-di-GMP-regulated genes in V. vulnificus

hyb_protocol: 1) Activate slide in pre-Hybridization buffer for 30-60 min at 42°C. 2) Wash the slide with D.W.. 3) Dry the slide with centrifugation (700 rpm) for 5 min. 4) Add the 35 µl of hybridization buffer into the dried labeled sample tube. 5) Denaturation (95°C, 5min). 6) Centrifuge for 2 min at 11,000 rpm. 7) Mix two labeled samples well. 8) Attach the MAUI lid (heating 65°C). 9) Inject the labeled samples. 10) Sealing. 11) Mix in Lid + slide MAUI Hybridization system (42°C, 16 hrs).

scan_protocol: After hybridization, the arrays were washed, dried and scanned using GenePix 4000B (Axon Instruments, Foster City, CA).

data_processing: Data from three independent experiments were normalized and then analyzed using the GenePix Pro 3.0 software (Axon Instruments).

organism: Vibrio vulnificus CMCP6

source_name: Total cellular RNA from the V. vulnificus cells grown under normal c-di-GMP condition

label_protocol: To synthesize aminoallyl-cDNA, reactions were performed with an Amino Allyl cDNA Labeling Kit (Ambion, Austin, TX) according to the manufacturer’s procedures with 50 µg of total RNA. The aminoallyl-cDNA from the cells grown under normal c-di-GMP condition and the cells grown under high c-di-GMP condition were respectively labeled with Cy3 or Cy5 (Ambion).

growth_protocol: The V. vulnificus strains containing pJH0311 (control empty vector) or pJN1002 (pJH0311 with dcpA, diguanylate cyclase) were grown in AB (autoinducer bioassay) medium.

extract_protocol: Total cellular RNA from the V. vulnificus strains grown to OD600 0.7 was isolated using an RNeasy® Mini Kit (Qiagen, Valencia, CA) and any residual DNA was removed using DNase I (NEB, Ipswich, MA).

source_name: Total cellular RNA from the V. vulnificus cells grown under high c-di-GMP condition


title: CLL-3 24h uncapped

value: electoporated with uncapped ZAP-70 mRNA


title: VV000862_dn


title: Δrse2 s mat - Replicate 2

tag: biosource 3 growth conditon


title: rse2Y326D-rse3G642V s mat - Replicate 3

tag: name biosource 3


title: VV000862_up


title: CLL-8 24h capped


title: CLL-1 24h uncapped 2


title: Cortical Bone rep1

value: Baboon cortical bone


title: CLL-4 24h capped


title: VV000861_dn


title: VV000860_up


title: rse2Y326D-rse3G642V s mat - Replicate 2

tag: biosource 4 growth conditon


title: VV000860_dn


title: CLL-8 24h uncapped


title: rse2Y326D-rse3G642V s mat - Replicate 1

tag: name biosource 4


title: CLL-4 24h uncapped


title: CLL-1 24h uncapped


title: rse3G642V s mat - Replicate 4

source_name: rse3G642V s

tag: strain

value: rse3G642V s


title: CLL-1 24h capped


title: pCR+npCR mamma breast cancer BC_5342587013_F

city: Amsterdam

first: Jelle

middle: Johannes

last: ten Hoeve

address: Plesmanlaan 121

department: Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing: The data were between-array normalised using simple scaling (SSN) subsequently log2 transformed

source_name: 14G core needle breast tumor biopsy

label_protocol: Total RNA was amplified and biotin labeled using the Illumina® TotalPrep™-96 RNA kit. All steps were performed according to standard protocol.

extract_protocol: From the frozen biopsies approximately 30 sections of 30-μm thickness were used for total RNA isolation with RNABee (Campro Scientific, Amersfoort, The Netherlands). Isolated total RNA was subsequently DNase-treated by using the Qiagen RNase-free DNase kit and RNeasy spin columns (Qiagen, West Sussex, U.K.) and dissolved in RNase-free H2O.

tag: response breast

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

tag: response

value: NOCR [No complete response]

tag: ihc er percentage

tag: ihc pr percentage

tag: intrinsic molecular subtype

value: Normal

value: PTC

tag: clinical subtype

tag: tissue

value: breast cancer tumor


title: pCR+npCR mamma breast cancer BC_5342587008_A

value: CR [(pathological) complete response]

tag: treatment


title: pCR+npCR mamma breast cancer BC_5342587014_E

value: CR+kl [(pathological) complete response breast, positive lymph nodes]


title: CLL-3 3h uncapped

tag: patient nr

tag: time

value: 3 h


title: CLL-1 3h uncapped 2


title: rse3G642V s mat - Replicate 3

tag: mating type

value: mat -

tag: growth condition

value: harvested after 48 hours of growth in darkness, on M2 media covered with a sheet of cellophane

tag: biosource 1 growth conditon

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane

tag: name biosource 1

tag: biosource 2 growth conditon

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: rse3G642V s mat - Replicate 2

tag: name biosource 2

tag: biosource 3 growth conditon

tag: name biosource 3

tag: biosource 4 growth conditon

tag: name biosource 4


title: pCR+npCR mamma breast cancer BC_5342587027_E

tag: response breast

tag: response

tag: ihc er percentage

tag: ihc pr percentage


title: pCR+npCR mamma breast cancer BC_5342587009_A

tag: intrinsic molecular subtype

tag: treatment

tag: clinical subtype

tag: tissue


title: NA breast cancer BC_5342587015_D

value: NA [Not Available]

value: NE [Not evaluable]


title: rse2Y326D s mat - Replicate 3

source_name: rse2Y326D s

tag: strain

value: rse2Y326D s

tag: mating type

tag: growth condition


title: pCR+npCR mamma breast cancer BC_5357957045_C

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

value: LumB


title: pCR+npCR mamma breast cancer BC_5342587008_F


title: pCR+npCR mamma breast cancer BC_5342587009_E


title: pCR+npCR mamma breast cancer BC_5357957053_E


title: CLL-2 3h capped

tag: patient nr

tag: time

value: electoporated with capped ZAP-70 mRNA


title: CLL-1 3h capped 2


title: rse3G642V s mat - Replicate 1

value: rse3G642V s

tag: biosource 1 growth conditon

tag: name biosource 1

tag: biosource 2 growth conditon

tag: name biosource 2

tag: biosource 3 growth conditon


title: CLL-2 3h uncapped

value: electoporated with uncapped ZAP-70 mRNA


title: CLL-8 3h uncapped


title: rse2Y326D s mat - Replicate 4

tag: name biosource 3

tag: biosource 4 growth conditon

tag: name biosource 4


title: rse2Y326D s mat - Replicate 2


title: pCR+npCR mamma breast cancer BC_5357957044_B

tag: response breast

tag: response

value: CR [(pathological) complete response]

tag: ihc er percentage

tag: ihc pr percentage

tag: intrinsic molecular subtype

value: Basal

value: PTC

value: breast cancer tumor


title: PR+NR breast cancer BC_5357957054_C

value: PR+NR [Partial Response + No Response]

value: NOCR [No complete response]

tag: treatment

tag: clinical subtype

tag: tissue


title: rse2Y326D s mat - Replicate 1

tag: strain

tag: mating type

value: mat -

tag: growth condition

value: harvested after 48 hours of growth in darkness, on M2 media covered with a sheet of cellophane

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: PR+NR breast cancer BC_5357957052_D

value: Normal


title: CLL-8 3h capped

tag: patient nr

tag: time

value: 3 h


title: CLL-1 3h uncapped


title: pCR+npCR mamma breast cancer BC_5357957053_A

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

value: CR+kl [(pathological) complete response breast, positive lymph nodes]

value: LumA


title: Wilde type s mat -  Replicate 2

source_name: Wilde type s

value: Wilde type s

tag: biosource 1 growth conditon

tag: name biosource 1

tag: biosource 2 growth conditon

tag: name biosource 2

tag: biosource 3 growth conditon

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: pCR+npCR mamma breast cancer BC_5357957054_A

tag: response breast

tag: response


title: CLL-4 3h capped

value: electoporated with capped ZAP-70 mRNA


title: Wilde type s mat -  Replicate 3

tag: name biosource 3

tag: biosource 4 growth conditon

tag: name biosource 4


title: pCR+npCR mamma breast cancer BC_4560224029_D

tag: ihc er percentage

tag: ihc pr percentage

tag: intrinsic molecular subtype

tag: treatment

value: PTC

tag: clinical subtype


title: pCR+npCR mamma breast cancer BC_4560224015_B

value: CR [(pathological) complete response]

tag: tissue

value: breast cancer tumor


title: pCR+npCR mamma breast cancer BC_4560224029_C


title: pCR+npCR mamma breast cancer BC_4560224027_C

value: NOCR [No complete response]


title: LNCaP REST siRNA3

city: Copenhagen

first: Charlotte

last: Svensson

state: Please select one

address: Blegdamsvej 3

department: Novo Nordisk foundation center for protein research

country: Denmark

institute: University of copenhagen

description:
rest knockdown
LNCaP transfected with REST siRNA3

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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LNCaP REST siRNA3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LNCaP cells were transfected with control and REST siRNA, harvested 3 days after transfection

extract_protocol: Qiagen's RNAeasy RNA extraction kit

treatment_protocol: No treatment

tag: cell line

value: LNCaP

value: REST knockdown


title: Wilde type s mat -  Replicate 1

tag: strain

tag: mating type

value: mat -

tag: growth condition

value: harvested after 48 hours of growth in darkness, on M2 media covered with a sheet of cellophane

tag: biosource 1 growth conditon

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane


title: PR+NR breast cancer BC_4560224064_D

value: PR+NR [Partial Response + No Response]

value: Normal


title: Wilde type s mat -  Replicate 4

tag: name biosource 1

tag: biosource 2 growth conditon

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3 growth conditon


title: pCR+npCR mamma breast cancer BC_5357957058_E

tag: response breast

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

tag: response


title: pCR+npCR mamma breast cancer BC_4560224035_C

tag: ihc er percentage

value: LumA


title: CLL-4 3h uncapped

tag: patient nr

tag: time

value: 3 h

value: electoporated with uncapped ZAP-70 mRNA


title: LNCaP REST siRNA2

description:
rest knockdown
LNCaP transfected with REST siRNA2

source_name: LNCaP REST siRNA2

tag: treatment


title: CLL-1 3h capped

value: electoporated with capped ZAP-70 mRNA


title: LNCaP REST siRNA1

description:
rest knockdown
LNCaP transfected with REST siRNA1

source_name: LNCaP REST siRNA1


title: pCR+npCR mamma breast cancer BC_5357957058_C

tag: ihc pr percentage

tag: intrinsic molecular subtype

value: LumB

value: PTC

tag: clinical subtype


title: pCR+npCR mamma breast cancer BC_4560224027_B

value: CR [(pathological) complete response]

tag: tissue

value: breast cancer tumor


title: LNCaP Control siRNA

description:
control knockdown
LNCaP transfected with Control siRNA4

source_name: LNCaP Control siRNA

tag: cell line

value: LNCaP

value: control


title: pCR+npCR mamma breast cancer BC_4560224053_E


title: LNCaP_ DCC+R1881_2

description:
androgen status, positive
LNCaP grown in DCC medium treated with R1881_2

source_name: LNCaP cells, DCC serum containing medium, R1881 treated

growth_protocol: LNCaP cells wre grown in RPMI1648 supplemented with 10%FBS or alternatively supplemented with 5% dextran-coated charcoal stripped(DCC) FBS.

treatment_protocol: Steroid depletion was achieved by incubating with DCC containing medium for 5 days and treatment of DCC cultured cells with synthestic androgen (R1881, 10nM) was perfomed overnight (16h).

value: DCC serum containing medium + R1881 treated