title: colorectal cancer cell line, SW948

source_name: ECACC(Supplier ID 91030714)


title: colorectal cancer cell line, TC71

status: Public on Jul 07 2017

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: SST RMA expression values at the gene-level derived using Expression Console software

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing:
Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Received from INSERM, R. Hamelin, Paris

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

growth_protocol: Grown in medium according to supplier recommendations with added fetal bovine serum, antibiotics Streptomycin and Penicillin, along with amino acid L-glutamine.

extract_protocol: Total RNA was isolated from cell pellets using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

tag: cell line

tag: sample type

value: colorectal cancer cell line


title: genomic DNA from  psoriatic skin sample 083

type: genomic

city: Hefei

first: Fusheng

last: Zhou

address: No 96 Meishan Road, Hefei, China

country: China

institute: Anhui Medical University

description: psoriatic skin sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: psoriatic skin sample 083

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from skin samples using Omega bio-tek system (D3396-02) according to standard instructions

tag: gender

value: Female

tag: tissue

value: Skin

tag: disease state

value: Psoriasis


title: genomic DNA from  psoriatic skin sample 079

description: psoriatic skin sample

source_name: psoriatic skin sample 079

value: Male


title: genomic DNA from  psoriatic skin sample 085

description: psoriatic skin sample

source_name: psoriatic skin sample 085


title: PS20 whole blood cells_stimulated_rep1

city: Montreal

first: Erwin

last: Schurr

address: 1001 boulevard Decarie

country: Canada

institute: McGill University Health Centre

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R. Probes with Detection P val < 0.05 in at least 3 samples were kept for analysis.

source_name: whole blood cells,stimulated

label_protocol: The 102 RNA samples were labelled using the Illumina TotalPrep RNA Amplification Kit from Ambion

extract_protocol: Total RNA was then extracted employing a modified protocol of the LeukoLOCK RNA extraction kit (Ambion, CA, USA) and cleaned with the RNAeasy kit (Qiagen, Germany)

tag: age

value: female

tag: duration of stimulation

tag: dose


title: PS21 whole blood cells_stimulated_rep1

value: male


title: genomic DNA from  psoriatic skin sample 077

description: psoriatic skin sample

source_name: psoriatic skin sample 077


title: genomic DNA from  psoriatic skin sample 076

description: psoriatic skin sample

source_name: psoriatic skin sample 076


title: colorectal cancer cell line, SW837

source_name: ATCC(Supplier ID CCL-235)


title: PS19 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, SW620

source_name: ECACC(Supplier ID 87051203)


title: PS18 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, SW480

source_name: ECACC(Supplier ID 87092801)


title: genomic DNA from  psoriatic skin sample 074

description: psoriatic skin sample

source_name: psoriatic skin sample 074


title: genomic DNA from  psoriatic skin sample 075

description: psoriatic skin sample

source_name: psoriatic skin sample 075


title: PS17 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, SW48

source_name: ATCC(Supplier ID CCL-231)


title: PS16 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, SW403

source_name: ECACC(Supplier ID 87071008)


title: PS10 whole blood cells_stimulated_rep1


title: PS9 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, SW1116

source_name: ECACC(Supplier ID 87071006)


title: colorectal cancer cell line, RKO

source_name: ATCC(Supplier ID CRL-2577)

value: RKO


title: genomic DNA from  psoriatic skin sample 072

description: psoriatic skin sample

source_name: psoriatic skin sample 072


title: genomic DNA from  psoriatic skin sample 066

description: psoriatic skin sample

source_name: psoriatic skin sample 066


title: PS13 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 073

description: psoriatic skin sample

source_name: psoriatic skin sample 073


title: genomic DNA from  psoriatic skin sample 070

description: psoriatic skin sample

source_name: psoriatic skin sample 070


title: PS15 whole blood cells_stimulated_rep1


title: PS11 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 067

description: psoriatic skin sample

source_name: psoriatic skin sample 067


title: colorectal cancer cell line, SW1463

source_name: ATCC(Supplier ID CCL-234)


title: genomic DNA from  psoriatic skin sample 069

description: psoriatic skin sample

source_name: psoriatic skin sample 069


title: genomic DNA from  psoriatic skin sample 065

description: psoriatic skin sample

source_name: psoriatic skin sample 065


title: colorectal cancer cell line, NCI-H508

source_name: ATCC(Supplier ID CCL-253)


title: PS7 whole blood cells_stimulated_rep1

source_name: whole blood cells,stimulated


title: colorectal cancer cell line, LS1034

source_name: ATCC(Supplier ID CRL-2158)


title: colorectal cancer cell line, LoVo

source_name: ATCC(Supplier ID CCL-229)

value: LoVo


title: PS3 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, LS174T

source_name: ATCC(Supplier ID CL-188)


title: genomic DNA from  psoriatic skin sample 064

description: psoriatic skin sample

source_name: psoriatic skin sample 064


title: genomic DNA from  psoriatic skin sample 063

description: psoriatic skin sample

source_name: psoriatic skin sample 063


title: PS8 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, IS3

source_name: Received from INSERM, R. Hamelin, Paris


title: genomic DNA from  psoriatic skin sample 062

description: psoriatic skin sample

source_name: psoriatic skin sample 062


title: colorectal cancer cell line, IS1


title: colorectal cancer cell line, KM12

source_name: NCI60(Supplier ID )


title: PS5 whole blood cells_stimulated_rep1


title: PS2 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 061

description: psoriatic skin sample

source_name: psoriatic skin sample 061


title: genomic DNA from uninvolved psoriatic skin sample 211

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 211


title: PS63_NS whole blood cells_non-stimulated_rep51

source_name: whole blood cells,non-stimulated


title: genomic DNA from  psoriatic skin sample 060

description: psoriatic skin sample

source_name: psoriatic skin sample 060


title: colorectal cancer cell line, HT29

source_name: ATCC(Supplier ID HTB-38)


title: colorectal cancer cell line, HCT116

source_name: ATCC(Supplier ID CCL-247)


title: colorectal cancer cell line, HCT15

source_name: ATCC(Supplier ID CCL-225)


title: genomic DNA from uninvolved psoriatic skin sample 210

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 210


title: PS62_NS whole blood cells_non-stimulated_rep50


title: genomic DNA from uninvolved psoriatic skin sample 208

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 208


title: genomic DNA from uninvolved psoriatic skin sample 209

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 209


title: PS1 whole blood cells_stimulated_rep1

source_name: whole blood cells,stimulated


title: PS59_NS whole blood cells_non-stimulated_rep47


title: PS60_NS whole blood cells_non-stimulated_rep48


title: colorectal cancer cell line, HCC2998


title: genomic DNA from uninvolved psoriatic skin sample 207

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 207


title: colorectal cancer cell line, EB

value: EB


title: colorectal cancer cell line, FRI

value: FRI


title: PS6 whole blood cells_stimulated_rep1


title: genomic DNA from uninvolved psoriatic skin sample 205

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 205


title: PS56_NS whole blood cells_non-stimulated_rep45


title: colorectal cancer cell line, DLD-1

source_name: ATCC(Supplier ID CCL-221)


title: colorectal cancer cell line, Colo678

source_name: DSMZ(Supplier ID ACC 194)


title: genomic DNA from uninvolved psoriatic skin sample 202

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 202


title: PS58 whole blood cells_stimulated_rep1


title: genomic DNA from uninvolved psoriatic skin sample 206

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 206


title: PS54_NS whole blood cells_non-stimulated_rep44


title: colorectal cancer cell line, Colo320

source_name: DSMZ(Supplier ID ACC 144)


title: PS52_NS whole blood cells_non-stimulated_rep42


title: PS53_NS whole blood cells_non-stimulated_rep43


title: genomic DNA from uninvolved psoriatic skin sample 201

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 201


title: colorectal cancer cell line, Colo205

source_name: ATCC(Supplier ID CCL-222)


title: PS50_NS whole blood cells_non-stimulated_rep41

source_name: whole blood cells,non-stimulated


title: colorectal cancer cell line, Co115

source_name: Received from INSERM, R. Hamelin, Paris


title: PS49_NS whole blood cells_non-stimulated_rep40


title: colorectal cancer cell line, CL-34

source_name: DSMZ(Supplier ID ACC 520)


title: colorectal cancer cell line, CL-40

source_name: DSMZ(Supplier ID ACC 535)


title: genomic DNA from uninvolved psoriatic skin sample 196

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 196


title: genomic DNA from uninvolved psoriatic skin sample 199

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 199


title: PS44_NS whole blood cells_non-stimulated_rep37


title: genomic DNA from uninvolved psoriatic skin sample 195

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 195


title: genomic DNA from uninvolved psoriatic skin sample 204

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 204


title: genomic DNA from uninvolved psoriatic skin sample 192

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 192


title: PS45_NS whole blood cells_non-stimulated_rep38


title: genomic DNA from uninvolved psoriatic skin sample 200

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 200


title: PS41_NS whole blood cells_non-stimulated_rep34


title: genomic DNA from uninvolved psoriatic skin sample 194

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 194


title: colorectal cancer cell line, CaCo2

source_name: ATCC(Supplier ID HTB-37)


title: PS42_NS whole blood cells_non-stimulated_rep35


title: PS46_NS whole blood cells_non-stimulated_rep39


title: PS40_NS whole blood cells_non-stimulated_rep33


title: genomic DNA from uninvolved psoriatic skin sample 188

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 188


title: PS43_NS whole blood cells_non-stimulated_rep36


title: PS37_NS whole blood cells_non-stimulated_rep31


title: PS38_NS whole blood cells_non-stimulated_rep32


title: genomic DNA from uninvolved psoriatic skin sample 193

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 193


title: genomic DNA from uninvolved psoriatic skin sample 197

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 197


title: genomic DNA from uninvolved psoriatic skin sample 187

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 187


title: genomic DNA from uninvolved psoriatic skin sample 190

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 190


title: PS36_NS whole blood cells_non-stimulated_rep30

source_name: whole blood cells,non-stimulated


title: genomic DNA from uninvolved psoriatic skin sample 191

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 191


title: PS35_NS whole blood cells_non-stimulated_rep29


title: genomic DNA from uninvolved psoriatic skin sample 185

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 185


title: PS34_NS whole blood cells_non-stimulated_rep28


title: PS30_NS whole blood cells_non-stimulated_rep26


title: genomic DNA from uninvolved psoriatic skin sample 176

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 176


title: genomic DNA from uninvolved psoriatic skin sample 184

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 184


title: PS33_NS whole blood cells_non-stimulated_rep27


title: PS29_NS whole blood cells_non-stimulated_rep25


title: genomic DNA from uninvolved psoriatic skin sample 179

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 179


title: PS28_NS whole blood cells_non-stimulated_rep24


title: PS27_NS whole blood cells_non-stimulated_rep23


title: PS26_NS whole blood cells_non-stimulated_rep22


title: genomic DNA from uninvolved psoriatic skin sample 174

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 174


title: PS23_NS whole blood cells_non-stimulated_rep20


title: PS24_NS whole blood cells_non-stimulated_rep21


title: colorectal cancer cell line, CL-11

source_name: DSMZ(Supplier ID ACC 467)


title: Phage-P4_13_rep3

type: SRA

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
Phage RNA recovered after 13min post infection
processed data file: Phage-infect-P4_T3.5-T13_statistics.xls

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced were mapped to Pseudomonas aeruginosa PAK whole genome sequence or Phage P4 sequence complemented by the manually annotated ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES -l 20
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 13M value as a reference for reporting the expression data of 0M.
Genome_build: Pseudomonas aeruginosa PAK (KK037225.1), Pseudomonas phage PAK_P4 (NC_022986)
Supplementary_files_format_and_content: Genome annotation (Gene ID), Raw Counts (0M, 13M), Normalized Counts (0M, 13M), Statistics (FC, pvalue, significant)

organism: Pseudomonas phage PAK_P4

source_name: Pseudomonas phage PAK P4

growth_protocol: Pseudomonas cells were grown in LB supplemented with 10mM MgCl2 at 37°C until OD600nm   ̴ 0,3

extract_protocol:
Cells were then lyzed in TRIzol,® total RNA was purified through a standard organic extraction and ethanol precipitation followed by DNase treatment (TURBO DNAse®) and rRNA depletion (Ribo-Zero rRNA Removal Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols using the Truseq stranded RNA seq kit.

treatment_protocol: Synchronous infection with bacteriophage PAK_P4 for 0min, 3,5min or 13min (MOI = 50) and halted by rapid cooling in diluted phenol

tag: subsp.

value: phage PAK

tag: strain

tag: time point

value: 13 min post infection


title: Phage-P4_13_rep2


title: Host-P4_13_rep1

description:
Host RNA recovered after 13min post infection
processed data file: Host-infect-P4_T0-T13_statistics.xls

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PAK

value: Host PAK

value: PAK


title: SigB4-cy5_WT4-cy3

description: Biological replicate 4 of 4.

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: sigB mutant grown 10h TY

label_protocol: 5 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strain C630E WT and sigB mutant were grown in TY

extract_protocol: Total RNA was extracted using QIAgen RNAeasy kit.

value: C630E Mullany

tag: genotype/variation

source_name: WT grown 10h TY

value: WT


title: genomic DNA from uninvolved psoriatic skin sample 175

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 175


title: SigB2-cy5_WT2-cy3

description: Biological replicate 2 of 4.


title: Phage-P4_13_rep1


title: genomic DNA from uninvolved psoriatic skin sample 171

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 171


title: Phage-P4_3.5_rep3

description:
Phage RNA recovered after 3.5min post infection
processed data file: Phage-infect-P4_T3.5-T13_statistics.xls

value: 3.5 min post infection


title: Host-P4_0_rep3

description:
Host RNA recovered after 0min post infection
processed data file: Host-infect-P4_T0-T13_statistics.xls

value: 0 min post infection


title: PS22_NS whole blood cells_non-stimulated_rep19


title: Host-P4_0_rep2


title: Phage-P4_3.5_rep2


title: genomic DNA from uninvolved psoriatic skin sample 172

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 172

value: Female

value: Skin


title: Host-P4_0_rep1


title: Phage-P4_3.5_rep1


title: genomic DNA from uninvolved psoriatic skin sample 166

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 166

value: Male

value: Psoriasis


title: genomic DNA from uninvolved psoriatic skin sample 170

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 170


title: Host-P4_13_rep3


title: SigB1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: genomic DNA from uninvolved psoriatic skin sample 168

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 168


title: genomic DNA from uninvolved psoriatic skin sample 165

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 165


title: SigB3-cy3_WT3-cy5

description: Biological replicate 3 of 4.


title: Host-P4_13_rep2


title: TN Breast cancer stromal sample 70

status: Public on Jul 06 2017

first: Morag

last: Park

state: QC

address: The Cancer Research Building 1160 Pine Avenue, Room 602

institute: Mcgill University

description: Tumor stromal sample isolated via laser capture microdissection

hyb_protocol: Agilent Technlogies SurePrint G3 Hmn GE 8x60K Microarrays (Cat#G4851A) were used for all experiments. RNA samples (300 ng) were subjected to fragmentation followed by 17 h hybridization, washing, and scanning (Agilent Technologies, model G2505C) according to the manufacturer’s protocol (manual ID #G4140-90050). Cy3-labeled samples were hybridized against Cy5-labeled Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA).

scan_protocol: Scanned on Agilent G2505C scanner according to the manufacturer’s protocol (manual ID #G4140-90050).

data_processing: Microarray data were feature extracted using Agilent Feature Extraction Software (v. 10.7.3.1) with the default parameters. R/Bioconductor (vers 3.20; Bioconductor 3.1) and the limma package were used for loading the data and normalization, where loess was applied for dye bias correction, and quantile normalization was used across arrays. Replicates of non-control probes were aggregated by taking their mean value.

source_name: Reference

label_protocol: For samples (ch1), 100 pg to 5 ng of total RNA was subjected to two rounds of T7 linear amplification using the Arcturus® RiboAmp® HS PLUS Kit (Catalog number: KIT0525) and labeled with Cy3 dye (Arcturus® Cy3 Turbo Labeling™ Kit Catalog number: KIT0609)  according to the manufacturer’s protocol. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA). For reference (ch2), RNA was subjected to two rounds of T7 linear amplification using the Arcturus® RiboAmp® HS PLUS Kit (Catalog number: KIT0525) and labeled with Cy5 dye (Arcturus® Cy3 Turbo Labeling™ Kit Catalog number: KIT0610)  according to the manufacturer’s protocol. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

extract_protocol: Tumor epithelium and stroma were separately microdissected from tissue samples using a PixCell IIe LCM system (Arcturus). All microdissections were performed within three hours of tissue staining. Total RNA was extracted from each population of microdissected cells using an Arcturus PicoPure RNA Isolation Kit (Cat# 12204-01).

treatment_protocol: Tissue compartments isolated from OCT-embedded frozen human tissue samples by laser capture microscopy following HistoGene staining and pathologist's evaluation

value: Universal Human Reference RNA (Stratagene)

source_name: microdissected TNBC stromal tissue

tag: event

value: FALSE

tag: er

value: Negative

tag: grade

value: High

tag: lymph

tag: chemo

value: Yes

tag: tamoxifen

value: No

tag: herceptin

tag: size

value: Tumor-stroma

tag: replicate

value: TRUE


title: genomic DNA from uninvolved psoriatic skin sample 169

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 169

tag: gender

tag: tissue

tag: disease state


title: genomic DNA from uninvolved psoriatic skin sample 161

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 161


title: genomic DNA from uninvolved psoriatic skin sample 177

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 177


title: TN Breast cancer stromal sample 62

tag: sample type

value: Positive

tag: age


title: TN Breast cancer stromal sample 67


title: genomic DNA from uninvolved psoriatic skin sample 167

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 167


title: TN Breast cancer stromal sample 59

description: Adjacent normal stromal sample isolated via laser capture microdissection

value: Normal-Stroma


title: TN Breast cancer stromal sample 57


title: TN Breast cancer stromal sample 64


title: TN Breast cancer stromal sample 65


title: TN Breast cancer stromal sample 68


title: genomic DNA from uninvolved psoriatic skin sample 163

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 163


title: genomic DNA from uninvolved psoriatic skin sample 173

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 173


title: TN Breast cancer stromal sample 66


title: TN Breast cancer stromal sample 60


title: TN Breast cancer stromal sample 69


title: TN Breast cancer stromal sample 63


title: genomic DNA from uninvolved psoriatic skin sample 164

description: uninvolved psoriatic skin sample

source_name: uninvolved psoriatic skin sample 164


title: TN Breast cancer stromal sample 58


title: TN Breast cancer stromal sample 61


title: TN Breast cancer stromal sample 56


title: TN Breast cancer stromal sample 55


title: TN Breast cancer stromal sample 53


title: TN Breast cancer stromal sample 54


title: TN Breast cancer stromal sample 47


title: TN Breast cancer stromal sample 52


title: TN Breast cancer stromal sample 50


title: TN Breast cancer stromal sample 44


title: TN Breast cancer stromal sample 48


title: TN Breast cancer stromal sample 45


title: TN Breast cancer stromal sample 36


title: TN Breast cancer stromal sample 41

value: Intermediate


title: TN Breast cancer stromal sample 51


title: TN Breast cancer stromal sample 33


title: TN Breast cancer stromal sample 43


title: TN Breast cancer stromal sample 46


title: TN Breast cancer stromal sample 49


title: TN Breast cancer stromal sample 40


title: TN Breast cancer stromal sample 39


title: TN Breast cancer stromal sample 38


title: TN Breast cancer stromal sample 35


title: TN Breast cancer stromal sample 37


title: TN Breast cancer stromal sample 42


title: TN Breast cancer stromal sample 34


title: TN Breast cancer stromal sample 31


title: TN Breast cancer stromal sample 28


title: TN Breast cancer stromal sample 22


title: TN Breast cancer stromal sample 25


title: TN Breast cancer stromal sample 29


title: TN Breast cancer stromal sample 21


title: TN Breast cancer stromal sample 30


title: TN Breast cancer stromal sample 26


title: TN Breast cancer stromal sample 20


title: TN Breast cancer stromal sample 32


title: TN Breast cancer stromal sample 18


title: TN Breast cancer stromal sample 11


title: TN Breast cancer stromal sample 19


title: TN Breast cancer stromal sample 14


title: TN Breast cancer stromal sample 23


title: TN Breast cancer stromal sample 17


title: TN Breast cancer stromal sample 27


title: TN Breast cancer stromal sample 12


title: TN Breast cancer stromal sample 9


title: TN Breast cancer stromal sample 15


title: TN Breast cancer stromal sample 16


title: TN Breast cancer stromal sample 24


title: TN Breast cancer stromal sample 10


title: TN Breast cancer stromal sample 13


title: TN Breast cancer stromal sample 6


title: TN Breast cancer stromal sample 7


title: TN Breast cancer stromal sample 8


title: TN Breast cancer stromal sample 5

value: ND


title: TN Breast cancer stromal sample 4


title: TN Breast cancer stromal sample 3


title: TN Breast cancer stromal sample 1


title: ZD6474 resistant human xenograft 1

city: Houston

first: Tina

last: Cascone

state: TX

address: 1515 Holcombe Blvd.

department: Cancer Medicine

country: USA

institute: UT MD Anderson Cancer Center

description: replicate 1

hyb_protocol: Each of 1.5 ug of biotinylated cRNAs was hybridized to both human WG-6 v3.0 and mouse WG-6 v2.0 Expression BeadChips Illumina microarrays at the same time.  Each of 1.5 ug of biotinylated cRNAs was hybridized to both Illumina Human WG-6 V3 and Mouse WG-6 V2 microarrays at the same time.

scan_protocol: Signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Health care Bio-Sciences, Little Chalfont, UK). Gene expression data were collected by using Illumina bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc.)

data_processing: Quantile normalization was performed on the average signal intensity values of the probes. The normalized expression data were logarithm transformed (base 2) for further analysis.

source_name: Mouse xenograft

label_protocol: Biotin labeled cRNA samples for hybridization were prepared by using Illumina Total Prep RNA Amplification Kit (Ambion Inc., Austin, TX). One microgram of total RNA was used for the synthesis of cDNA and followed by an amplification and biotin labeling.

extract_protocol: Total RNA was isolated from the cancer tissues by using mirVanaTM miRNA isolation Kit (Ambion Inc., Austin, TX) according to manufacturer’s protocol.

treatment_protocol: H1975 lung adenocarcinoma cells (2.0 × 106 per mouse) were injected subcutaneously into male athymic nude mice (NCI-nu). When tumor volumes reached ~ 270 mm3, mice were treated with either AZD2171 (cediranib) 6 mg/kg p.o. daily or ZD6474 (vandetanib) 50 mg/kg p.o. daily. Tumor xenografts were considered resistant when their volume tripled compared to pretreatment volume. Parallel short-term treatment (14 days) studies were conducted when tumor volumes reached ~350 mm3 (sensitive).

tag: mouse host strain

value: Nci-nu

value: tumor xenograft


title: TN Breast cancer stromal sample 2


title: ZD6474 sensitive human xenograft 3

description: replicate 3


title: AZD2171 resistant human xenograft 1

description: replicate 1


title: ZD6474 resistant human xenograft 2

description: replicate 2


title: AZD2171 resistant human xenograft 3

description: replicate 3


title: ZD6474 sensitive human xenograft 1

description: replicate 1


title: AZD2171 resistant human xenograft 2

description: replicate 2


title: ZD6474 sensitive human xenograft 2

description: replicate 2


title: AZD2171 sensitive human xenograft 2

description: replicate 2


title: AZD2171 sensitive human xenograft 3

description: replicate 3


title: AZD2171 sensitive human xenograft 1

description: replicate 1


title: SAV-rep3

city: Loughborough

first: Neil

last: Graham

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Samples were hybridised at the NASC microarray core facility according to manufactures' instructions. GeneChips were washed and stained in the Affymetrix Fluidics station 450.

scan_protocol: Scanning was performed accordinf to manufactures' instruction using an Affymetrix 3000 7G scanner

data_processing: RNA data was analysed using Genespring GX 11 software (Agilent technologies) using the RMA probe sumarisation algorithm. Each gene signal was then normalised to the median of the gene signal across all samples

organism: Brassica oleracea

source_name: Fully expanded leaf from 8 week old plant

label_protocol: RNA was amplified, fragmented and labeled using the Ambion WT expression kit.

growth_protocol: Plants were gerown in 17 cm pots containing a peat based compost (Lentse potgrond)

extract_protocol: Qiagen RNAeasy kit as per manufactures instructions

tag: variety

value: Savoy cabbage

value: 8 weeks

value: fully expanded leaf


title: WIN7-rep1

value: Winspit 7


title: ZD6474 sensitive mouse xenograft 3

description: replicate 3

organism: Mus musculus

tag: strain

value: stroma


title: ZD6474 sensitive mouse xenograft 1

description: replicate 1


title: PSB-rep4

value: Purple sprouting Broccoli


title: AZD2171 resistant mouse xenograft 3

description: replicate 3


title: ZD6474 sensitive mouse xenograft 2

description: replicate 2


title: ZD6474 resistant mouse xenograft 1

description: replicate 1


title: WIN9-rep1

value: Winspit 9


title: ZD6474 resistant mouse xenograft 2

description: replicate 2


title: SAV-rep4


title: SAV-rep1


title: WIN14-rep1

value: Winspit 14


title: PSB-rep2


title: AZD2171 sensitive mouse xenograft 2

description: replicate 2


title: AZD2171 resistant mouse xenograft 2

description: replicate 2


title: AZD2171 sensitive mouse xenograft 1

description: replicate 1


title: PSB-rep3


title: SAV-rep2


title: WIN5-rep1

value: Winspit 5


title: PSB-rep1


title: AZD2171 resistant mouse xenograft 1

description: replicate 1


title: AZD2171 sensitive mouse xenograft 3

description: replicate 3


title: ketamine_3

city: Miami

first: Eléonore

last: Beurel

state: FL

address: 1011 NW 15th Street

department: Departments of Psychiatry and Biochemistry

institute: University of Miami

description:
Array C, blocks 17-24 of raw data file
741C_600_H23

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon Genepix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split in to four subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 10327 features on each microarray by subtracting the median local background from the median local foreground for each spot. Detection Thresholds for each array were determined by calculating the 10% trim mean intensity of the negative controls spots and adding 5X the standard deviation of the background (non-spot area). The spot intensities and the Threshold (T) were transformed by taking the log (base 2) of each value.  The mean probe intensities for each of the 1262 mouse probes on each of the 19 arrays were then determined by averaging the triplicate spot intensities. Spots flagged as poor quality during data extraction were omitted prior to averaging and spots that have an average saturated signal were removed prior to normalization, which yielded 1209 mouse non-saturated probes intensities. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the mouse probes intensities above Threshold in > 90% of samples. The log2-transformed spot intensities for all 10327 features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays.  The 1209 mouse non-control non-saturated log2-transformed, normalized, and averaged probe intensities were filtered to obtain a list of 747 mouse microRNA probes showing probe intensity above Threshold in at least 10% of samples. The data was untransformed using the formula 2^N.

source_name: hippocampus (right)

label_protocol: The samples were DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

extract_protocol: RNA were extracted using the TRIzol method and small RNA concentrated using Ocean ridge method

treatment_protocol: mice were treated intranasally with 10 ug siRNA for GSK3b, or 60 ug L808mts every other day  for 3 days, or with 10 mg/kg ketamine ip  for 24 h, or with 2% lithium chow for 4 weeks  and sacrificed 24 h later, RNA were extracted from hippocampus and sequenced

value: C57BL/6 male adult

tag: treatment

value: ketamine

tag: dose, route, time'

value: 10 mg/kg, ip, 24 h


title: A673/TR/shEF_SI_shMKL1_2_con_2

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm

source_name: Asp14 Clone of Ewing's sarcoma A673 cell line with doxicyclin inducible EWS-FLI1 knockdown construct

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol:
serum-starved overnight+60 minutes of serum-induction (SI) with 20% FBS-DMEM
see growth condition in SAMPLES section

extract_protocol: RNA was extrated using the Qiagen RNeasy extraction kit according to the manufacturer's instructions.

treatment_protocol:
transfected with pLKO sh-MKL-1/2 plasmid
not treated
see treatment in SAMPLES section

tag: cell line

value: A673/TR/shEF clone of A673 EwS cell line stably carrying a doxycycline-inducible sh-EWS-FLI1 construct


title: lithium_2

description:
Array B, blocks 9-16 of raw data file
740B_600_H17

value: lithium

value: in the chow (0.2%)  for 4 weeks


title: lithium_3

description:
Array C, blocks 17-24 of raw data file
740C_600_H18


title: ketamine_2

description:
Array B, blocks 9-16 of raw data file
741B_600_H22


title: lithium_1

description:
Array A, blocks 1-8 of raw data file
740A_600_H16


title: lithium_4

description:
Array D, blocks 25-32 of raw data file
740D_600_H19


title: L803mts_4

description:
Array D, blocks 25-32 of raw data file
739D_600_H15

value: 61 ug, 5 uL/nostril, in, every other day for 3 days


title: ketamine_1

description:
Array A, blocks 1-8 of raw data file
741A_600_H21


title: A673/TR/shEF_starved_shNS_doxy_1

growth_protocol:
serum starved: 0.2% FBS-DMEM overnight
see growth condition in SAMPLES section

treatment_protocol:
transfected with pLKO sh-NS (non silencing) control plasmid
1µg/ml doxycycline for 48 h
see treatment in SAMPLES section


title: A673/TR/shEF_SI_shNS_doxy_1


title: A673/TR/shEF_SI_shMKL1_2_doxy_2

treatment_protocol:
transfected with pLKO sh-MKL-1/2 plasmid
1µg/ml doxycycline for 48 h
see treatment in SAMPLES section


title: L803mts_3

description:
Array C, blocks 17-24 of raw data file
739C_600_H13

value: 60 ug, 5 uL/nostril, in, every other day for 3 days


title: A673/TR/shEF_SI_shMKL1_2_con_1


title: A673/TR/shEF_starved_shMKL1_2_doxy_1


title: L803mts_2

description:
Array A, blocks 1-8 of raw data file
747A_600_H12


title: A673/TR/shEF_starved_shMKL1_2_con_1


title: L803mts_1

description:
Array A, blocks 1-8 of raw data file
739A_600_H11


title: A673/TR/shEF_starved_shMKL1_2_con_2


title: A673/TR/shEF_SI_shNS_con_2

treatment_protocol:
transfected with pLKO sh-NS (non silencing) control plasmid
not treated
see treatment in SAMPLES section


title: A673/TR/shEF_SI_shNS_con_1


title: siGSK3b_4

description:
Array D, blocks 25-32 of raw data file
738D_600_H9

value: siRNA GSK3beta

value: 11 ug, 5 uL/nostril, in, every other day for 3 days


title: siGSK3b_3

description:
Array C, blocks 17-24 of raw data file
738C_600_H8

value: 10 ug, 5 uL/nostril, in, every other day for 3 days


title: A673/TR/shEF_starved_shNS_con_1


title: A673/TR/shEF_starved_shMKL1_2_doxy_2


title: siGSK3b_2

description:
Array B, blocks 9-16 of raw data file
738B_600_H7


title: A673/TR/shEF_starved_shNS_doxy_2


title: A673/TR/shEF_SI_shNS_doxy_2


title: A673/TR/shEF_starved_shNS_con_2


title: A673/TR/shEF_SI_shMKL1_2_doxy_1


title: siGSK3b_1

description:
Array A, blocks 1-8 of raw data file
738A_600_H6


title: control_4

description:
Array D, blocks 25-32 of raw data file
737D_600_H4

value: vehicle

value: 5 uL/nostril, in, every other day for 3 days


title: control_3

description:
Array C, blocks 17-24 of raw data file
737C_600_H3


title: control_2

description:
Array B, blocks 9-16 of raw data file
737B_600_H2


title: control_1

description:
Array A, blocks 1-8 of raw data file
737A_600_H1


title: BP343

status: Public on Jul 04 2017

first: Jeverson

last: Moreira

address: 4 Avenue de l'Observatoire

institute: INSERM

description: Gene expression data from lymphoblastoid cell lines cultured during 4 days in presence/absence of LiCl 1 mM

hyb_protocol: Biotin-labelled sample was then hybridized to GeneChip® miRNA 3,0 microarrays at 48°C for 17 h  and microarrays were washed on the fluidic station FS450 according to the specific manufacturer’s intructions (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The microarrays were washed on the fluidic station FS450 according to the specific manufacturer’s protocols

data_processing: GeneChips were scanned using theAffymetrix GeneArray Scanner GCS3000 7G.

source_name: lymphoblastoid cell line from NR treated 4 days with control

label_protocol: 130 ng of total RNA was biotin-labelled according to the manufacturer’s instructions.

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with 10 % of fetal bovine serum, 1 % penicillin/streptomycin/L-glutamine (Life Technologies®, France)  at 37 °C in the presence of 5 % CO2.

extract_protocol: Total RNA from 5,000000 cells was isolated from cell pellets using miRNeasy Mini Kit (Qiagen®, France)

treatment_protocol: Cell lines were seeded at 200,000 cells/ml into separate flasks, either in the presence of lithium chloride (LiCl) or in a lithium-free medium for 4 days after which cell pellets were collected and frozen at −80 °C

value: bipolar disorder

tag: response phenotype, alda scale

value: non-responders

tag: cell type

value: lymphoblastoid cell line


title: 5753693028_D

status: Public on Jul 05 2017

city: Lebanon

first: Angeline

last: Andrew

state: NH

address: 7927 Rubin Building

institute: Dartmouth

description:
5753693028_D
replicate 2

data_processing: Data were normalized using cubic spline in the Illumina software.

source_name: UROtsa cell line, anti miR-34a

label_protocol: Biotinylated cRNA were prepared  for Illumina arrays

growth_protocol: UROtsa cells were grown in DME (Sigma D6046) modified with 5% FBS, glucose, and Penicillin / Streptomycin.

extract_protocol: RNA was extracted using Trizol reagent followed by  clean-up (Qiagen kit).

treatment_protocol: Cells were transfected with 30nM anti-miR-34a or negative control (Applied Biosystems Inc) using siPort NeoFX reagent (Ambion).

value: UROtsa

value: normal urothelial cells


title: BP268Li

source_name: lymphoblastoid cell line from NR treated 4 days with LiCl 1 mM


title: BP282


title: BB112Li


title: 5753693028_K

description:
5753693028_K
replicate 1

source_name: UROtsa cell line, negative control


title: BP268


title: 5753693028_F

description:
5753693028_F
replicate 2


title: BP343Li


title: BP282Li

hyb_protocol: Biotin-labelled cDNA was then hybridized to GeneChip® Human Gene 2.1ST microarrays at 45°C for 17 h  and microarrays were washed on the fluidic station FS450 according to the specific manufacturer’s intructions (Affymetrix, Santa Clara, CA, USA).

label_protocol: 50 ng of total RNA was reverse-transcribed using the Ovation PicoSL WTA System V2 (NuGEN Technologies, West Cumbria, UK), according to the manufacturer’s instructions.


title: BP026

source_name: lymphoblastoid cell line from ER treated 4 days with control

value: excellent responders


title: BB112


title: BP343Li


title: 5753693028_L

description:
5753693028_L
replicate 1


title: BP026Li

source_name: lymphoblastoid cell line from ER treated 4 days with LiCl 1 mM


title: BP282


title: BB112Li


title: BP282Li


title: BP411


title: BP268Li


title: BP024Li


title: BP380Li


title: BP411Li


title: BP380


title: 5753693028_E

description:
5753693028_E
replicate 2


title: BP343


title: BB112


title: BP268


title: 5753693028_J

description:
5753693028_J
replicate 1


title: BP024


title: BP024Li


title: BP411


title: BP026


title: BP380Li


title: BP026Li


title: BP380


title: BP411Li


title: Oenococcus oeni 217T [OoC3]

status: Public on Jul 03 2017

city: Tarragona

first: Cristina

last: Reguant

state: Tarragona

address: Marcel·lí Domingo 1

department: Biochemistry and Biotechnology

country: Spain

institute: University Rovira i Virgili

description: Oenococcus oeni total RNA from cells in the initial point of fermentation

hyb_protocol: Cy3-labeled DNA was precipitated with 1 volume isopropanol. Hybridization mixture including 2mg labeled DNA was prepared using Nimblegen hybridization kit (cat.#05583683001). 090324_Ooen_exp Nimblegen arrays were hybridized in Nimblegen hybridization system 4 station for 16-18 h at 42ºC, and then washed in 1XWash solution I, II and III (cat.#5584507001).Hybridization buffers and washes were completed according to manufacturer's protocol

scan_protocol: Arrays were scanned on a Genepix 4000B scanner

data_processing: Pair reports (raw data) listing the probe  intensities of the arrays were extracted and processed using Nimblescan software v2.6

organism: Oenococcus oeni

source_name: Oenococcus oeni 217T

label_protocol: dsDNA was generated from 10 mg RNA following Nimblegen array user's guide protocol. 1mg dsDNA was labeled by Klenow random priming with Cy3 nonamers with Nimblegen One-color DNA labeling kit (cat.# 06370411001) following manufacturer's user's guide

growth_protocol: O. oeni was cultured at 30ºC in MRS broth medium supplemented with L-malic acid (4 g l-1) and fructose (5 g l-1) at pH 5.0.

extract_protocol: Total RNA extractions were performed using the Roche RNeasy kit according to the manufacturer’s instructions (Mannheim, Germany).

treatment_protocol: When cultures reached the late exponential phase (OD600nm ≈ 1) they were collected by centrifugation and inoculated in flasks of 500ml with wine like medium (2 g/L fructose, 2 g/L tartaric acid, 0.5 g/L citric acid, 0.6 g/L L-malic acid, 5 g/L yeast extract, 0.1 g/L acetic acid, 5 g/L glycerol and 12 % ethanol v/v, it was adjusted to a pH 3.4 with NaOH 1N)


title: Oenococcus oeni 217T [OoC1]

description: Oenococcus oeni total RNA from cells before inoculation in wine like medium (12% ethanol v/v)


title: BP024


title: Oenococcus oeni 217T [OoC2]

description: Oenococcus oeni total RNA from cells after 1 hour of inoculation in wine like medium (12% ethanol v/v)


title: VLX60_1uM

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description: Gene expression data from HCT116 cells treated with VLX60 for 6 hours.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: colorectal carcinoma cell line HCT116

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

treatment_protocol: HCT116 cells treated with 1 microM VLX60 for 6 hours.

tag: perturbagen

value: small molecule

tag: type

value: treatment

tag: name

tag: concentration

tag: vehicle

value: DMSO

tag: duration


title: Oenococcus oeni 2T2 [OoB3]

source_name: Oenococcus oeni 2T2


title: control_DMSO

description: Gene expression data from HCT116 cells treated with DMSO for 6 hours.

value: control


title: VLX60_2uM

treatment_protocol: HCT116 cells treated with 2 microM VLX60 for 6 hours.


title: Oenococcus oeni 2T2 [OoB2]


title: BE2C_3DBioR_R2

city: Heidelberg

first: Emily

last: Koeneke

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
3DBioR_B
5504654016_G_Grn.idat

scan_protocol: The standard Illumina scanning protocol was used

data_processing: The data were quantile normalized using Illumina BeadStudio Data Analysis Software version v4_r2

source_name: neuroblastoma cells

label_protocol: 1mcg total RNA per sample was amplified and biotin labeled using Invitrogen Illumina total Prep reagents, following the standard protocol

extract_protocol: Total RNA was isolated using the RNeasy MiniKit (Qiagen)

tag: growth conditions

value: grown in 3D scaffolds within a bioreactor system


title: BE2C_3DBioR_R1

description:
3DBioR_A
5504654016_F_Grn.idat


title: BE2C_2D_R3

description:
2D_C
5617835023_C_Grn.idat

value: grown in 2D monolayers


title: BE2C_2D_R2

description:
2D_B
5617835023_B_Grn.idat


title: Oenococcus oeni 2T2 [OoB1]


title: 200643150051_H

city: Singapore

first: Jing Quan

last: Lim

address: 30 Hospital Boulevard

department: CMR

country: Singapore

institute: National Cancer Centre Singapore

description: cholangiocarcinoma

hyb_protocol: 750ng of biotin-labeled cRNA were hybridized on the Illumina HT-12 version 4 beadchip according to Manufacturer’s instruction (Illumina, Inc., San Diego, CA)

scan_protocol: Beadchips were washed and stained according to Manufacturer’s instruction and scanned using Illumina BeadArray Reader (Illumina, Inc., San Diego, CA)

data_processing: GenomeStudio v2011.1 + Gene Expression v1.9.0 (raw - noNormalization and noBackground, normalized - Quantile normalization and noBackground)

source_name: tumor

label_protocol: Biotin-labeled cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion Inc.) from 250ng-500ng of total RNA

extract_protocol: RNA was extracted from tumor tissue using RNeasy mini kit (Qiagen), quantified by measuring Abs260 with a UV spectrophotometer and the quality was assessed with the Agilent 2100 Bioanalyzer

tag: tissue

value: bile duct


title: 200643150051_K

description: cholangiocarcinoma


title: VLX50_10uM

description: Gene expression data from HCT116 cells treated with VLX50 for 6 hours.

treatment_protocol: HCT116 cells treated with 10 microM VLX50 for 6 hours.


title: 200643150051_L

description: cholangiocarcinoma


title: BE2C_Tumor_R3

description:
Tumor_C
5504654016_I_Grn.idat

source_name: neuroblastoma

value: neuroblastoma tumor


title: 200643150051_I

description: cholangiocarcinoma


title: BE2C_Tumor_R1

description:
Tumor_A
5617835013_K_Grn.idat


title: BE2C_3DBioR_R3

description:
3D_BioR_C
5617835013_H_Grn.idat


title: BE2C_3DStatic_R1

description:
3DStatic_A
5504654016_C_Grn.idat

value: grown in 3D scaffolds


title: 200643150051_J

description: cholangiocarcinoma


title: 200643150051_E

description: cholangiocarcinoma


title: BE2C_3DStatic_R3

description:
3DStatic_C
5504654016_E_Grn.idat


title: BE2C_3DStatic_R2

description:
3DStatic_B
5504654016_D_Grn.idat


title: BE2C_Tumor_R2

description:
Tumor_B
5617835013_L_Grn.idat


title: BE2C_2D_R1

description:
2D_A
5617835023_A_Grn.idat


title: Oenococcus oeni 3P2 [OoA3]

source_name: Oenococcus oeni 3P2


title: 200643150051_D

description: cholangiocarcinoma


title: Oenococcus oeni 3P2 [OoA2]


title: Oenococcus oeni 3P2 [OoA1]


title: 200643150051_C

description: cholangiocarcinoma


title: 200643150051_B

description: cholangiocarcinoma


title: 200643150072_L

description: cholangiocarcinoma


title: 200643150051_G

description: cholangiocarcinoma


title: 200643150051_A

description: cholangiocarcinoma


title: 200643150051_F

description: cholangiocarcinoma


title: sCLE skin lesion_H4_015_52_SCLE

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from human sCLE skin lesion

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Human Gene 2.1  ST arrays (Santa Clara, CA) according to the manufacturer protocol.

scan_protocol: GeneChip arrays were scanned by using the Affymetrix GeneTitan system (software version 3.2.4.1515) according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using R software version 3.1.3 using custom CDF version 19 and modified Affymetrix_1.44.1 package from BrainArray: RMA method and Human Entrez Gene custom CDF annotation version 19 were used for the normalization; and Combat for batch correction.

source_name: sCLE skin lesion

label_protocol: Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6) following the manufacturer's protocol.

extract_protocol: Total RNA was isolated using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek) following manufacturer’s instructions.

value: Skin

tag: disease state

value: sCLE


title: sCLE skin lesion_H4_010_47b_SCLE


title: 200643150072_G

description: cholangiocarcinoma


title: 200643150072_I

description: cholangiocarcinoma


title: 200643150072_E

description: cholangiocarcinoma


title: 200643150072_F

description: cholangiocarcinoma


title: 200643150072_D

description: cholangiocarcinoma


title: 200643150072_K

description: cholangiocarcinoma


title: sCLE skin lesion_H4_011_49_SCLE


title: 200643150072_C

description: cholangiocarcinoma


title: 200643150072_B

description: cholangiocarcinoma


title: sCLE skin lesion_H4_001_32r_SCLE


title: 200739030011_L

description: cholangiocarcinoma


title: 200643150072_J

description: cholangiocarcinoma


title: 200643150072_A

description: cholangiocarcinoma


title: 200739030011_K

description: cholangiocarcinoma


title: sCLE skin lesion_H4_012_50_SCLE


title: 200643150072_H

description: cholangiocarcinoma


title: 200739030011_J

description: cholangiocarcinoma


title: sCLE skin lesion_H3_065_SCLE


title: sCLE skin lesion_H3_064_SCLE


title: 200739030011_I

description: cholangiocarcinoma


title: sCLE skin lesion_H3_071_SCLE


title: sCLE skin lesion_H3_063_SCLE


title: 200739030011_G

description: cholangiocarcinoma


title: 200739030011_H

description: cholangiocarcinoma


title: 200739030011_F

description: cholangiocarcinoma


title: sCLE skin lesion_H3_057_SCLE


title: sCLE skin lesion_H3_060_SCLE


title: sCLE skin lesion_H2_012_42r_SCLE


title: sCLE skin lesion_H2_006_36b_SCLE


title: 200739030011_A

description: cholangiocarcinoma


title: 200739030011_C

description: cholangiocarcinoma


title: 200739030011_D

description: cholangiocarcinoma


title: 200739030011_E

description: cholangiocarcinoma


title: 200647550008_L

description: cholangiocarcinoma


title: 200739030011_B

description: cholangiocarcinoma


title: 200647550008_I

description: cholangiocarcinoma


title: 200647550008_K

description: cholangiocarcinoma


title: 200647550008_H

description: cholangiocarcinoma


title: 200647550008_E

description: cholangiocarcinoma


title: 200647550008_J

description: cholangiocarcinoma


title: sCLE skin lesion_H1_022_SCLE


title: sCLE skin lesion_H1_014_SCLE


title: 200647550008_F

description: cholangiocarcinoma


title: 200643150050_L

description: cholangiocarcinoma


title: sCLE skin lesion_H1_019_SCLE


title: 200647550008_B

description: cholangiocarcinoma


title: sCLE skin lesion_H2_004_33_SCLE


title: 200643150050_J

description: cholangiocarcinoma


title: 200647550008_A

description: cholangiocarcinoma


title: 200643150050_K

description: cholangiocarcinoma


title: sCLE skin lesion_H2_002_31_SCLE


title: 200647550008_C

description: cholangiocarcinoma


title: 200647550008_D

description: cholangiocarcinoma


title: 200647550008_G

description: cholangiocarcinoma


title: 200643150050_G

description: cholangiocarcinoma


title: sCLE skin lesion_H1_005_SCLE


title: sCLE skin lesion_H1_003a_SCLE


title: DLE skin lesion_H4_009_44_DLE

description: Gene expression data from human DLE skin lesion

source_name: DLE skin lesion

value: DLE


title: sCLE skin lesion_H1_013_SCLE


title: DLE skin lesion_H4_007_43b_DLE


title: 200643150050_C

description: cholangiocarcinoma


title: 200647720045_L

description: cholangiocarcinoma


title: 200643150050_F

description: cholangiocarcinoma


title: sCLE skin lesion_H1_002a_SCLE


title: 200643150050_B

description: cholangiocarcinoma


title: DLE skin lesion_H4_005_41_DLE


title: 200643150050_H

description: cholangiocarcinoma


title: 200643150050_A

description: cholangiocarcinoma


title: 200643150050_D

description: cholangiocarcinoma


title: 200643150050_I

description: cholangiocarcinoma


title: 200643150050_E

description: cholangiocarcinoma


title: 200647720045_K

description: cholangiocarcinoma


title: 200647720045_I

description: cholangiocarcinoma


title: 200647720045_H

description: cholangiocarcinoma


title: DLE skin lesion_H3_073_DLE


title: DLE skin lesion_H3_074_DLE


title: 200647720045_F

description: cholangiocarcinoma


title: DLE skin lesion_H4_004_40_DLE


title: 200647720045_J

description: cholangiocarcinoma


title: 200647720045_B

description: cholangiocarcinoma


title: 200647720045_D

description: cholangiocarcinoma


title: DLE skin lesion_H3_069_DLE


title: 200647720045_G

description: cholangiocarcinoma


title: DLE skin lesion_H3_058_DLE


title: DLE skin lesion_H3_068_DLE


title: DLE skin lesion_H3_056_DLE


title: DLE skin lesion_H3_059_DLE


title: 3998386019_J

description: cholangiocarcinoma


title: 3998386019_H

description: cholangiocarcinoma


title: DLE skin lesion_H2_015_46_DLE


title: DLE skin lesion_H3_072_DLE


title: 3998386019_L

description: normal bile duct

source_name: normal


title: 200647720045_C

description: cholangiocarcinoma


title: DLE skin lesion_H3_067_DLE


title: DLE skin lesion_H3_062_DLE


title: 3998386019_G

description: cholangiocarcinoma


title: DLE skin lesion_H2_009_39_DLE


title: 200647720045_E

description: cholangiocarcinoma


title: 200647720045_A

description: cholangiocarcinoma


title: 3998386019_K

description: normal bile duct


title: 3998386019_I

description: cholangiocarcinoma


title: DLE skin lesion_H1_016_DLE


title: DLE skin lesion_H1_021_DLE


title: 3998386019_F

description: cholangiocarcinoma


title: 3998386019_D

description: cholangiocarcinoma


title: 3998386019_C

description: cholangiocarcinoma


title: DLE skin lesion_H1_017_DLE


title: DLE skin lesion_H1_009_DLE


title: DLE skin lesion_H1_012_DLE


title: DLE skin lesion_H1_006_DLE


title: 3998386019_B

description: cholangiocarcinoma


title: DLE skin lesion_H1_007_DLE


title: DLE skin lesion_H1_015_DLE


title: DLE skin lesion_H1_001a_DLE


title: DLE skin lesion_H1_008_DLE


title: 3998386019_E

description: cholangiocarcinoma


title: 3998386005_K

description: cholangiocarcinoma


title: 3998386005_J

description: cholangiocarcinoma


title: Normal skin_H3_076_N

description: Gene expression data from human normal skin biopsy

source_name: Normal skin

value: healthy


title: 3998386019_A

description: cholangiocarcinoma


title: 3998386005_D

description: cholangiocarcinoma


title: 3998386005_G

description: cholangiocarcinoma


title: Normal skin_H1_025_N


title: 3998386005_H

description: cholangiocarcinoma


title: Normal skin_H2_024_55_N


title: 3998386005_F

description: cholangiocarcinoma


title: Normal skin_H3_078_N


title: 3998386005_I

description: cholangiocarcinoma


title: 3998386005_E

description: cholangiocarcinoma


title: Normal skin_H1_023_N


title: sCLE skin lesion_H3_075_SCLE


title: Normal skin_H1_024_N


title: 3998386005_A

description: cholangiocarcinoma


title: Normal skin_H4_016_54_N


title: 3998386005_C

description: cholangiocarcinoma


title: 3998386005_L

description: cholangiocarcinoma


title: 3998386024_H

description: cholangiocarcinoma


title: 3998386024_F

description: cholangiocarcinoma


title: 3998386024_C

description: cholangiocarcinoma


title: 3998386024_K

description: cholangiocarcinoma


title: 3998386024_J

description: cholangiocarcinoma


title: 3998386024_I

description: cholangiocarcinoma


title: 3998386005_B

description: cholangiocarcinoma


title: 3998386024_L

description: cholangiocarcinoma


title: Glomerular compartment from IgAN human kidney S27_F_23_6_IgAN

description: Gene expression data from the glomerular compartment of human IgAN kidney

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Human Genechip U133 2.0 arrays (Santa Clara, CA) according to the manufacturer protocol.

source_name: Kidney biopsy from human IgAN

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit (Qiagen, Venlo, the Netherlands) following manufacturer’s instructions.

value: Glomeruli from kidney biopsy


title: Glomerular compartment from IgAN human kidney S25_M_48_6_IgAN


title: 3998386024_A

description: cholangiocarcinoma


title: 3998386026_G

description: cholangiocarcinoma


title: 3998386026_H

description: cholangiocarcinoma


title: 3998386026_J

description: cholangiocarcinoma


title: 3998386024_G

description: cholangiocarcinoma


title: 3998386024_E

description: cholangiocarcinoma


title: 3998386026_K

description: cholangiocarcinoma


title: 3998386024_D

description: cholangiocarcinoma


title: 3998386026_I

description: cholangiocarcinoma


title: 3998386026_L

description: cholangiocarcinoma


title: Glomerular compartment from IgAN human kidney S24_M_65_6_IgAN


title: U251_Control_8

city: Utrecht

first: Elly

middle: M

last: Hol

address: Universiteitsweg 100

department: Department of Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

description:
raw data in Cy5 channel of file:
US12302316_252665217637_S01_GE2-v5_95_Feb07_1_2.txt

hyb_protocol: A mix of 825 ng of Cy3 and Cy5 labelled cRNA samples was hybridized to Human GE 4x44K v2 Microarrays (Agilent, Amstelveen, NL) according to the manufacturer’s protocol.

scan_protocol: cRNA fluorescence intensity was scanned using an Agilent Technologies Scanner G2505A. Scans were made with 100% and 10% photon multiplier tube intensity, at 5 um resolution. Scan data were extracted using Agilent Feature Extraction software (version 9.5.3.1 Agilent).

data_processing: Using the limma package in bioconductor, spot intensities were imported into R software for statistical computing (R version 3.1). Spots labelled by the Feature Extraction software as saturated or non-uniformly distributed foregrounds and backgrounds, as well as visually identified artefacts on the array were omitted. In these cases the statistical analysis of differential expression was based on the remaining spots. Intensities were normalized separately for U251 and U373, but within these subsets a quantile normalization was performed between all arrays and channels. Sample intensities were extracted for an intensity-based analysis. Redundant probes detecting identical transcripts were averaged.

source_name: U251 astrocytoma line, recombinant mCherry expression

label_protocol: cRNA was made from 100 ng RNA using a Low Input Quick Amp Labeling Kit, two-color (Agilent, Amstelveen, NL), as per manufacturer’s protocol.

growth_protocol: The serum concentration in the cell culture medium was changed from 10% to 2% FBS three days before an experiment. U251 cells with rec-GFAP or rec-mCherry expression or U373 cells with shRNA targeting GFAP or NTC were plated in medium with 2% FBS in 6-well flexible bottom Bioflex plates coated with the laminin derived peptide YIGSR (Flexcell International, Hillsborough NC, US; Dunn Labortechnik, Asbach, DE), at a density of 5 * 10^4 cells/cm2.   Cells were allowed to adhere for 6 hours followed by a replacement of the culture medium with FBS free medium.

extract_protocol: RNA was isolated by adding TRIsure (Bioline, London, UK; GC biotech B.V., Alphen aan den Rijn, NL) directly to the cell culture wells. RNA was extracted according to the manufacturer’s protocol, and precipitated in isopropyl alcohol in the presence of glycogen at  -20°C overnight (Roche; Almere)31. Samples were centrifuged at 4°C at a speed of 2.0*104 g for 45 minutes (min), washed twice with cold 75% ethanol (in MilliQ), and the RNA pellet was dissolved in MilliQ (Millipore). The 260/280 absorbance ratio was measured by spectrophotometry (NanoDrop; Thermo Scientific) to assess RNA concentration and purity.

tag: tumour line

tag: construct

value: recombinant mCherry

tag: substrate

value: PDMS coated with YIGSR peptide


title: 3998386026_F

description: cholangiocarcinoma


title: 3998386024_B

description: cholangiocarcinoma


title: Glomerular compartment from IgAN human kidney S23_M_61_6_IgAN


title: 3998386026_E

description: cholangiocarcinoma


title: Glomerular compartment from IgAN human kidney S19_M_24_6_IgAN


title: U251_Control_7

description:
raw data in Cy5 channel of file:
US12302316_252665217636_S01_GE2-v5_95_Feb07_1_4.txt


title: 3998386026_D

description: cholangiocarcinoma


title: U251_GFAPdelta_8

description:
raw data in Cy5 channel of file:
US12302316_252665217636_S01_GE2-v5_95_Feb07_1_1.txt

source_name: U251 astrocytoma line, recombinant GFAPdelta-IRES-mCherry expression

value: recombinant GFAPdelta - IRES - mCherry


title: Glomerular compartment from IgAN human kidney S17_M_53_6_IgAN


title: Glomerular compartment from IgAN human kidney S16_F_23_6_IgAN


title: Glomerular compartment from IgAN human kidney S6_M_35_4_IgAN


title: 3998386026_B

description: cholangiocarcinoma


title: U251_GFAPalpha_8

description:
raw data in Cy5 channel of file:
US12302316_252665217635_S01_GE2-v5_95_Feb07_1_4.txt

source_name: U251 astrocytoma line, recombinant GFAPalpha-IRES-GFP expression

value: recombinant GFAPalpha - IRES - GFP


title: U251_GFAPdelta_7

description:
raw data in Cy5 channel of file:
US12302316_252665217635_S01_GE2-v5_95_Feb07_1_3.txt


title: U251_GFAPalpha_7

description:
raw data in Cy5 channel of file:
US12302316_252665217635_S01_GE2-v5_95_Feb07_1_1.txt


title: Glomerular compartment from IgAN human kidney S4_F_45_4_IgAN


title: U251_Control_5

description:
raw data in Cy5 channel of file:
US12302316_252665217634_S01_GE2-v5_95_Feb07_1_2.txt


title: Glomerular compartment from IgAN human kidney S3_M_58_4_IgAN


title: Glomerular compartment from IgAN human kidney S7_M_53_4_IgAN


title: Glomerular compartment from IgAN human kidney S8_F_41_4_IgAN


title: U251_GFAPalpha_5

description:
raw data in Cy5 channel of file:
US12302316_252665217633_S01_GE2-v5_95_Feb07_1_3.txt


title: U251_GFAPalpha_6

description:
raw data in Cy5 channel of file:
US12302316_252665217634_S01_GE2-v5_95_Feb07_1_1.txt


title: 3998386026_C

description: cholangiocarcinoma


title: 3998386026_A

description: cholangiocarcinoma


title: U251_Control_6

description:
raw data in Cy5 channel of file:
US12302316_252665217634_S01_GE2-v5_95_Feb07_1_4.txt


title: U251_GFAPdelta_6

description:
raw data in Cy5 channel of file:
US12302316_252665217633_S01_GE2-v5_95_Feb07_1_4.txt


title: Glomerular compartment from IgAN human kidney S9_M_58_3_IgAN


title: Glomerular compartment from IgAN human kidney S15_M_20_3_IgAN


title: U251_GFAPalpha_4

description:
raw data in Cy3 channel of file:
US12302316_252665217637_S01_GE2-v5_95_Feb07_1_2.txt


title: Glomerular compartment from IgAN human kidney S1_F_54_4_IgAN


title: Glomerular compartment from IgAN human kidney S14_M_30_3_IgAN


title: U251_GFAPdelta_4

description:
raw data in Cy3 channel of file:
US12302316_252665217636_S01_GE2-v5_95_Feb07_1_4.txt


title: U251_GFAPdelta_3

description:
raw data in Cy3 channel of file:
US12302316_252665217635_S01_GE2-v5_95_Feb07_1_4.txt


title: Glomerular compartment from IgAN human kidney S12_M_49_3_IgAN


title: Glomerular compartment from IgAN human kidney S10_M_34_3_IgAN


title: Glomerular compartment from IgAN human kidney S13_F_17_3_IgAN


title: Glomerular compartment from control human kidney H25_M_57_3_Con_L

description: Gene expression data from the glomerular compartment of human normal kidney

source_name: Kidney biopsy from human control


title: Glomerular compartment from control human kidney H1_F_22_4_Con_L


title: U251_GFAPalpha_3

description:
raw data in Cy3 channel of file:
US12302316_252665217636_S01_GE2-v5_95_Feb07_1_1.txt


title: Glomerular compartment from IgAN human kidney S2_M_46_4_IgAN

description: Gene expression data from the glomerular compartment of human IgAN kidney


title: Glomerular compartment from control human kidney H2_M_65_4_Con_L


title: U251_GFAPdelta_5

description:
raw data in Cy5 channel of file:
US12302316_252665217633_S01_GE2-v5_95_Feb07_1_1.txt


title: Glomerular compartment from control human kidney H3_M_68_4_Con_L


title: Glomerular compartment from control human kidney H24_F_40_3_Con_L


title: U251_Control_2

description:
raw data in Cy3 channel of file:
US12302316_252665217633_S01_GE2-v5_95_Feb07_1_3.txt


title: U251_Control_3

description:
raw data in Cy3 channel of file:
US12302316_252665217635_S01_GE2-v5_95_Feb07_1_1.txt


title: Glomerular compartment from control human kidney H26_M_52_3_Con_L


title: U373_NTC_6

description:
raw data in Cy5 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_4.txt

source_name: U373 astrocytoma line, shRNA Non targeting control

value: shRNA NTC


title: U251_Control_4

description:
raw data in Cy3 channel of file:
US12302316_252665217635_S01_GE2-v5_95_Feb07_1_3.txt


title: U251_Control_1

description:
raw data in Cy3 channel of file:
US12302316_252665217633_S01_GE2-v5_95_Feb07_1_1.txt


title: U251_GFAPdelta_2

description:
raw data in Cy3 channel of file:
US12302316_252665217634_S01_GE2-v5_95_Feb07_1_2.txt


title: U251_GFAPalpha_2

description:
raw data in Cy3 channel of file:
US12302316_252665217634_S01_GE2-v5_95_Feb07_1_4.txt


title: U251_GFAPdelta_1

description:
raw data in Cy3 channel of file:
US12302316_252665217634_S01_GE2-v5_95_Feb07_1_1.txt


title: Glomerular compartment from control human kidney H22_F_46_3_Con_L


title: Glomerular compartment from control human kidney H21_M_52_3_Con_L


title: U251_GFAPalpha_1

description:
raw data in Cy3 channel of file:
US12302316_252665217633_S01_GE2-v5_95_Feb07_1_4.txt


title: U373_GFAPpanKD_5

description:
raw data in Cy5 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_3.txt

source_name: U373 astrocytoma line, shRNA GFAPpan knockdown

value: shRNA GFAPpan


title: Glomerular compartment from control human kidney H20_F_47_3_Con_L


title: Glomerular compartment from control human kidney H18_F_45_2_Con_L


title: Glomerular compartment from control human kidney H17_M_41_2_Con_L


title: Glomerular compartment from control human kidney H19_M_65_2_Con_L


title: U373_GFAPalphaKD_4

description:
raw data in Cy5 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_1.txt

source_name: U373 astrocytoma line, shRNA GFAPalpha knockdown

value: shRNA GFAPalpha


title: Glomerular compartment from control human kidney H16_F_37_2_Con_L


title: U373_GFAPpanKD_4

description:
raw data in Cy5 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_2.txt


title: Glomerular compartment from control human kidney H15_M_35_2_Con_L


title: U373_GFAPalphaKD_5

description:
raw data in Cy5 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_2.txt


title: Glomerular compartment from control human kidney H8_M_34_1_Con_L

description: Gene expression data from the glomerular compartment of human normal kidney


title: Glomerular compartment from control human kidney H9_F_49_1_Con_L


title: U373_GFAPalphaKD_3

description:
raw data in Cy3 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_4.txt


title: U373_NTC_3

description:
raw data in Cy3 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_3.txt


title: U373_NTC_5

description:
raw data in Cy5 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_4.txt


title: U373_GFAPpanKD_3

description:
raw data in Cy5 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_3.txt


title: Glomerular compartment from control human kidney H7_F_40_1_Con_L


title: U373_NTC_2

description:
raw data in Cy3 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_2.txt


title: U373_NTC_4

description:
raw data in Cy5 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_1.txt


title: U373_NTC_1

description:
raw data in Cy3 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_2.txt


title: Glomerular compartment from control human kidney H14_F_38_1_Con_L


title: U373_GFAPpanKD_2

description:
raw data in Cy3 channel of file:
US12302316_252665225265_S02_GE2-v5_95_Feb07_1_1.txt


title: Glomerular compartment from control human kidney H6_M_68_1_Con_L


title: U373_GFAPalphaKD_2

description:
raw data in Cy3 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_4.txt


title: U373_GFAPalphaKD_1

description:
raw data in Cy3 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_3.txt


title: U373_GFAPpanKD_1

description:
raw data in Cy3 channel of file:
US12302316_252665218297_S03_GE2-v5_95_Feb07_1_1.txt


title: HV9_HEH

status: Public on Jul 02 2017

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

hyb_protocol: Three µg labeled cRNA were hybridized onto Human Genome U133 Plus 2.0 GeneChips (Affymetrix), revealed and washed using FS4, 168h after treatment administration50 fluidic station.

scan_protocol: GeneChips were scanned using a 5G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

data_processing: Raw data were normalized using the GC-RMA algorithm . Batch effects were removed using COMBAT

source_name: Whole blood_healthy control

label_protocol: Double-stranded cDNA was prepared from total RNA and an oligo-dT primer using GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, United States).

growth_protocol: Whole blood samples were collected into PAXGene tubes.

extract_protocol: Total RNA was extracted with PAXgene Blood RNA kit (PreAnalytix, Hilden, Germany). RNA integrity and quality were assessed using Agilent 2100 Bioanalyser (Agilent Technologies, Waldbrom, Germany) and Lab-on-chip RNA 6000 Nano Assay  (Agilent Technologies).

treatment_protocol: PAXGene tubes were stored at -80°C until extraction.

value: blood

tag: patient id

tag: sample type

value: HV

tag: treatment

tag: survival (d28)

tag: Sex

tag: age

tag: tbsa


title: HV3_HEH


title: HV5_HEH


title: Glomerular compartment from control human kidney H11_F_27_1_Con_L


title: Glomerular compartment from control human kidney H13_M_53_1_Con_L


title: HV6_HEH


title: HV4_HEH


title: HV8_HEH


title: P_B32_S3_SV

description: P_B32_S3, 120h after treatment administration_SV

source_name: Whole blood_S3, 120h after treatment administration_Placebo

value: Placebo

value: Survivor

value: F


title: P_B19BY_S3_NS

description: P_B19BY_S3, 120h after treatment administration_NS

value: Non survivor


title: HV7_HEH


title: P_B32_S1_SV

source_name: Whole blood_S1, before treatment administration_Placebo


title: C_B31_S2_SV

description: C_B31_S2, one day after treatment administration_SV

source_name: Whole blood_S2, one day after treatment administration_Hydrocortisone

value: Hydrocortisone

value: M


title: P_B19BY_S2_NS

description: P_B19BY_S2, one day after treatment administration_NS

source_name: Whole blood_S2, one day after treatment administration_Placebo


title: HV13_HEH


title: HV11_HEH


title: HV1_HEH


title: P_B19BY_S4_NS

description: P_B19BY_S4, 168h after treatment administration_NS

source_name: Whole blood_S4, 168h after treatment administration_Placebo


title: HV2_HEH


title: HV12_HEH


title: C_B31_S3_SV

description: C_B31_S3, 120h after treatment administration_SV

source_name: Whole blood_S3, 120h after treatment administration_Hydrocortisone


title: HV10_HEH


title: P_B19BY_S1_NS


title: C_B31_S1_SV

source_name: Whole blood_S1, before treatment administration_Hydrocortisone


title: C_B30_S3_NS

description: C_B30_S3, 120h after treatment administration_NS


title: C_B27_S1_SV


title: C_B30_S1_NS


title: C_B28_S2_SV

description: C_B28_S2, one day after treatment administration_SV


title: P_B26_S2_SV

description: P_B26_S2, one day after treatment administration_SV


title: P_B26_S3_SV

description: P_B26_S3, 120h after treatment administration_SV


title: C_B27_S3_SV

description: C_B27_S3, 120h after treatment administration_SV


title: P_B25_S3_NS

description: P_B25_S3, 120h after treatment administration_NS


title: P_B21_S3_SV

description: P_B21_S3, 120h after treatment administration_SV


title: C_B22_S3_SV

description: C_B22_S3, 120h after treatment administration_SV


title: C_B27_S2_SV

description: C_B27_S2, one day after treatment administration_SV


title: C_B24_S3_NS

description: C_B24_S3, 120h after treatment administration_NS


title: P_B25_S2_NS

description: P_B25_S2, one day after treatment administration_NS


title: C_B28_S3_SV

description: C_B28_S3, 120h after treatment administration_SV


title: C_B20_S4_NS

description: C_B20_S4, 168h after treatment administration_NS

source_name: Whole blood_S4, 168h after treatment administration_Hydrocortisone


title: P_B26_S1_SV


title: C_B24_S1_NS


title: C_B28_S1_SV


title: P_B21_S1_SV


title: P_B25_S1_NS


title: P_B23_S2_SV

description: P_B23_S2, one day after treatment administration_SV


title: P_B23_S4_SV

description: P_B23_S4, 168h after treatment administration_SV


title: P_B23_S1_SV


title: P_B32_S2_SV

description: P_B32_S2, one day after treatment administration_SV


title: C_B22_S2_SV

description: C_B22_S2, one day after treatment administration_SV


title: P_B21_S4_SV

description: P_B21_S4, 168h after treatment administration_SV


title: P_B23_S3_SV

description: P_B23_S3, 120h after treatment administration_SV


title: C_B22_S1_SV


title: C_B24_S2_NS

description: C_B24_S2, one day after treatment administration_NS


title: P_B21_S2_SV

description: P_B21_S2, one day after treatment administration_SV


title: C_B20_S3_NS

description: C_B20_S3, 120h after treatment administration_NS


title: P_B18_S4_SV

description: P_B18_S4, 168h after treatment administration_SV


title: C_B20_S1_NS


title: P_B18_S1_SV


title: P_B17_S4_SV

description: P_B17_S4, 168h after treatment administration_SV


title: P_B18_S3_SV

description: P_B18_S3, 120h after treatment administration_SV


title: P_B18_S2_SV

description: P_B18_S2, one day after treatment administration_SV


title: P_B17_S1_SV


title: P_B16_S4_SV

description: P_B16_S4, 168h after treatment administration_SV


title: Glomerular compartment from control human kidney H12_M_67_1_Con_L

description: Gene expression data from the glomerular compartment of human normal kidney


title: P_B16_S1_SV


title: P_B17_S2_SV

description: P_B17_S2, one day after treatment administration_SV


title: C_B14_S4_SV

description: C_B14_S4, 168h after treatment administration_SV


title: C_B14_S2_SV

description: C_B14_S2, one day after treatment administration_SV


title: C_B14_S3_SV

description: C_B14_S3, 120h after treatment administration_SV


title: C_B14_S1_SV


title: P_B12_S2_SV

description: P_B12_S2, one day after treatment administration_SV


title: P_B12_S3_SV

description: P_B12_S3, 120h after treatment administration_SV


title: C_B11_S1_SV


title: C_B11_S4_SV

description: C_B11_S4, 168h after treatment administration_SV


title: P_B17_S3_SV

description: P_B17_S3, 120h after treatment administration_SV


title: C_B11_S2_SV

description: C_B11_S2, one day after treatment administration_SV


title: C_B13_S3_NS

description: C_B13_S3, 120h after treatment administration_NS


title: P_B12_S4_SV

description: P_B12_S4, 168h after treatment administration_SV


title: C_B11_S3_SV

description: C_B11_S3, 120h after treatment administration_SV


title: P_B16_S2_SV

description: P_B16_S2, one day after treatment administration_SV


title: C_B13_S1_NS


title: P_B12_S1_SV


title: P_B16_S3_SV

description: P_B16_S3, 120h after treatment administration_SV


title: C_B13_S2_NS

description: C_B13_S2, one day after treatment administration_NS


title: P_B10_S4_SV

description: P_B10_S4, 168h after treatment administration_SV


title: C_B09_S4_SV

description: C_B09_S4, 168h after treatment administration_SV


title: P_B08_S1_SV


title: P_B10_S1_SV


title: P_B08_S2_SV

description: P_B08_S2, one day after treatment administration_SV


title: P_B10_S2_SV

description: P_B10_S2, one day after treatment administration_SV


title: P_B07_S3_SV

description: P_B07_S3, 120h after treatment administration_SV


title: P_B07_S1_SV


title: C_B05_S4_SV

description: C_B05_S4, 168h after treatment administration_SV


title: C_B05_S3_SV

description: C_B05_S3, 120h after treatment administration_SV


title: C_B09_S3_SV

description: C_B09_S3, 120h after treatment administration_SV


title: P_B10_S3_SV

description: P_B10_S3, 120h after treatment administration_SV


title: C_B09_S2_SV

description: C_B09_S2, one day after treatment administration_SV


title: C_B09_S1_SV


title: CD73+CD105+, biological  rep3

city: Lausanne

first: Jean-Paul

last: Abbuehl

department: ISREC

country: Switzerland

institute: Ecole Polytechnique Federale de Lausanne

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in manual from Affymetrix at the Lausanne DNA Array Facility (DAFL)

data_processing: Data processed with RMA and quantile normalized using BioC aroma.affymetrix. Batch was corrected with ComBat in sva package

source_name: primary bone marrow

label_protocol: biotin

extract_protocol: FACS Sorted cell populations were directly subjected to RNA isolation and purification using miRNA easy kit

treatment_protocol: Tissue was dissociated and cells were flow sorted.

tag: cell type


title: C_B05_S1_SV


title: CD73+CD105+, biological  rep2

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in manual from Affymetrix at the Lausanne DNA Array Facility (DAFL)


title: P_B08_S3_SV

description: P_B08_S3, 120h after treatment administration_SV


title: P_B03_S3_SV

description: P_B03_S3, 120h after treatment administration_SV


title: C_B06_S1_NS


title: P_B04_S3_SV

description: P_B04_S3, 120h after treatment administration_SV


title: C_B05_S2_SV

description: C_B05_S2, one day after treatment administration_SV


title: P_B04_S4_SV

description: P_B04_S4, 168h after treatment administration_SV


title: P_B03_S4_SV

description: P_B03_S4, 168h after treatment administration_SV


title: P_B04_S1_SV


title: P_B03_S2_SV

description: P_B03_S2, one day after treatment administration_SV


title: P_B04_S2_SV

description: P_B04_S2, one day after treatment administration_SV


title: P_B07_S2_SV

description: P_B07_S2, one day after treatment administration_SV


title: P_B07_S4_SV

description: P_B07_S4, 168h after treatment administration_SV


title: P_B03_S1_SV


title: C_B02_S4_SV

description: C_B02_S4, 168h after treatment administration_SV


title: C_B02_S2_SV

description: C_B02_S2, one day after treatment administration_SV


title: C_B02_S1_SV


title: C_B01_S4_NS

description: C_B01_S4, 168h after treatment administration_NS


title: C_B02_S3_SV

description: C_B02_S3, 120h after treatment administration_SV


title: C_B01_S2_NS

description: C_B01_S2, one day after treatment administration_NS


title: CD73+CD105+, biological  rep1


title: CD73+CD105-, biological  rep2


title: isp-1/isp-1;ceh-23 replicate 1

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 526 Campus Road, 341 Biotech

department: MBG

institute: Cornell University

description: Biological replicate 1

hyb_protocol: Fragmented cRNA with the In Situ Hybridization kit Plus (agilent), and hybridize overnight on Agilent 4X44K C.elegans arrays at 60C

scan_protocol: Scanned on an Agilent G2505C US83000170,

data_processing: Image were quantified using Agilent Feature Extraction Software (FE10.5) with protocol GE2_105_Dec08. data were normalized by background subtraction with Linear and LOWESS normalization.

organism: Caenorhabditis elegans

label_protocol: cRNA was synthesized and linearly amplified from 100 ng of total RNA with the Low RNA Input Linear Amplification Kit (Agilent), labeled with Cy3 and Cy5- CTP dyes (Perkin Elmer)

growth_protocol: Synchronized mid-L4 worms grown at 20C on 100mm NGM plates seeded with OP50 E. coli.

extract_protocol: Total RNA was isolated using Tri-reagent (Molecular Research Center, Inc.) and purified with the RNeasy kit (Qiagen).

treatment_protocol: all strains were treated the same

tag: genotype/variation

tag: larval stage


title: isp-1/isp-1;ceh-23 replicate 2

description: Biological replicate 2


title: C_B01_S3_NS

description: C_B01_S3, 120h after treatment administration_NS


title: CD73+CD105-, biological  rep1


title: CD73+CD105-, biological  rep3


title: isp-1/isp-1;ceh-23 replicate 1 dye flip

description: Biological replicate 1 dye flip


title: C_B01_S1_NS


title: isp-1/isp-1;ceh-23 replicate 3

description: Biological replicate 3


title: embryos wild-type 25°C 1-2h common reference rep3

status: Public on Jul 01 2017

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

hyb_protocol: Hybridization was performed in buffer consisting of 1M NaCl, 0.5% SLS, 50mM MES pH 6.5, 33% formamide at 42°C.  Slides were washed once in 6X SSPE and 0.005% SLS, then once for 5 min in 0.06X SSPE.

scan_protocol: Arrays were scanned using an Agilent scanner.

data_processing: Array images were quantified with Imagene software and normalized by the lowess method with R software.  To calculate the log(2)ratio for the common reference experiments, the wild-type log(2)ratio was subtracted from the pum mutant log(2)ratio.

organism: Drosophila melanogaster

source_name: [common reference] oocytes wild-type stage 14

label_protocol: cDNA from total RNA, with incorporated AA-dUTP, was generated by random priming according to the protocol of Kapranov et al (2007) using Superscript II (Invitrogen) and was then labelled with Cy3 and Cy5 dyes (GE Healthcare).  Labelled cDNA was purified on Qiagen PCR purification columns.

growth_protocol: All fly lines were maintained at 25C.

extract_protocol: Total embryonic RNA was extracted using Trizol (Invitrogen), followed by purification on Rneasy columns (Qiagen).

treatment_protocol: pumET7/pumMsc embryos and corresponding wild-type controls were collected on apple juice agar plates for 1 hour at 25°C and allowed to develop to 1-2h, 2-3h, 3-4h or 4-5h after egg laying (AEL) at 25°C.  pum13/pumMsc embryos and corresponding wild-type controls were collected on apple juice agar plates for 1 hour at 25°C, then transferred to 18°C and allowed to develop to 2-3h, 5-6h, 8-9h or 11-12h AEL.

tag: developmental stage

value: oocyte

value: wild-type

tag: time point

value: stage 14

source_name: embryos wild-type 25°C 1-2h

value: embryo

tag: temperature


title: embryos pumET7/pumMsc 25°C 0-1h common reference rep2

source_name: embryos pumET7/pumMsc 25°C 0-1h


title: embryos pumET7/pumMsc 25°C 1-2h common reference rep3

source_name: embryos pumET7/pumMsc 25°C 1-2h


title: embryos pumET7/pumMsc 25°C 4-5h common reference rep2

description:
Raw data file: 251987110028C_201202221422_S01.datatable
Cy3: wild-type stage 14 oocytes
Cy5: pumET7/pumMsc 25°C 4-5h
Raw data file: 251987110028D_201202221422_S01.datatable.txt
Cy3: pumET7/pumMsc 25°C 4-5h
Cy5: wild-type stage 14 oocytes

source_name: embryos pumET7/pumMsc 25°C 4-5h


title: embryos wild-type 25°C 3-4h common reference rep3

source_name: embryos wild-type 25°C 3-4h


title: embryos pumET7/pumMsc 25°C 0-1h common reference rep3


title: embryos pumET7/pumMsc 25°C 3-4h common reference rep3

source_name: embryos pumET7/pumMsc 25°C 3-4h


title: embryos wild-type 25°C 3-4h common reference rep2


title: embryos pumET7/pumMsc 25°C 2-3h common reference rep2

source_name: embryos pumET7/pumMsc 25°C 2-3h


title: embryos wild-type 25°C 2-3h common reference rep2

source_name: embryos wild-type 25°C 2-3h


title: embryos wild-type 25°C 4-5h common reference rep2

description:
Raw data file: 251987110028A_201202221422_S01.datatable
Cy3: wild-type stage 14 oocytes
Cy5: wild-type 25°C 4-5h
Raw data file: 251987110028B_201202221422_S01.datatable.txt
Cy3: wild-type 25°C 4-5h
Cy5: wild-type stage 14 oocytes

source_name: embryos wild-type 25°C 4-5h


title: embryos wild-type 25°C 1-2h common reference rep2


title: embryos wild-type 25°C 0-1h common reference rep3

source_name: embryos wild-type 25°C 0-1h


title: embryos pumET7/pumMsc 25°C 3-4h common reference rep2


title: embryos pumET7/pumMsc 25°C 3-4h common reference rep1


title: embryos wild-type 25°C 0-1h common reference rep2


title: embryos pumET7/pumMsc 25°C 1-2h common reference rep2


title: embryos pumET7/pumMsc 25°C 2-3h common reference rep3


title: embryos wild-type 25°C 4-5h common reference rep1

description:
Raw data file: 251987110027A_201202221413_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: wild-type 25°C 4-5h
Raw data file: 251987110027B_201202221413_S01.datatable
Cy3: wild-type 25°C 4-5h
Cy5: wild-type stage 14 oocytes


title: embryos pumET7/pumMsc 25°C 2-3h common reference rep1


title: embryos pumET7/pumMsc 25°C 4-5h common reference rep1

description:
Raw data file: 251987110027C_201202221413_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: pumET7/pumMsc 25°C 4-5h
Raw data file: 251987110027D_201202221413_S01.datatable.txt
Cy3: pumET7/pumMsc 25°C 4-5h
Cy5: wild-type stage 14 oocytes


title: embryos wild-type 25°C 2-3h common reference rep3


title: embryos wild-type 25°C 1-2h common reference rep1


title: embryos pum13/pumMsc 18°C 11-12h common reference

description:
Raw data file: 20080626_251987110012C_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: pum13/pumMsc 18°C 11-12h
Raw data file: 20080626_251987110012D_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 11-12h
Cy5: wild-type stage 14 oocytes

source_name: embryos pum13/pumMsc 18°C 11-12h


title: embryos wild-type 25°C 0-1h common reference rep1


title: embryos wild-type 25°C 3-4h common reference rep1


title: embryos pumET7/pumMsc 25°C 0-1h common reference rep1


title: embryos pumET7/pumMsc 25°C 1-2h common reference rep1


title: embryos wild-type 18°C 11-12h common reference

description:
Raw data file: 20080626_251987110010A_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: wild-type 18°C 11-12h
Raw data file: 20080626_251987110010B_S01.datatable.txt
Cy3: wild-type 18°C 11-12h
Cy5: wild-type stage 14 oocytes

source_name: embryos wild-type 18°C 11-12h


title: embryos wild-type 25°C 0-1h common reference

description:
Raw data file: 20080626_251987110008A_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: wild-type 25°C 0-1h
Raw data file: 20080626_251987110008B_S01.datatable.txt
Cy3: wild-type 25°C 0-1h
Cy5: wild-type stage 14 oocytes


title: embryos pum13/pumMsc 18°C 8-9h common reference

description:
Raw data file: 20080626_251987110012A_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: pum13/pumMsc 18°C 8-9h
Raw data file: 20080626_251987110012B_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 8-9h
Cy5: wild-type stage 14 oocytes

source_name: embryos pum13/pumMsc 18°C 8-9h


title: embryos pum13/pumMsc 18°C 5-6h common reference

description:
Raw data file: 20080626_251987110011C_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: pum13/pumMsc 18°C 5-6h
Raw data file: 20080626_251987110011D_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 5-6h
Cy5: wild-type stage 14 oocytes

source_name: embryos pum13/pumMsc 18°C 5-6h


title: embryos pum13/pumMsc 18°C 0-1h common reference

description:
Raw data file: 20080626_251987110010C_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: pum13/pumMsc 18°C 0-1h
Raw data file: 20080626_251987110010D_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 0-1h
Cy5: wild-type stage 14 oocytes

source_name: embryos pum13/pumMsc 25°C 0-1h


title: embryos wild-type 18°C 5-6h vs pum13/pumMsc 18°C 5-6h direct comparison

description:
Raw data file: 20080610_251987110006C_S01.datatable.txt
Cy3: wild-type 18°C 5-6h
Cy5: pum13/pumMsc 18°C 5-6h
Raw data file: 20080610_251987110006D_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 5-6h
Cy5: wild-type 18°C 5-6h

source_name: embryos wild-type 18°C 5-6h


title: embryos wild-type 18°C 5-6h common reference

description:
Raw data file: 20080626_251987110009A_S02.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: wild-type 18°C 5-6h
Raw data file: 20080626_251987110009B_S02.datatable.txt
Cy3: wild-type 18°C 5-6h
Cy5: wild-type stage 14 oocytes

source_name: [common reference] oocytes wild-type stage 14


title: embryos wild-type 18°C 11-12h vs pum13/pumMsc 18°C 11-12h direct comparison

description:
Raw data file: 20080610_251987110007C_S01.datatable.txt
Cy3: wild-type 18°C 11-12h
Cy5: pum13/pumMsc 18°C 11-12h
Raw data file: 20080610_251987110007D_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 11-12h
Cy5: wild-type 18°C 11-12h


title: embryos pum13/pumMsc 18°C 2-3h common reference

description:
Raw data file: 20080626_251987110011A_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: pum13/pumMsc 18°C 2-3h
Raw data file: 20080626_251987110011B_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 2-3h
Cy5: wild-type stage 14 oocytes

source_name: embryos pum13/pumMsc 18°C 2-3h


title: Nras mutant mm415

city: San Francisco

first: Xu

last: Chen

state: CA

address: 1450 3rd street, HD200

department: Dermatology

institute: UCSF

description: Gene expression data from tissue culture cells

hyb_protocol: The labeled cDNA was hybridized to human Transcriptome 2.0 microarrays from Affymetrix according to manufacture’s standard protocol.

scan_protocol: The signal intensity fluorescent images produced during affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).

data_processing: The array data were normalized at gene level with standard RMA method by using Affymetrix expression console software and analyzed by using Affymetrix Transcriptome Analysis Console (TAC) software.

source_name: tissue culture cell line

label_protocol: The GeneChip WT PLUS Reagent kit from Affymetrix was used for amplification, fragmentation and biotin-labeling.

growth_protocol: Melanoma cell lines were maintained in RPMI 1640 with 10% FBS.

extract_protocol: Extraction of total RNA was performed using PureLink RNA mini kit from Life technologies according to the manufacturer's instructions.

tag: genotype

value: Nras mutant


title: Nras mutant mm485


title: embryos wild-type 25°C 0-1h vs pum13/pumMsc 25°C 0-1h direct comparison

description:
Raw data file: 20080610_251987110005C_S02.datatable.txt
Cy3: wild-type 25°C 0-1h
Cy5: pum13/pumMsc 25°C 0-1h
Raw data file: 20080610_251987110005D_S02.datatable.txt
Cy3: pum13/pumMsc 25°C 0-1h
Cy5: wild-type 25°C 0-1h


title: embryos wild-type 18°C 8-9h common reference

description:
Raw data file: 20080626_251987110009C_S02.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: wild-type 18°C 8-9h
Raw data file: 20080626_251987110009D_S02.datatable.txt
Cy3: wild-type 18°C 8-9h
Cy5: wild-type stage 14 oocytes

source_name: embryos wild-type 18°C 8-9h


title: Braf mutant sk-mel-5

value: Braf mutant


title: embryos wild-type 18°C 8-9h vs pum13/pumMsc 18°C 8-9h direct comparison

description:
Raw data file: 20080610_251987110007A_S01.datatable.txt
Cy3: wild-type 18°C 8-9h
Cy5: pum13/pumMsc 18°C 8-9h
Raw data file: 20080610_251987110007B_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 8-9h
Cy5: wild-type 18°C 8-9h


title: embryos wild-type 18°C 2-3h common reference

description:
Raw data file: 20080626_251987110008C_S01.datatable.txt
Cy3: wild-type stage 14 oocytes
Cy5: wild-type 18°C 2-3h
Raw data file: 20080626_251987110008D_S01.datatable.txt
Cy3: wild-type 18°C 2-3h
Cy5: wild-type stage 14 oocytes

source_name: embryos wild-type 18°C 2-3h