title: Breast tumor 202

description: 4418463155_G: GP202

value: IDC

tag: tumor grade

tag: ln positive (total)

tag: recurrence free time (months)

tag: location of recurrence


title: Breast tumor 204

status: Public on Jun 19 2014

type: RNA

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

description: 4418463227_A: GP204

hyb_protocol: 750 ng of labeled cRNA were applied to Illimuna whole-genome gene expression HumanRef-8 v2 BeadChips for an overnight hybridization at 58°C.

scan_protocol: Signal is developed with streptavidin-Cy3 and the BeadChip is scanned with the Illumina BeadArray Reader.

data_processing: Image data were processed by GenomeStudio software using background subtraction and quantile normalization. Methods to adjust the normalized intensity values see MAQC Consortium’s description [PMID: 16964229]. Log2 expression ratio of a normalized intensity value to the average signal in all samples for each transcript was calculated.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human primary breast tumor

label_protocol: 200 ng of total RNA were converted to cDNA, followed by an in vitro transcription amplification step to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX).

extract_protocol: RNA was extracted from fine needle aspirates of tumors with QIAGEN RNAeasy Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: age

tag: margin (cm)

tag: tumor type

value: DCIS/IDC

tag: tumor size (cm)

tag: lvi

tag: eic

tag: er

tag: pr

tag: cmtc

tag: recurrence

value: no

tag: used in the 284bc dataset?

tag: rin


title: Breast tumor 203

description: 4418463155_H: GP203

value: No

value: Negative


title: Aldh1l1-GFP positive cells, age E18.5 biological rep. 3

city: San Francisco

first: David

last: Rowitch

state: CA

address: 35 Medical Center Way, RMB 932D

department: Institute for Regenerative Medicine

country: USA

institute: University of California-San Francisco

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
data preprocessed in R using Bioconductor suite- oligo package/RMA algorithm used to background correct, normalize, and summarize. Two types of analyses then performed: 1)  Limma package/treat algorithm used to assess differential expression, 2) Gene coexpression modules determined as described in Molofsky et al, Glia (2013) 61:1518
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.na30.mm9.probeset.csv

label: biotin

organism: Mus musculus

source_name: Aldh1L1-GFP flow sorted  spinal cord

label_protocol: purified RNA was amplified and biotin labeled (WT ovation, NuGen)

growth_protocol: mouse spinal cords from Aldh1l1-GFP transgenic mice on a swiss-webster background, various ages

extract_protocol: RNA was trizol purified with glycogen as a carrier molecule, DNAse digested, and further purified on an RNAeasy mini column (Qiagen)

treatment_protocol: papain dissociated and flow sorted on a BD facs aria II to isolate astrocytes (aldh1l1-GFP positive) and non-astrocytes (Aldh1l1-GFP negative),

tag: genetic background

value: Swiss-Webster

tag: cell type

value: Aldh1l1-GFP positive cells


title: Large cell carcinoma 007

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

hyb_protocol: see miRNA Labeling and Microarray Hybricization Protocol Version 0.1 (Agilent Technologies)

scan_protocol: Cy3-sample RNA were generated and hybridized to a Human miRNA Microarray and scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software.

data_processing: Raw data was normalized by a 75 percentile shift.

source_name: Large cell carcinoma

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I.

tag: tissue type

value: Large cell carcinoma

tag: histology

value: LA


title: All live sorted spinal cord cells, age E14.5 biological rep. 3

value: whole spinal cord


title: Large cell carcinoma 006

label_protocol: see miRNA Labeling and Microarray Hybricization Protocol Version 0.1 (Agilent Technologies)


title: Squamous cell carcinoma 024

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma

value: SQ


title: Large cell carcinoma 008


title: Large cell carcinoma 015


title: Large cell carcinoma 005


title: Large cell carcinoma 001


title: adenosquamous carcinoma 004

source_name: Adenosquamous carcinoma

value: Adenosquamous carcinoma

value: AS


title: adenosquamous carcinoma 002


title: adenosquamous carcinoma 003


title: Adenocarcinoma 088

source_name: Adenocarcinoma

value: Adenocarcinoma

value: AD


title: Adenocarcinoma 086


title: Adenocarcinoma 087


title: Large cell carcinoma 004


title: Adenocarcinoma 084


title: Adenocarcinoma 083


title: Breast tumor 200

description: 4418463155_E: GP200

tag: tumor grade

tag: ln positive (total)

value: Positive

tag: recurrence free time (months)

tag: location of recurrence


title: Breast tumor 198

description: 4418463155_C: GP198

tag: age

tag: margin (cm)

tag: tumor type

value: IDC

tag: tumor size (cm)

value: yes


title: Adenocarcinoma 082


title: All live sorted spinal cord cells, age E14.5 biological rep. 1


title: adenosquamous carcinoma 001


title: Breast tumor 199

description: 4418463155_D: GP199

tag: lvi

tag: eic

tag: er

tag: pr

value: no


title: Aldh1l1-GFP positive cells, age E14.5 biological rep. 2


title: Breast tumor 201

description: 4418463155_F: GP201

value: No

value: Yes

tag: cmtc

tag: recurrence

tag: used in the 284bc dataset?

tag: rin


title: Adenocarcinoma 080

tag: tissue type

tag: histology


title: Aldh1l1-GFP positive cells, age E14.5 (mislabeled sample, exclude from analysis)

source_name: ID unknown

tag: genetic background

value: Swiss-Webster

tag: cell type

value: ID unknown


title: Aldh1l1-GFP positive cells, age E14.5 biological rep. 1

value: Aldh1l1-GFP positive cells


title: Squamous cell carcinoma 025


title: Adenocarcinoma 081


title: Breast tumor 197

description: 4418463155_B: GP197

tag: tumor grade

tag: ln positive (total)

value: Negative

tag: recurrence free time (months)

tag: location of recurrence


title: Breast tumor 195

description: 4334518108_G: GP195

tag: age

tag: margin (cm)

tag: tumor type

value: DCIS

tag: tumor size (cm)


title: All live sorted spinal cord cells, age E13.5 biological rep. 1

value: whole spinal cord


title: Adenocarcinoma 079


title: All live sorted spinal cord cells, age E13.5 biological rep. 2


title: Adenocarcinoma 078


title: All live sorted spinal cord cells, age E13.5 biological rep. 3


title: Adenocarcinoma 077


title: Adenocarcinoma 076


title: Aldh1l1-GFP positive cells, age E13.5 biological rep. 3


title: Breast tumor 196

description: 4418463155_A: GP196

tag: lvi

tag: eic

tag: er

tag: pr


title: Adenocarcinoma 075


title: Adenocarcinoma 074


title: Adenocarcinoma 073


title: Aldh1l1-GFP positive cells, age E13.5 biological rep. 1


title: Adenocarcinoma 071


title: Adenocarcinoma 072


title: Adenocarcinoma 069


title: Adenocarcinoma 066


title: Adenocarcinoma 067


title: Adenocarcinoma 065


title: BMPC ZBTB20 TRAP_4

city: Saint Louis

first: Yinan

state: Missouri

address: 660 South Euclid Avenue

department: Immunology and Pathology

institute: Washington University in St. Louis

hyb_protocol: Hybridization to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix) was performed by the Genome Technology Access Center core facility at Washington University in St. Louis

scan_protocol: Scanning and image acquisition were performed by the Genome Technology Access Center core facility at Washington University in St. Louis

data_processing: 8 CEL files were imported into ArrayStar (DNASTAR) for analysis. Data was normalized with RMA algorithm. Genes with greater than a 2-fold difference in mean expression between the two genotypes were selected.

source_name: Zbtb20-deficient bone marrow B220low/-CD138+ cells

label_protocol: cDNA synthesis and amplification was performed with Ovation Pico WTA system V2 (NuGEN), 5ug of amplified cDNA per sample was labelled with Encore Biotin Module (NuGEN).

growth_protocol: Chimeras were generated using Zbtb20-sufficient or Zbtb20-deficient E14.5 fetal livers. Donor cells were harvested from chimeras after 3-4 months following reconstitution.

extract_protocol: Total RNA was extracted from RLT-lyzed cells with the RNeasy Micro Kit (Qiagen).

treatment_protocol: Bones were crushed with pestle and mortar and marrow was separated from bone bits through a density gradient polysucrose solution. Bone marrow cells were stained with antibodies specific to B220, CD138, CD45.2 (donor) for purification via MACS and FACS. FACS-purified B220low/-CD138 cells were lyzed immediately with RLT buffer (Qiagen).

value: bone marrow B220low/-CD138+ cells

tag: source

value: Zbtb20-deficient E14.5 fetal livers


title: Breast tumor 192

description: 4334518108_D: GP192

tag: cmtc

tag: recurrence

value: chest

tag: used in the 284bc dataset?

tag: rin


title: adenosquamous carcinoma 003

hyb_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.

scan_protocol: Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version A.7.5.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Feature Extraction Software (version A.7.5.1).

source_name: Primary lung tumor

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: tissue type

value: Primary lung tumor

tag: histology

value: AS

tag: cell line

value: mixture of 20 cell ines


title: Breast tumor 193

description: 4334518108_E: GP193

value: IDC

tag: tumor grade

tag: ln positive (total)

value: Positive

tag: recurrence free time (months)

tag: location of recurrence


title: Breast tumor 194

description: 4334518108_F: GP194

tag: age

tag: margin (cm)

tag: tumor type

tag: tumor size (cm)

value: no

value: yes


title: Lymph node stromal cell line BLS12 unstimulated

city: Hirakata

first: Tomoya

last: Katakai

state: Osaka

address: 2-5-1 Shinmachi

department: Department of Molecular Genetics, Institute of Biomedical Science

institute: Kansai Medical University

description: Gene expression data from established stromal cell line

hyb_protocol: The labeled ssDNAwas hybridized with Mouse Gene 1.0 ST Array (Affymetrix).

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

data_processing: The image was quantified by using Affymetrix GeneChip Command Console Software version 1.0 and Affymetrix Expression Console Software version 1.1.

source_name: BALB/c mouse lymph node derived stromal cell line

label_protocol: RNA was subjected to amplification and cRNA/cDNA synthesis by using cDNA Synthesis and Amplification Kit (Affymetrix). Single-strand DNA was synthesized with Super Script II and biotinilated with Terminal Labeling Kit (Affymetrix).

growth_protocol: C57BL/6JJcl mice were maintained and bred under specific pathogen-free conditions in the animal facility of Kansai Medical University. BALB/cA mice derived lymph node stromal (BLS) cell lines were cultured in DMEM supplemented with 10% FCS and antibiotics. To prepare mouse embryonic fibroblasts, E11.5-13.5 embryos digested with 0.125% trypsin, 0.025% EDTA-HBSS at 37°C for 30 min and cultured in DMEM supplemented with 10% FCS and antibiotics.

extract_protocol: Total RNA was isolated using RNeasy Plus Mini Kit (QIAGEN).

treatment_protocol: BLS cells were stimulated with or without 1μg/ml goat polyclonal anti-mouse LTβR agonistic antibody (R&D systems) for 2 days.

tag: strain

value: BALB/cA-derived

tag: tissue

value: adult lymph node


title: Lymph node stromal cell line BLS12 stimulated with LTβR agonistic antibody

description: Gene expression data from established stromal cell line stimulated with LTβR agonistic antibody

source_name: BALB/c mouse lymph node derived stromal cell line with stimulation


title: Breast tumor 191

description: 4334518108_C: GP191

tag: lvi

value: No

tag: eic

value: Yes

tag: er

tag: pr

tag: cmtc


title: Adenocarcinoma 062

tag: tissue type

value: Adenocarcinoma

tag: histology

value: AD


title: Adenocarcinoma 063


title: Aldh1l1-GFP positive cells, age E13.5 biological rep. 2

tag: genetic background

value: Swiss-Webster

tag: cell type

value: Aldh1l1-GFP positive cells


title: Lymph node stromal cell line BLS4 unstimulated

tag: cell line


title: Breast tumor 188

description: 4334518100_H: GP188

tag: tumor grade

tag: ln positive (total)

value: Negative

tag: recurrence

tag: recurrence free time (months)

tag: location of recurrence

tag: used in the 284bc dataset?

tag: rin


title: Adenocarcinoma 061


title: Adenocarcinoma 060


title: Breast tumor 189

description: 4334518108_A: GP189

tag: age

tag: margin (cm)

tag: tumor type

value: ILC

tag: tumor size (cm)

tag: lvi


title: Adenocarcinoma 064

tag: tissue type


title: Adenocarcinoma 059

tag: histology


title: Adenocarcinoma 058


title: Lymph node stromal cell line BLS4 stimulated with LTβR agonistic antibody

tag: strain

tag: tissue


title: Adenocarcinoma 057


title: Adenocarcinoma 056


title: Breast tumor 187

description: 4334518100_G: GP187

tag: eic

tag: er

tag: pr

tag: cmtc


title: Adenocarcinoma 054


title: Adenocarcinoma 053


title: Adenocarcinoma 055


title: LN stromal cell fraction

description: Gene expression data from stromal cell fraction freshly isolated from enzyme digested lymph node

source_name: C57BL/6 mouse adult lymph node stromal cell fraction


title: Adenocarcinoma 052


title: Breast tumor 190

description: 4334518108_B: GP190

tag: tumor grade

tag: ln positive (total)

tag: recurrence

tag: recurrence free time (months)


title: Embryonic fibroblast

description: Gene expression data from cultured enbryonic fibroblast

source_name: C57BL/6 mouse E11.5-13.5 embryo derived fibroblast

value: embryo


title: Adenocarcinoma 051


title: Breast tumor 186

description: 4334518100_F: GP186

tag: age

tag: location of recurrence

tag: used in the 284bc dataset?

tag: rin


title: Breast tumor 185

description: 4334518100_E: GP185

tag: margin (cm)

tag: tumor type

tag: tumor size (cm)

tag: lvi


title: Adenocarcinoma 050

tag: tissue type

tag: histology


title: Breast tumor 182

description: 4334518100_B: GP182

tag: eic

tag: er


title: Adenocarcinoma 049


title: MCFDCIS rep 1

city: Dallas

first: Xiaoyu

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

description:
biological replicate 1
5983368004_K
Pearson_061011

hyb_protocol: Direct Hybridization Assay Protocols in Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide

scan_protocol: illumina HiScan®SQ System User Guide

data_processing: Raw data were generated by GenomeStudioTM Gene Expression Module v1.0 without background subtraction and normalization

source_name: Cell line

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit protocol

growth_protocol: Cells were grown in the recomended culture media for 48 h.

extract_protocol: Total RNA was extracted following manufacturer's protocol for Qiagen Rneasy Plus, Cat. No. 74134, Appendix D: Purification of Total RNA containing small RNAs from cells

treatment_protocol: Cells were approx 70% confluent at the time of lysis and RNA extraction.

tag: cell line

value: MCFDCIS

tag: majority phenotype

value: noninvasive


title: HCC1806 rep 2

description:
biological replicate 2
5983368004_J
Pearson_061011


title: Breast tumor 184

description: 4334518100_D: GP184

value: DCIS

tag: tumor grade

tag: ln positive (total)

tag: pr

tag: cmtc


title: Breast tumor 183

description: 4334518100_C: GP183

tag: age

value: IDC

value: Positive

tag: recurrence

tag: recurrence free time (months)

tag: location of recurrence


title: Breast tumor 181

description: 4334518100_A: GP181

tag: margin (cm)

tag: tumor type

value: no

tag: used in the 284bc dataset?

value: yes

tag: rin


title: Adenocarcinoma 047

tag: tissue type

tag: histology


title: Adenocarcinoma 046


title: HCC1954 rep 2

description:
biological replicate 2
5983368004_H
Pearson_061011


title: HCC1806 rep 1

description:
biological replicate 1
5983368004_I
Pearson_061011


title: Adenocarcinoma 044


title: Adenocarcinoma 045


title: Adenocarcinoma 043


title: Breast tumor 178

description: 4334518087_E: GP178

tag: tumor size (cm)

tag: lvi

tag: eic

tag: er


title: T47D rep 2

description:
biological replicate 2
5713595010_F
Pearson_022211_part2

tag: cell line

tag: majority phenotype


title: Adenocarcinoma 042


title: Adenocarcinoma 041


title: Breast tumor 179

description: 4334518087_F: GP179

tag: tumor grade

tag: ln positive (total)

tag: pr

tag: cmtc


title: Adenocarcinoma 037


title: Adenocarcinoma 039


title: Adenocarcinoma 036


title: T47D rep 1

description:
biological replicate 1
5713595010_E
Pearson_022211_part2


title: Adenocarcinoma 035


title: All live sorted spinal cord cells, age E14.5 biological rep. 2

tag: genetic background

tag: age

tag: cell type

value: whole spinal cord


title: HCC1954 rep 1

description:
biological replicate 1
5983368004_G
Pearson_061011


title: Breast tumor 180

description: 4334518087_G: GP180

tag: margin (cm)

tag: tumor type

value: No

tag: recurrence

tag: recurrence free time (months)

tag: location of recurrence

value: left breast, bone, lung

tag: used in the 284bc dataset?


title: Adenocarcinoma 034

tag: tissue type

value: Adenocarcinoma

tag: histology


title: MCFDCIS rep 2

description:
biological replicate 2
5983368004_L
Pearson_061011

tag: cell line


title: Adenocarcinoma 040

value: AD


title: HCC1428 rep 2

description:
biological replicate 2
5713595010_D
Pearson_022211_part2

tag: majority phenotype


title: Breast tumor 177

description: 4334518087_D: GP177

tag: tumor size (cm)

tag: tumor grade

tag: lvi

tag: eic

tag: er

tag: rin


title: Adenocarcinoma 033


title: Adenocarcinoma 032


title: Adenocarcinoma 031


title: Breast tumor 175

description: 4334518087_B: GP175

tag: age

tag: ln positive (total)

value: Yes

tag: pr

tag: cmtc


title: Breast tumor 176

description: 4334518087_C: GP176

tag: margin (cm)

tag: tumor type

tag: recurrence

tag: recurrence free time (months)


title: Adenocarcinoma 028

tag: tissue type

tag: histology


title: MCF7 rep 2

description:
biological replicate 2
5713595010_B
Pearson_022211_part2

tag: cell line

tag: majority phenotype


title: HCC1428 rep 1

description:
biological replicate 1
5713595010_C
Pearson_022211_part2


title: Breast tumor 173

description: 4334518081_G: GP173

tag: tumor size (cm)

tag: tumor grade

tag: location of recurrence

tag: used in the 284bc dataset?


title: Adenocarcinoma 027


title: Adenocarcinoma 026


title: MCF7 rep 1

description:
biological replicate 1
5713595010_A
Pearson_022211_part2


title: Breast tumor 172

description: 4334518081_F: GP172

tag: lvi

tag: eic

tag: er

tag: rin


title: Adenocarcinoma 023


title: Adenocarcinoma 020


title: Breast tumor 174

description: 4334518087_A: GP174

tag: age

tag: ln positive (total)

tag: pr

tag: cmtc


title: Adenocarcinoma 030


title: HS578T rep 1

description:
biological replicate 1
7196763039_C
Pearson_031512

value: invasive


title: Adenocarcinoma 019


title: Adenocarcinoma 029


title: Breast tumor 170

description: 4334518081_D: GP170

tag: margin (cm)

tag: tumor type

value: Negative

tag: recurrence

tag: recurrence free time (months)


title: Adenocarcinoma 018

tag: tissue type

tag: histology


title: Adenocarcinoma 025


title: Breast tumor 171

description: 4334518081_E: GP171

value: IMC

tag: tumor size (cm)

tag: tumor grade


title: Adenocarcinoma 014


title: Breast tumor 169

description: 4334518081_C: GP169

tag: location of recurrence

tag: used in the 284bc dataset?


title: HS578T rep 2

description:
biological replicate 2
7196763039_D
Pearson_031512

tag: cell line

tag: majority phenotype


title: SUM159-Trailblazer rep 2

description:
biological replicate 2
5983368004_B
Pearson_061011


title: Adenocarcinoma 011


title: Breast tumor 167

description: 4334518081_A: GP167

value: ILC

tag: lvi

tag: eic

tag: er

tag: rin


title: Adenocarcinoma 012


title: SUM159-Opportunist rep 2

description:
biological replicate 2
5983368004_C
Pearson_061011


title: SUM159-Opportunist rep 1

description:
biological replicate 1
5713595001_F
Pearson_022211_part1


title: Breast tumor 168

description: 4334518081_B: GP168

tag: age

tag: ln positive (total)

tag: pr

tag: cmtc


title: Breast tumor 166

description: 4256290013_G: GP166

tag: margin (cm)

tag: tumor type

tag: recurrence

tag: recurrence free time (months)


title: SUM159-Parental rep 1

description:
biological replicate 1
5713595001_D
Pearson_022211_part1


title: HCC1143-Opportunist rep 1

description:
biological replicate 1
5713595001_C
Pearson_022211_part1


title: Breast tumor 164

description: 4256290013_E: GP164

tag: tumor size (cm)

tag: tumor grade


title: Breast tumor 165

description: 4256290013_F: GP165

value: Benign

tag: location of recurrence

tag: used in the 284bc dataset?


title: Adenocarcinoma 009

tag: tissue type

tag: histology


title: SUM159-Trailblazer rep 1

description:
biological replicate 1
5713595001_E
Pearson_022211_part1

tag: cell line

tag: majority phenotype


title: Adenocarcinoma 006


title: Adenocarcinoma 007


title: Adenocarcinoma 008


title: Adenocarcinoma 010


title: Adenocarcinoma 004


title: Adenocarcinoma 003


title: Adenocarcinoma 002


title: Adenocarcinoma 001


title: Breast tumor 163

description: 4256290013_D: GP163

tag: lvi

tag: eic

tag: er

tag: rin


title: Adenocarcinoma 005


title: Breast tumor 162

description: 4256290013_C: GP162

tag: age

tag: ln positive (total)

tag: pr

tag: cmtc


title: HCC1143-Trailblazer rep 2

description:
biological replicate 2
5983368004_E
Pearson_061011


title: HCC1143-Trailblazer rep 1

description:
biological replicate 1
5713595001_B
Pearson_022211_part1


title: HCC1143-Parental rep 2

description:
biological replicate 2
5983368004_D
Pearson_061011

value: noninvasive


title: HCC1143-Opportunist rep 2

description:
biological replicate 2
5983368004_F
Pearson_061011


title: HCC1143-Parental rep 1

description:
biological replicate 1
5713595001_A
Pearson_022211_part1


title: siAR DHT

city: Itabashi-ku

first: Takao

last: Susa

state: Tokyo

department: Department of Biochemistry

institute: Teikyo University School of Medicine

description: Gene expression after DHT treatment for 24hr in siAR LNCaP

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: LNCaP, siAR, DHT, replicate 1

label_protocol: The cRNA was amplified and labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc. CA, USA).

growth_protocol: LNCaP cells were maintained in monolayer cultures in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with 5% (v/v) fetal bovine serum and antibiotics (Life Technologies) in humidified 5% CO2-95% air at 37°C.

extract_protocol: Total RNAs of LNCaP cells were isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA samples were quantified by an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality was confirmed with an Experion System (Bio-Rad Laboratories, Hercules, CA).

treatment_protocol: 24 h before hormone treatment, serum-free media were used and the cells were exposed to the indicated hormones for another 24 h. The ligand concentration was  2.0 × 10−7 M.

tag: cell type

value: LNCaP

tag: transfectant

value: siRNA for AR


title: SUM159-Parental rep 2

description:
biological replicate 2
5983368004_A
Pearson_061011


title: siAR v

description: Gene expression after vehicle treatment for 24hr in siAR LNCaP

source_name: LNCaP, siAR, vehicle, replicate 1


title: Apc null A

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

country: Spain

institute: IRB Barcelona

description: Apc null

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: Gene expression data was pre-processed and normalized using RMA algorithm as implemented in Bioconductor's affy package. The data  was quantile normalized, and the summarization was obtained via median  polish.

source_name: Apc null

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Adenoma/tumor organoid media (Control media): 50% advanced DMEM (Life Technologies, 12491-023), 1X Glutamax (Gibco 35050), 1X HEPES (1M Gibco 15630), 1X N-2 (Life Technologies 17502-048), 1X B-27 (12587-010), 50ng/mL EGF (LifeTechnologies PHG0311) and 10 μM Rock inhibitor Y-27623 (Merk) when passaging. Media replacement was performed every 2 days.    See  Colon adenoma growth conditions in Sato T et al., Gastroenterology, 2011), for more details.

extract_protocol: Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies) and quantified using a Nanodrop spectrophotometer. Quality was assessed using a Bioanalyzer (Agilent) and only high quality samples (RIN ≥9) were used for hybridization.

treatment_protocol: 3D cultures of Apc null or compound Gata6/Apc tumor organoids were grown for 7 days following the growth protocol outlined above.

tag: batch

value: A

tag: genotype

value: Apc null

tag: tissue

value: colon adenoma tumor organoids

tag: genetic background


title: siAR E2

description: Gene expression after E2 treatment for 24hr in siAR LNCaP

source_name: LNCaP, siAR, E2, replicate 1


title: siAR R5020

description: Gene expression after R5020 treatment for 24hr in siAR LNCaP

source_name: LNCaP, siAR, R5020, replicate 1


title: siRNA polQ replication timing 2

type: genomic

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

description: Biological replicate 2 of 2. polQ siRNA

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray (SurePrint G3 Human CGH Microarray Kit, 4x180K, AGILENT Technologies, genome reference Hg18) that covers the whole genome with one probe every 13 Kb (11 KB in RefSeq sequences).

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 2 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.

molecule: genomic DNA

source_name: neosynthetized DNA in early S phase

label_protocol: Microarray hybridization requires a minimum of 500 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification was conducted (WGA, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Human RKO cell line was purchased from ATCC and grown in Dulbecco’s Modified Eagle Medium with GlutaMAX™ I, High glucose, Sodium Pyruvate (Gibco, Life technologies, Paisley, UK), supplemented with 10% Foetal Bovine Serum (Lonza, Basel, CH), penicillin (100U/ml) and streptomycin (100µg/ml) (Gibco) at 37°C, 5% CO2 and 5% O2 (standard culture conditions).

extract_protocol: 24h after transfection with POLQ-1 or CTRL siRNA, RKO cells were incubated with BrdU (50µM) for one hour, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) as described by Hiratani et al 2008. To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with CAV2 oligonucleotides (early control) and with bgGRM8 oligonucleotides (late control).

treatment_protocol: RKO cells were transfected with siRNA targeting either POLQ by two independent pools of siRNA : POLQ-1 siRNA: ON-TARGET plus smart pool of 4 POLQ siRNA from Dharmacon (Thermo Fisher Scientific, Waltham, USA): CCUUAAGACUGUAGGUACU, ACACAGUAGGCGAGAGUAU, CGACUAAGAUAGAUCAUUU, CAAACAACCCUUAUCGUAAA; siRNA POLQ-2: ON-TARGET plus smart pool of 4 POLQ siRNA from Dharmacon: UCAGAGGGAUGGAGCUAAU, GAGAUUACCCUUUCACCUA, CAAUUUUACAGUACGGAAA, UGAUAGAUUAGCCUAGUA) or Luciferase (CTRL) (5’-CGUACGCGGAAUACUUCGAdTdT-3’ from Sigma-Aldrich, Saint-Louis, USA) at the final concentration of 50nM, by using Lipofectamine 2000 transfection reagent (Invitrogen, Carlsbad, USA) following the manufacturer’s suggestions. Transfection medium was changed 8 hours later to complete medium.

value: RKO

tag: transfection

value: polQ siRNA

source_name: neosynthetized DNA in late S phase


title: siRNA control replication timing 2

description: Biological replicate 2 of 2. Control siRNA

tag: cell line

value: control siRNA


title: siRNA polQ replication timing 1

description: Biological replicate 1 of 2. polQ siRNA


title: Gata6 null/Apc null B

description: Gata6 null/Apc null

source_name: Gata6 null/Apc null

value: B

value: Gata6 null/Apc null


title: siRNA control replication timing 1

description: Biological replicate 1 of 2. Control siRNA


title: Gata6 null/Apc null A

description: Gata6 null/Apc null


title: Leukocyte_child_affected_N9

city: PARIS

first: Anne

last: Philippi

address: 10 avenue de Verdun

institute: INSERM

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations (GeneChip Fluidics Station 450), and scanned using Affymetrix scanner GCS3000-7G.

data_processing: Genotype Call (SNP call): AA, AB, BB, and NoCall;

source_name: Leukocyte peripheral blood N9

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from leukocyte obtained from peripheral blood using the Wizard Kit. DNA quality and quantity was assessed using both Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Leukocyte peripheral blood

tag: disease status

value: affected

tag: gender

value: male


title: siCT R5020

description: Gene expression after R5020 treatment for 24hr in siCT LNCaP

source_name: LNCaP, siCT, R5020, replicate 1


title: Leukocyte_child_affected_N8

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N8


title: Apc null B

description: Apc null


title: siCT DHT

description: Gene expression after DHT treatment for 24hr in siCT LNCaP

source_name: LNCaP, siCT, DHT, replicate 1


title: Leukocyte_child_affected_N5

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N5


title: Leukocyte_child_unaffected_N6

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N6

value: unaffected


title: siCT v

description: Gene expression after vehicle treatment for 24hr in siCT LNCaP

source_name: LNCaP, siCT, vehicle, replicate 1


title: siCT E2

description: Gene expression after E2 treatment for 24hr in siCT LNCaP

source_name: LNCaP, siCT, E2, replicate 1


title: Leukocyte_child_affected_N4

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N4


title: Leukocyte_child_unaffected_N3

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N3


title: E13.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model tongue bud 3

status: Public on Jun 18 2014

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description: Whole genome transcriptome profile of tongue bud, collected at embryonic day 13.5, from mouse with a conditional inactivation of the Alk5 gene in the cranial neural crest.

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: Standard Affymetrix scanning protocol was used.

data_processing: Samples were processed by RMA normalization and log2-scaled expression values were generated through the WebArray tool (URL: http://www.webarraydb.org/webarray/index.html) with default options. p-values for significance testing were adjusted using the SPLOSH (Spacings LOESS Histogram) method as implemented by WebArray.

label_protocol: Standard Affymetrix cRNA labeling protocol was used.

growth_protocol: Standard IACUC protocols were used

extract_protocol: Embryo was harvested at the designated time point. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from murine tongue bud tissue at E13.5.

treatment_protocol: Mice were maintained under standard IACUC protocols.

value: Alk5 fl/fl; Wnt1-Cre

tag: strain

value: tongue bud

value: Not determined


title: E13.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model tongue bud 4


title: Leukocyte_child_unaffected_N7

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N7


title: Leukocyte_mother_unaffected_N2

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N2

value: female


title: E13.5 Alk5 fl/fl control mouse tongue bud 4

description: Whole genome transcriptome profile of tongue bud, collected at embryonic day 13.5, from control mouse

source_name: E13.5 Control Mouse tongue bud 4

value: Alk5 fl/fl


title: E13.5 Alk5 fl/fl control mouse tongue bud 1

source_name: E13.5 Control Mouse tongue bud 1


title: E13.5 Alk5 fl/fl control mouse tongue bud 2

source_name: E13.5 Control Mouse tongue bud 2


title: E13.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model tongue bud 1


title: E11.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model mandibular arch 3

description: Whole genome transcriptome profile of mandibular arch, collected at embryonic day 11.5, from mouse with a conditional inactivation of the Alk5 gene in the cranial neural crest.

extract_protocol: Embryo was harvested at the designated time point. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from murine mandibular arch tissue at E11.5.

value: Mandibular arch


title: E13.5 Alk5 fl/fl control mouse tongue bud 3

source_name: E13.5 Control Mouse tongue bud 3


title: neoplasitc epithelium 3_MeDIP_chip

city: Shanghai

first: yun

middle: xiao

last: zhang

address: Room 305, Building #1,639 Zhi Zao Ju Road

department: Oral Mucosal Diseases

country: China

institute: Shanghai Ninth People's Hospital Affiliated Shanghai JiaoTong University School of Medicine

description: MeDIP-chip neoplastic epithelium cells promoter methylation

hyb_protocol: standard Nimblegen protocol

scan_protocol: Arrays were scanned on an GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: get the Peaks data with specified parameters (sliding window width: 750bp; mini probes per peak: 2; P-value minimum cutoff: 2; maximum spacing between nearby probes within peak: 500bp)

source_name: MeDIP DNA from neoplastic epithelium 3

label_protocol: standard Nimblegen protocol

extract_protocol: Cut tissue into small pieces, and place in a 1.5 ml microcentrifuge tube. Add 180 μl Buffer ATL and 20 μl proteinase K and vortex; incubate at 56°C until the tissue is completely lysed. Add 4 μl RNase A (100 mg/ml) and vortex, incubate for 2 min at room temperature. Vortexes for 15 s, add 200 μl Buffer AL and vortex. Then add 200μl ethanol (96%) and vortex. Pipet the mixture into the DNeasy Mini spin column placed in a 2 ml collection tube. Centrifuge at 6000g for 1 min. Discard flow-through and place the spin column in a new 2 ml collection tube, add 500 μl Buffer AW1, and centrifuge for 1 min at 6000 g. Discard flow-through and place the column in a new 2 ml collection tube, add 500 μl Buffer AW2, centrifuge for 3 min at 20000g. Discard flow-through and place the column in a clean 1.5 ml microcentrifuge tube, pipet 200 μl Buffer AE directly onto the DNeasy membrane. Incubate at room temperature for 1 min, then centrifuge for 1 min at 6000g to elute.

value: neoplastic epithelium 3

tag: ethnicity

value: chinese

source_name: Input DNA from neoplastic epithelium 3


title: Leukocyte_father_unaffected_N1

description: Hybridized to 250K_Nsp

source_name: Leukocyte peripheral blood N1


title: E11.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model mandibular arch 4


title: E11.5 Alk5 fl/fl control mouse mandibular arch 2

description: Whole genome transcriptome profile of mandibular arch, collected at embryonic day 11.5, from control mouse

source_name: E11.5 Control Mouse Mandibular Arch 2


title: E11.5 Alk5 fl/fl control mouse mandibular arch 3

source_name: E11.5 Control Mouse Mandibular Arch 3


title: E11.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model mandibular arch 2


title: E13.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model tongue bud 2


title: E11.5 Alk5 fl/fl control mouse mandibular arch 4

source_name: E11.5 Control Mouse Mandibular Arch 4


title: E11.5 Wnt1-Cre;Alk5 fl/fl conditional knockout mouse model mandibular arch 1


title: normal epithelium 2_MeDIP_chip

description: MeDIP-chip normal epithelium cells promoter methylation

source_name: MeDIP DNA from normal epithelium 2

value: normal epithelium 2

source_name: Input DNA from normal epithelium 2


title: normal epithelium 1_MeDIP_chip

source_name: MeDIP DNA from normal epithelium 1

value: normal epithelium 1

source_name: Input DNA from normal epithelium 1


title: neoplasitc epithelium 1_MeDIP_chip

source_name: MeDIP DNA from neoplastic epithelium 1

value: neoplastic epithelium 1

source_name: Input DNA from neoplastic epithelium 1


title: Biopsy_No_Graft_Loss_20

city: Bronx

first: Pilib

last: Ó Broin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Gene expression data from graft functioning biopsy

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeometric p-values for over or under-representation of each GO term.

source_name: Biopsy from graft functioning patient

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: One biopsy core was collected into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation. Renal tissue and glomerular content in all cores was verified by Pathology department technical personnel using a dissecting microscope and any non-renal tissue was removed.

value: kidney

tag: tissue source

value: biopsy


title: Biopsy_No_Graft_Loss_15


title: Biopsy_No_Graft_Loss_18


title: Biopsy_No_Graft_Loss_13


title: Biopsy_No_Graft_Loss_17


title: normal epithelium 3_MeDIP_chip

source_name: MeDIP DNA from normal epithelium 3

value: normal epithelium 3

source_name: Input DNA from normal epithelium 3


title: E11.5 Alk5 fl/fl control mouse mandibular arch 1

source_name: E11.5 Control Mouse Mandibular Arch 1

tag: age


title: Biopsy_No_Graft_Loss_16


title: Biopsy_No_Graft_Loss_8


title: Biopsy_No_Graft_Loss_7


title: Biopsy_No_Graft_Loss_11


title: Biopsy_No_Graft_Loss_12


title: Biopsy_No_Graft_Loss_9


title: Biopsy_No_Graft_Loss_2


title: neoplasitc epithelium 2_MeDIP_chip

source_name: MeDIP DNA from neoplastic epithelium 2

value: neoplastic epithelium 2

source_name: Input DNA from neoplastic epithelium 2


title: Biopsy_No_Graft_Loss_5


title: Biopsy_No_Graft_Loss_1


title: Biopsy_No_Graft_Loss_6


title: Biopsy_Graft_Loss_7

description: Gene expression data from graft loss biopsy

source_name: Biopsy from graft loss patient


title: Biopsy_Graft_Loss_8


title: Biopsy_Graft_Loss_6


title: Biopsy_No_Graft_Loss_10


title: Biopsy_No_Graft_Loss_3


title: Biopsy_No_Graft_Loss_4


title: Mutant RNA Sample 5.5_rep2

city: Freiburg

first: Jan

last: Mitschke

address: Schaenzlestr. 1

department: Biologie III

country: Germany

institute: University of Freiburg

hyb_protocol: For RNA hybridizations, the labelled RNA mix was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA. Hybridization of labelled genomic DNA was performed similar to RNA hybridization, but omittingt the fragmentation step in the Agilent protocol. For DNA hybridization 0.5 to 3.8 µg of labeled DNA were used.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the modified protocol GE1_107_Sep09 Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: Mutant RNA Sample 5.5

label_protocol: The RNA mix was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. DNA was fragmented by 3h incubation at 95°C in H2O and Cy3 labeled with the Kreatech kit mentioned before.

growth_protocol: Cells were grown in liquid cultures under constant illumination with white light at 50 µmol photons m^-2 s^-1 in BG11 medium (Rippka et al., 1979) supplemented with 10 mM TES pH 8 at 30 °C. After three days, cultures were shifted to light-dark conditions (12h:12h light:dark cycle). Cells were harvested by filtering through Supor-800 0.8 µm membrane filters during the first period of alternated illumination at timepoints CT 17.5 (timepoint 17.5) and CT 5.5 (timepoint 5.5) and after six days of growth in a light-dark cycle at timepoint CT 5.5 (timepoint 0).

extract_protocol: Each membrane filter was immediately put into PGTX reagent (Pinto et al., 2009), fragmented by vortexing, frozen in liquid nitrogen and stored at ―20 °C. The samples were thawed at 95 °C and vortexed in between. After incubation on ice for 5 min, 150 µl of cold bromochloropropane were added. Following an incubation at room temperature for 15 min, the phases were separated by centrifugation at 4 °C. The aqueous phase was treated with an equal volume of phenol/chloroform/isoamylalcohol (25:24:1) and centrifuged at 4°C. The RNA in the supernatant was precipitated over night at ―20 °C by addition of an equal volume of isopropanol, pelleted by centrifugation at 13.000 rpm for 30 min at 4°C, washed with 1 ml of 75 % v/v ethanol and pelleted again. The RNA was air dried and resuspended in DEPC-treated ddH2O. The total extracted RNA was quantified using a Nanodrop spectrophotometer. Prior to the microarray analysis, the RNA was treated with DNaseI (Invitrogen). Integrity of the RNA was examined by electrophoretic separation on a 1.3% (w/v) formaldehyde agarose gel.

tag: timepoint

value: deletion of kaiAB1C1


title: Biopsy_Graft_Loss_5


title: Biopsy_Graft_Loss_4


title: Mutant RNA Sample 5.5_rep1


title: Biopsy_Graft_Loss_3


title: Mutant RNA Sample 17.5_rep1

source_name: Mutant RNA Sample 17.5


title: Biopsy_Graft_Loss_2


title: WT RNA Sample 5.5_rep2

source_name: WT RNA Sample 5.5

value: wildtype


title: Biopsy_Graft_Loss_1


title: Mutant RNA Sample 0_rep1

source_name: Mutant RNA Sample 0


title: WT RNA Sample 5.5_rep1


title: Mutant RNA Sample 17.5_rep2


title: WT RNA Sample 17.5_rep1

source_name: WT RNA Sample 17.5


title: WT RNA Sample 17.5_rep2


title: WT RNA Sample 0_rep2

source_name: WT RNA Sample 0


title: Male 11d EB E1 exposure 2

city: Jerusalem

first: Daniel

last: Ronen

address: Edmond J. Safra Campus, Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

hyb_protocol: Fragmented, labeled cDNA was hybridized for 17h at 45 C at 60 RPM. Following hybridization array was washed using Affymetrix® GeneChip® Fluidics Station 450

scan_protocol: Arrays  were scanned  using GeneChip® Scanner 3000 7G with Autoloader

data_processing:
The data were analyzed with Robust Multi-array Average (RMA) using Affymetrix default analysis settings. Using Affymetrix "Expression Console" software;
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: 11d EB exposed to 100nM E1

label_protocol: cDNA was generation and labeled with biotin-TdT according  to manufactures protocol (Ambion® WT Expression Kit)

growth_protocol: Human ES cells were maintained on mitomycin arrested mouse embryonic fibroblasts (MEF) feeder layer and cultures in KnockOut DMEM (Gibco-Invitrogen) containing, 15% Knockout serum (Gibco-Invitrogen), 2mM L-Glutamine (Sigma-Aldrich), 1x non-essential amino acids (biological industries, Israel), 0.1mM b-Mercatoethanol (Sigma-Aldrich), 8ng,ml Basic FGF (Peprotech) and 50 units/ml of penicillin and 50ug/ml streptomycin (biological industries, Israel).

extract_protocol: Total RNA was extracted using 5 Prime PerfectPure RNA Cultured Cell Kit. All samples were DNAse treated according to the manufacturer's instructions.

treatment_protocol: Medium was replaced with starvation medium composed of Phenol-red free DMEM supplemented with 1% Knockout serum, 2mM L-Glutamine (Sigma-Aldrich), 1x non-essential amino acids (biological industries, Israel), 0.1mM b-Mercatoethanol (Sigma-Aldrich), 8ng/ml Basic FGF (Peprotech), 1X Insulin-Transferrin-Selenium (Gibco-Invitrogen) and 50 units/ml of penicillin and 50ug/ml streptomycin (Biological Industries, Israel). and suplamented with 100nM estrone (Sigma-Aldrich).

value: male

value: embryonic stem (ES) cells

tag: exposed to

value: 100nM E1 for 11d


title: Female 3d E1 exposure

source_name: ES cells exposed to 100nM E1 for 3d

value: female

value: 100nM E1 for 3d


title: Male 3d E1 exposure


title: Female 11d EB E1 exposure 1


title: Male control

source_name: ES cells no treatment

value: none (0d control)


title: Female 11d EB E1 exposure 2


title: Mutant RNA Sample 0_rep2


title: WT RNA Sample 0_rep1


title: Male 11d EB E1 exposure 1


title: SAM636908 KM-12 PRPF6-4 3

city: South San Francisco

first: Jinfeng

last: Liu

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

description: ch1 treatment : PRPF6-4

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent G2505C scanner Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: KM12 PRPF6-4

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference.

growth_protocol: SW620 and KM-12 human colon cancer cell lines were grown in DMEM (high glucose) + 10% FBS media.

extract_protocol: Three days after transfection total RNA was harvested with the Qiagen RNeasy Mini kit with on-column DNase digestion.

treatment_protocol: Colon cancer cell line SW620 and KM-12 were transfected with siRNAs against a non-targeting control (NTC) or PRPF6 (three independent siRNAs), each treatment was done in three replicates.

source_name: Universal Human Reference RNA

tag: control type

value: Universal Human Reference RNA


title: Obese rat liver RNA original

city: Hyderabad

first: Vajreswari

last: Ayyalasomayajula

state: Telangana

address: Tarnaka

department: Lipid Chemistry Division

country: India

institute: National Institute of Nutrition

description: Gene expression data from liver of WNIN/Ob obese rat

hyb_protocol: Hybridization cocktail containing the labelled probes was prepared, using Genechip Hybridization, wash and stain kit (Affymetrix, California, USA). 200μl of hybridization cocktail was loaded on to Rat Gene 1.0 ST arrays (Affymetrix, California, USA) and incubated for 18h at 450C and 60rpm in hybridization oven. After incubation, arrays were washed and scanned according to the manufacturer’s instructions. Four chips were used for hybridization (one for lean sample and one for obese sample with one technical replicate each). Chip images were given in figure 22. The Rat Gene 1.0 ST array consists of 722,254 probes representing 27,342 well-annotaed genes (covers 99.98% coverage of NM sequences present in the April 3, 2007, RefSeq data base).

scan_protocol: Gene chips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: Chip images were checked for artefacts and quality control analyses were performed.  CEL files generated were pre-processed by Robust Multiarray analysis (RMA) and normalised by quantile method, using Array Star software (DNASTAR, Inc. Wisconsin, USA). To determine the differentially-expressed genes, intensity values from technical replicates from lean group were averaged and compared against the averaged intensity values from obese group. Genes with more than 2 fold differentially regulated (up or downregulated) were taken into consideration.

organism: Rattus norvegicus

source_name: Liver

label_protocol: Two pools of RNA were prepared (RNA from four lean and four obese animals was pooled separately) and 100ng of pooled, total RNA was taken and converted to antisense cRNA by in vitro-transcription through single stranded and double stranded cDNA steps using WT cDNA synthesis and amplification kit (Affymetrix, California, USA). From antisense cRNA, single stranded cDNA was synthesized and cRNA was hydrolysed by using the same kit. cDNA was fragmented and labelled with phycoerythrin using WT terminal labelling kit (Affymetrix, California, USA).

growth_protocol: All the experimental procedures were approved by the Institutional Animal Ethical Committee (IAEC) of National Center for Laboratory Animal Sciences, Hyderabad, India. Four-month-old, male, WNIN/Ob lean and obese rats (n=4 for each phenotype) were obtained from the National Center for the Laboratory Animal Sciences (NCLAS), Hyderabad, India. The animals were housed in cages and acclimatised for one week under controlled conditions of light (12 hours of light/12 hours of dark) and temperature (22±2oC). Stock-diet and water were provided ad libitum. After acclimatization, blood was drawn and animals were sacrificed by CO2 asphyxiation. Liver was immediately removed, frozen in liquid nitrogen, and stored at -80 o C.

extract_protocol: Total RNA was isolated and purified using QIAGEN RNeasy Mini Kit (Invitrogen, California, USA). RNA concentration and quality were determined by reading the absorbance at 230nm, 260nm, 270nm, 280nm, and 320nm. Along with the RNA concentration (260nm), we checked protein contamination (260nm/280nm, ratio≥2), phenol contamination (260nm/270nm, ratio≥1.2) and salt contamination (260nm/230nm, ratio≥2). RNA integrity was confirmed by agarose gel electrophoresis (1%).

treatment_protocol: No treatments were done. Baseline gene expression in lean and obese phenotypes were comapred.

value: Liver

value: WNIN/Ob strain

tag: phenotype

value: Obese phenotype


title: Femal control

tag: cell type


title: Obese rat liver RNA technical replicate

description: Gene expression data from techincal replicate of WNIN/Ob obese rat liver


title: SAM636906 KM-12 PRPF6-4 1

description: ch1 treatment : PRPF6-4


title: SAM636904 KM-12 PRPF6-3 2

description: ch1 treatment : PRPF6-3

source_name: KM12 PRPF6-3


title: SAM636905 KM-12 PRPF6-3 3

description: ch1 treatment : PRPF6-3


title: SAM636903 KM-12 PRPF6-3 1

description: ch1 treatment : PRPF6-3


title: serum_lung cancer population

status: Public on Jun 17 2014

city: Guangzhou

first: jinkun

last: huang

state: guangdong

address: 195 Dongfengxi Road, Guangzhou

department: school of public health

institute: Guangzhou Medical University

description: All study samples were obtained from The First Affiliated Hospital of Guangzhou Medical University (Guangzhou, China)

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: Serom from lung cancer patients

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: serum


title: Biopsy_No_Graft_Loss_19

source_name: Biopsy from graft functioning patient

value: kidney


title: serum_cigarette smoking population

source_name: Serom from smokers


title: serum_normal population

source_name: Serom from non-smokers


title: SAM636907 KM-12 PRPF6-4 2

description: ch1 treatment : PRPF6-4


title: SAM636896 SW620 PRPF6-4 3

description: ch1 treatment : PRPF6-4

source_name: SW620 PRPF6-4


title: Lean rat liver RNA technical replicate

description: Gene expression data from technical replicate of WNIN/Ob lean rat liver

value: Lean phenotype


title: SAM636902 KM-12 NTC 3

description: ch1 treatment : NTC

source_name: KM12 NTC


title: Obese rat 2 adipose tissue

description: Gene expression data from adipose tissue of WNIN/Ob obese rat

hyb_protocol: Hybridization cocktail containing the labelled probes was prepared using Genechip Hybridization, wash and stain kit (Affymetrix, California, USA).   200μl of hybridization cocktail was loaded on to Rat Gene 1.0 ST arrays (Affymetrix, California, USA) and incubated for 18h at 450C and 60rpm in hybridization oven. After incubation, arrays were washed and scanned. Four chips were used for hybridization (two for lean and two for obese animals). The Rat Gene 1.0 ST array consists of 722,254 probes representing 27,342 well-annotaed genes (covers 99.98% coverage of NM sequences present in the April 3, 2007, RefSeq data base).

data_processing: Chip images were checked for artefacts and quality control analyses were performed.  CEL files generated were pre-processed by Robust Multiarray analysis (RMA) and normalised by quantile method, using Array Star software (DNASTAR, Inc. Wisconsin, USA). To determine the differentially-expressed genes, intensity values from two lean rat samples were averaged and compared against the averaged intensity values from two obese samples. Genes with more than 2 fold differentially regulated (up or downregulated) were taken into consideration.

source_name: retroperitonal adipose tissue

label_protocol: 100ng of total RNA was taken and converted to antisense cRNA by in vitro-transcription through single stranded and  double stranded cDNA steps, using WT cDNA synthesis and amplification kit (Affymetrix, California, USA). From antisense cRNA, single stranded cDNA was synthesized and cRNA was hydrolysed by using the same kit. cDNA was fragmented and labelled with phycoerythrin using WT terminal labelling kit (Affymetrix, California, USA).

growth_protocol: Male, Four-month-old WNIN/Ob lean and obese rats (n=2 for each phenotype) were obtained from the National Center for the Laboratory Animal Sciences (NCLAS), Hyderabad, India. The animals were housed in cages and acclimatised for one week under controlled conditions of light (12 hours of light/12 hours of dark) and temperature (22±2oC). Stock-diet and water were provided ad libitum. All the experimental procedures were approved by the Institutional Animal Ethical Committee (IAEC). After acclimatization, blood was drawn and animals were sacrificed by CO2 asphyxiation. Retroperitoneal adipose tissue was immediately removed, frozen in liquid nitrogen, and stored at -80 o C.

extract_protocol: Total RNA was isolated using the Trizol RNA isolation method (Invitrogen, Carlsbad, CA) with slight modifications to increase the RNA purity and yield. Briefly, adipose tissue (500mg) was homogenized in 0.5mL Trizol reagent in 2mL eppendorf tube and later 0.5mL Trizol was added and vertexed. Fat layer was removed after centrifugation of the homogenate for 10,000g at 4oC for 5 minutes. Later steps were performed according to the manufacturer’s instructions with three times chloroform wash. RNA was precipitated with isopropanol and washed with alcohol (75%). After washing, alcohol was removed and tubes were centrifuged at 2000g for 2 minutes at room temperature  to remove the traces of the ethyl alcohol (which is the major contaminant that affect cRNA amplification step during microarray standardization) and dissolved in autoclaved milliQ water. RNA concentration and quality were determined by reading the absorbance at 230nm, 260nm, 270nm, 280nm, and 320nm. Along with the RNA concentration (260nm), we checked protein contamination (260nm/280nm, ratio≥2), phenol contamination (260nm/270nm, ratio≥1.2) and salt contamination (260nm/230nm, ratio≥2). RNA integrity was confirmed on 1% agarose gel electrophoresis. We haven’t used column methods for RNA purification, as we are getting low concentrations of RNA, which is not suitable for downstream microarray procedures.

value: retroperitonal adipose tissue


title: Lean rat liver RNA original

description: Gene expression data from liver of WNIN/Ob lean rat


title: Obese rat 1 adipose tissue


title: SAM636900 KM-12 NTC 1

description: ch1 treatment : NTC


title: obese-control_replicate6

city: Giessen

first: Janine

last: Keller

address: Heinrich-Buff-Ring 26-32

department: Inst. for Animal Nutrition

institute: JLU Giessen

description:
Biological replicate 6 from 6. obese control
sample number in normalized data file: 3

hyb_protocol: Labeled RNA samples were mixed pair-wise and hybridized according to the instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria).

scan_protocol: Afterwards, slides were scanned using the Agilent G2565BA Microarray scanner System (Agilent Technologies, Inc., USA).

data_processing: The image analysis was carried out using the ImaGene® 9 (mercury LNATM microRNA Array Analysis Software, Exiqon, Denmark). The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. The file "Normalized_data.txt contains the normalized signal intensities.

source_name: muscle obese control

label_protocol: 750 ng total RNA from both sample and reference was labeled using the mercury LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark).

extract_protocol: For miRNA microarray and qRT-PCR analysis total RNA, including small RNAs, was isolated from muscle samples using the Qiagen miRNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol.

value: Zucker

value: skeletal muscle


title: Biopsy_No_Graft_Loss_14

value: biopsy


title: obese-control_replicate5

description:
Biological replicate5 from 6. obese control
sample number in normalized data file: 2

value: male


title: Lean rat 1 adipose tissue

description: Gene expression data from adipose tissue of WNIN/Ob lean rat


title: Lean rat 2 adipose tissue


title: obese-carnitine_replicate5

description:
Biological replicate 5 from 6. obese carnitine
sample number in normalized data file: 15

source_name: muscle obese carnitine


title: SAM636901 KM-12 NTC 2

description: ch1 treatment : NTC


title: obese-carnitine_replicate4

description:
Biological replicate 4 from 6. obese carnitine
sample number in normalized data file: 18


title: obese-carnitine_replicate6

description:
Biological replicate 6 from 6. obese carnitine
sample number in normalized data file: 13


title: obese-control_replicate4

description:
Biological replicate 4 from 6. obese control
sample number in normalized data file: 6


title: SAM636894 SW620 PRPF6-4 1

description: ch1 treatment : PRPF6-4


title: obese-carnitine_replicate3

description:
Biological replicate 3 from 6. obese carnitine
sample number in normalized data file: 14


title: obese-carnitine_replicate2

description:
Biological replicate 2 from 6. obese carnitine
sample number in normalized data file: 17


title: obese-control_replicate3

description:
Biological replicate 3 from 6. obese control
sample number in normalized data file: 5


title: obese-control_replicate2

description:
Biological replicate 2 from 6. obese control
sample number in normalized data file: 1


title: obese-carnitine_replicate1

description:
Biological replicate 1 from 6. obese carnitine
sample number in normalized data file: 16


title: SAM636890 SW620 NTC 3

description: ch1 treatment :NTC

source_name: SW620 NTC


title: obese-control_replicate1

description:
Biological replicate 1 from 6. obese control
sample number in normalized data file: 4


title: SAM636892 SW620 PRPF6-3 2

description: ch1 treatment : PRPF6-3

source_name: SW620 PRPF6-3


title: SAM636893 SW620 PRPF6-3 3

description: ch1 treatment : PRPF6-3


title: SAM636891 SW620 PRPF6-3 1

description: ch1 treatment : PRPF6-3


title: SAM636895 SW620 PRPF6-4 2

description: ch1 treatment : PRPF6-4


title: SAM636888 SW620 NTC 1

description: ch1 treatment : NTC


title: SAM636889 SW620 NTC 2

description: ch1 treatment : NTC


title: RU-5 5

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description:
RU-5
5

hyb_protocol: Quiagen single amplification protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: skin

label_protocol: Quiagen single amplification protocol

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol

tag: time

value: week 12

tag: lesions

value: non lesional

tag: responder

value: responder

value: M

tag: scorad


title: RU-4 4

description:
RU-4
4

value: week 2

value: lesional


title: RU-4 6

description:
RU-4
6


title: RU-6 4

description:
RU-6
4


title: RU-6 2

description:
RU-6
2

value: day 1


title: RU-8 5

description:
RU-8
5

value: nonresponder


title: RU-5 2

description:
RU-5
2


title: RU-6 1

description:
RU-6
1


title: RU-7 3

description:
RU-7
3


title: RU-4 3

description:
RU-4
3


title: RU-6 6

description:
RU-6
6


title: RU-7 1

description:
RU-7
1


title: RU-4 5

description:
RU-4
5


title: RU-6 3

description:
RU-6
3


title: RU-4 1

description:
RU-4
1


title: RU-8 2

description:
RU-8
2


title: RU-5 4

description:
RU-5
4


title: RU-3 4

description:
RU-3
4


title: RU-7 2

description:
RU-7
2


title: RU-3 3

description:
RU-3
3


title: RU-8 4

description:
RU-8
4


title: RU-8 3

description:
RU-8
3


title: RU-8 1

description:
RU-8
1


title: RU-5 1

description:
RU-5
1


title: RU-6 5

description:
RU-6
5


title: RU-3 5

description:
RU-3
5


title: RU-4 2

description:
RU-4
2


title: RU-5 6

description:
RU-5
6


title: RU-10 2

description:
RU-10
2


title: RU-10 6

description:
RU-10
6


title: RU-10 3

description:
RU-10
3


title: RU-3 1

description:
RU-3
1


title: RU-10 4

description:
RU-10
4


title: RU-10 5

description:
RU-10
5


title: RU-1 4

description:
RU-1
4


title: RU-10 1

description:
RU-10
1


title: RU-3 2

description:
RU-3
2


title: I-6 4

description:
I-6
4

value: F


title: I-14 5

description:
I-14
5


title: RU-1 3

description:
RU-1
3


title: RU-1 2

description:
RU-1
2


title: I-6 5

description:
I-6
5


title: I-14 6

description:
I-14
6


title: RU-1 6

description:
RU-1
6


title: I-16 6

description:
I-16
6


title: I-16 5

description:
I-16
5


title: I-18 2

description:
I-18
2


title: RU-1 1

description:
RU-1
1


title: RU-3 6

description:
RU-3
6


title: RU-1 5

description:
RU-1
5


title: I-18 5

description:
I-18
5


title: I-18 4

description:
I-18
4


title: I-16 4

description:
I-16
4


title: I-16 3

description:
I-16
3


title: I-16 1

description:
I-16
1


title: I-18 1

description:
I-18
1


title: I-16 2

description:
I-16
2


title: I-18 3

description:
I-18
3


title: I-13 5

description:
I-13
5


title: I-18 6

description:
I-18
6


title: I-14 4

description:
I-14
4


title: I-13 6

description:
I-13
6


title: I-13 4

description:
I-13
4


title: I-13 3

description:
I-13
3


title: I-13 2

description:
I-13
2


title: I-13 1

description:
I-13
1


title: I-14 2

description:
I-14
2


title: I-11 5

description:
I-11
5


title: I-14 1

description:
I-14
1


title: I-11 6

description:
I-11
6


title: I-14 3

description:
I-14
3


title: I-11 2

description:
I-11
2


title: I-10 6

description:
I-10
6


title: I-10 5

description:
I-10
5


title: I-10 1

description:
I-10
1


title: I-11 3

description:
I-11
3


title: I-11 1

description:
I-11
1


title: RU-5 3

description:
RU-5
3


title: I-10 2

description:
I-10
2


title: I-10 3

description:
I-10
3


title: 24h rep-3 [control vs. infected skin]

city: AUBURN

first: chao

last: li

address: 203 swingle hall

institute: auburn university

description: blue catfish skin

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

scan_protocol: Following hybridization, the slides were scanned using a GenePix personal 4100A Scanner (Axon Instruments) and initial analysis were performed with Feature Extraction software v9.5.3 (Agilent).

data_processing: Agilent Feature Extraction Software v9.5.3 was used for background subtraction and LOWESS normalization.

organism: Ictalurus furcatus

source_name: 24h rep-3

label_protocol: cDNA was generated from 500 ng of each isolated RNA sample; cRNA was then made using Cy3-CTP or Cy5-CTP incorporation for labeling purposes. The fluorescently labeled cRNA probes were purified using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA), and the concentration, fluorescent intensities, and quality of labeled cRNA probes were determined using a Nano-drop spectrophotometer. At each timepoint, 3 Cy3 labeled cRNA and 3 Cy5 labeled cRNA were generated with randomized dye assignments between treatment and control samples.

growth_protocol: Fish were challenged in 3 control and 3 treatment groups per timepoint in each group. Aquaria were randomly divided into sampling timepoints-2 h treatment, 12 h treatment, 24 h treatment, 2 h control, 12 h control, and 24 h control with thirty fish in each aquarium.Immersion experiments were performed in a 25 L bucket with aeration. Briefly, 50 ml of overnight Aeromonas hydrophila cells 1.5×109 were added to water to give a final volume of 5 L (1.5×107 final exposure concentration). Thirty blue catfish were immersed in each bucket for 2 h. After the 2 h immersion, the catfish were distributed to 30 L glass aquaria.

extract_protocol: Total RNA was extracted from tissues using the RNeasy Plus Universal Mini Kit (Qiagen) following manufacturer’s instructions.

tag: reference group

value: skin from control group

tag: test group

value: skin after Aeromonas hydrophila infection


title: I-11 4

description:
I-11
4


title: I-10 4

description:
I-10
4


title: CMC rep3

city: Beijing

first: song

last: yajian

address: N0.1 Beichen Road

institute: institute of microbiology, chinese acadmy of science

description: Gene expression when cells grown on CMC to mid-logarithmic phase

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies, Santa Clara, CA, US)with default settings.

organism: Bacillus sp. N16-5

source_name: cells grown on CMC, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Cultures were grown under aerobic conditions at 37°C in round-bottom flasks on different substrates to mid-logarithmic phase.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: treatment

value: CMC


title: pectin rep3

description: Gene expression when cells grown on pectin to mid-logarithmic phase

source_name: cells grown on pectin, replicate 3

value: pectin


title: pectin rep2

source_name: cells grown on pectin, replicate 2


title: xylan rep3

description: Gene expression when cells grown on xylan to mid-logarithmic phase

source_name: cells grown on xylan, replicate 3

value: xylan


title: pectin rep1

source_name: cells grown on pectin, replicate 1


title: I-6 3

description:
I-6
3

tag: gender


title: 12h rep-3 [control vs. infected skin]

description: blue catfish skin

source_name: 12h rep-3


title: I-6 1

description:
I-6
1


title: I-5 6

description:
I-5
6


title: CMC rep2

source_name: cells grown on CMC, replicate 2


title: xylan rep2

source_name: cells grown on xylan, replicate 2


title: CMC rep1

source_name: cells grown on CMC, replicate 1


title: I-6 2

description:
I-6
2


title: galactomannan rep3

description: Gene expression when cells grown on galactomannan to mid-logarithmic phase

source_name: cells grown on galactomanan, replicate 3

value: galactomannan


title: 12h rep-1 [control vs. infected skin]

description: blue catfish skin

source_name: 12h rep-1


title: 24h rep-2 [control vs. infected skin]

description: blue catfish skin

source_name: 24h rep-2


title: 24h rep-1 [control vs. infected skin]

description: blue catfish skin

source_name: 24h rep-1


title: xylan rep1

source_name: cells grown on xylan, replicate 1


title: xylose rep3

description: Gene expression when cells grown on xylose to mid-logarithmic phase

source_name: cells grown on xylose, replicate 3

value: xylose


title: xylose rep2

source_name: cells grown on xylose, replicate 2


title: 12h rep-2 [control vs. infected skin]

description: blue catfish skin

source_name: 12h rep-2


title: xylose rep1

source_name: cells grown on xylose, replicate 1


title: arabinose rep3

description: Gene expression when cells grown on arabinose to mid-logarithmic phase

source_name: cells grown on arabinose, replicate 3

value: arabinose


title: 2h rep-3 [control vs. infected skin]

description: blue catfish skin

source_name: 2h rep-3


title: I-5 5

description:
I-5
5

source_name: skin

value: week 12


title: galactomannan rep1

source_name: cells grown on galactomanan, replicate 1


title: arabinose rep2

source_name: cells grown on arabinose, replicate 2


title: galactomannan rep2

source_name: cells grown on galactomanan, replicate 2


title: I-4 6


title: I-5 3

description:
I-5
3

value: non lesional


title: I-5 1

description:
I-5
1

value: responder


title: arabinose rep1

source_name: cells grown on arabinose, replicate 1


title: mannose rep2

description: Gene expression when cells grown on mannose to mid-logarithmic phase

source_name: cells grown on mannose, replicate 2

value: mannose


title: I-5 4

description:
I-5
4

value: week 2


title: mannose rep3

source_name: cells grown on mannose, replicate 3


title: I-4 4

value: lesional

value: M


title: I-5 2

description:
I-5
2

value: day 1


title: 2h rep-1 [control vs. infected skin]

description: blue catfish skin

source_name: 2h rep-1


title: galactose rep1

description: Gene expression when cells grown on galactose to mid-logarithmic phase

value: galactose


title: I-4 5


title: mannose rep1

source_name: cells grown on mannose, replicate 1


title: glucose rep2

description: Gene expression when cells grown on glucose to mid-logarithmic phase

source_name: cells grown on glucose, replicate 2

value: glucose


title: 2h rep-2 [control vs. infected skin]

description: blue catfish skin

source_name: 2h rep-2

value: skin from control group

value: skin after Aeromonas hydrophila infection


title: galactose rep2


title: fructose rep1

description: Gene expression when cells grown on fructose to mid-logarithmic phase

source_name: cells grown on fructose, replicate 1

value: fructose


title: fructose rep3

source_name: cells grown on fructose, replicate 3


title: I-4 3


title: glucose rep3

source_name: cells grown on glucose, replicate 3


title: fructose rep2

source_name: cells grown on fructose, replicate 2


title: glucose rep1

source_name: cells grown on glucose, replicate 1


title: I-4 2


title: I-4 1


title: galactose rep3

source_name: cells grown on galactomanan, replicate 3


title: I-3 5

source_name: skin

value: F


title: PCC6803_WT grown at 30°C rep2

first: Jens

last: Georg

address: Schänzlestr. 1

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.5.1.1 and the protocol GE1_105_Dec08  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized and internal replicate probes were averaged.

source_name: WT

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: The Synechocystis sp. strain PCC 6803 strains used in this study were wild-type and a strain in which crhR has been partially inactivated, crhRTR (Rosana et al., 2012b). Cells were cultured in BG-11 liquid medium at 30°C under continuous illumination (50 microeinsteins m−2s−1) with continuous bubbling with sterile, humidified air essentially as described previously (Chamot and Owttrim, 2000). Media supporting mutant cyanobacterial growth was supplemented with sodium thiosulphate (0.3%) and buffered with tricine (10 mM, pH 8.0) plus spectinomycin and spectinomycin (50 µg/mL each) for crhRTR.

extract_protocol: Mid-log phase Synechocystis cells were inactivated at the stated growth temperature by addition of a 1:1 (vol:vol) dilution of the culture with ice-cold 5% phenol in ethanol. Total RNA was subsequently extracted by glass bead lysis in the presence of phenol, followed by extensive phenol-chloroform extraction and lithium chloride precipitation (Chamot and Owttrim, 2000)

treatment_protocol: Cold stressed cells were produced by incubation as above at 20°C for three h (Chamot and Owttrim, 2000)

tag: genotype

value: WT

value: grown at 30C


title: I-3 6


title: WT_Aero_Rep3

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

description: Gene expression data from WT cells obtained under aerobic conditions.

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Microarray datasets were normalized by Robust Multichip Average (RMA) to log2 scale with background adjustment and quantile normalization.  Statistical analysis of normalized data to identify differentially expressed genes was done using the limma package.  Correction for multiple testing was done using Benjamini-Hochberg correction. All analyses were conducted in the R statistical programming environment.

organism: Cereibacter sphaeroides

source_name: WT cells grown aerobically

label_protocol: Synthesized cDNA was labeled with BioArray™ Terminal labeling kit with biotin-ddUTP

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles either photosynthetically (bubbling with 95% N2, 5% CO2) or aerobically (bubbling with 69% N2, 30% O2, 1% CO2) on Sistrom's minimal media and harvested at exponential phase.

extract_protocol: RNA was extracted from R. sphaeroides cells by hot acid phenol extraction.

tag: strain


title: WT_Aero_Rep1


title: I-3 3


title: I-3 1


title: RSP_0489_Rep3

description: Gene expression data from a ΔRSP_0489 markerless deletion strain obtained under aerobic conditions.

source_name: ΔRSP_0489 deletion cells grown aerobically


title: I-3 4


title: PCC6803_WT grown at 30°C rep1


title: I-1 6


title: PCC6803_WT grown at 30°C rep3


title: PCC6803_crhR_trunc_3h 20°C rep3

source_name: ΔcrhR

value: ΔcrhR

value: grown at 20C


title: PCC6803_WT 3h 20°C rep3


title: PCC6803_crhR_trunc_3h 20°C rep1


title: PCC6803_WT 3h 20°C rep2


title: PCC6803_crhR_trunc_grown at 30°C rep3


title: I-1 5

value: week 12

value: non lesional


title: WT_Aero_Rep2


title: RSP_0489_Rep2


title: PCC6803_crhR_trunc_3h 20°C rep2


title: WT_Photo_Rep3

description: Gene expression data from WT cells obtained under photosynthetic conditions.

source_name: WT cells grown photosynthetically


title: RSP_0489_Rep1


title: PCC6803_crhR_trunc_grown at 30°C rep1


title: PCC6803_WT 3h 20°C rep1


title: I-3 2

value: responder


title: RSP_3341_Rep2

description: Gene expression data from a ΔRSP_3341 markerless deletion strain obtained under photosynthetic conditions.

source_name: ΔRSP_3341 deletion cells grown photosynthetically


title: I-1 4

value: week 2


title: WT_Photo_Rep2


title: RSP_3341_Rep1


title: I-1 3


title: I-1 2

value: lesional


title: WT_Photo_Rep1


title: PCC6803_crhR_trunc_grown at 30°C rep2


title: G3361-ABCB5-KD Rep1

city: Boston

first: Markus

middle: Hermann

last: Frank

state: Massachusetts

address: 300 Longwood Avenue

department: Medicine

institute: Boston Children's Hospital

hyb_protocol: Refer to Dana Farber Cancer Institute Microarray Core

source_name: Melanoma cell-line, G3361, ABCB5 shRNA

extract_protocol: Qiagen miniprep kit with additional 15min on-column DNaseI digestion

tag: cell line

value: pigmented melanoma


title: A375-ABCB5-KD Rep2

scan_protocol: Refer to Dana Farber Cancer Institute Microarray Core

source_name: Melanoma cell-line, A375, ABCB5 shRNA

value: non-pigmented melanoma


title: G3361-Scrambled Rep2

data_processing: Refer to Dana Farber Cancer Institute Microarray Core

source_name: Melanoma cell-line, G3361, control


title: G3361-ABCB5-KD Rep3

label_protocol: Refer to Dana Farber Cancer Institute Microarray Core


title: G3361-Scrambled Rep3


title: G3361-Scrambled Rep1


title: G3361-ABCB5-KD Rep2


title: I-1 1

value: day 1

tag: age

value: M


title: A375-ABCB5-KD Rep3


title: A375-Vector Rep1

source_name: Melanoma cell-line, A375, control


title: A375-ABCB5-KD Rep1


title: 28 dpc_crush - left retina

city: Fort Worth

first: Tasneem

middle: Putliwala

last: Sharma

address: 3500 Camp Bowie Blvd

department: Cell Biology and Anatomy- Visual Sciences

institute: UNTHSC

description: gene expression data from retina following ONC

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

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade

data_processing: Data were collected using the using the GeneChip operating software (GCOS) v1.4 with Affymetrix default analysis settings and global scaling as normalization method

source_name: Retinas harvested at 28 dpc

label_protocol: Biotinylated cDNA were prepared using NuGen FL-Ovation cDNA Biotin Module according to manufacturers protocol.

growth_protocol: BALB/cJ mice aged 2-4 months were utilized for all the experiments and were obtained from the Jackson Laboratories.

extract_protocol: Retina samples were collected in 1ml of TRIzol and homogenized using 5mm steel beads in the TissueLyser LT for five minutes at 50 oscillations/second. For phase separation 50μl of BAN Phase Separation Reagent was added to the homogenized samples, and samples were centrifuged at 14,000rpm for 15 minutes. The upper aqueous phase was transferred to an RNeasy mini column and processed according to the manufacturer's protocol. Total RNA was pooled from each group (experimental or control group at each time point) and 50ng of RNA from pool was converted to cDNA

treatment_protocol: The ON of the left eye was crushed 0.5mm posterior from the globe for 4 seconds using the Nickell’s technique. For the microarray studies, five mice were used per time-point. After the retinal tissues were harvested samples were all pooled for each experimental (left, n=5) and control eye (right, n=5) group and sent for microarray analysis

value: BALB/cJ

tag: stress

value: ONC of left eye

tag: tissue

value: left retina

tag: timepoint

value: 28 dpc


title: A375-Vector Rep3


title: 28 dpc_control - right retina

value: right retina


title: 21 dpc_control - right retina

source_name: Retinas harvested at 21 dpc

value: 21 dpc


title: 21 dpc_crush - left retina


title: 7 dpc_crush - left retina

source_name: Retinas harvested at 7 dpc

value: 7 dpc


title: 14 dpc_control - right retina

source_name: Retinas harvested at 14 dpc

value: 14 dpc


title: 3 dpc_control - right retina

source_name: Retinas harvested at 3 dpc

value: 3 dpc


title: 7 dpc_control - right retina


title: 14 dpc_crush - left retina


title: 3 dpc_crush - left retina


title: Naïve control - right retina

source_name: Retinas harvested from naïve mice

value: Naïve control

value: naïve


title: rGRF3 B

city: Rosario

first: Juan

middle: Manuel

last: Debernardi

state: Santa Fe

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

hyb_protocol: Affymetrix instructions

scan_protocol: Affymetrix instructions

data_processing: The data were analyzed with Robina software (version_1.2.4), analysis strategy: Limma normalization method: gcrma

organism: Arabidopsis thaliana

source_name: Apices from rGRF3 plants

label_protocol: Affymetrix instructions

growth_protocol: Plants were grown on soil medium in short photoperiods (8 h light/16 h dark) at 23 °C.

extract_protocol: Total RNA was extracted from dissected vegetative apices  using the RNeasy plant mini kit (QIAGEN).

treatment_protocol: Vegetative apices together with the leaf primordia were dissected from plants of 20 days.

value: Apices from 20 day-old plants growth in shortdays

tag: phenotype

value: GRF3 overexpressor


title: 28 dpc_control - right optic nerve

description: gene expression data from optic nerve following ONC

source_name: Optic nerves harvested at 28 dpc

extract_protocol: ON samples were collected in 1ml of TRIzol and homogenized using 5mm steel beads in the TissueLyser LT for five minutes at 50 oscillations/second. For phase separation 50μl of BAN Phase Separation Reagent was added to the homogenized samples, and samples were centrifuged at 14,000rpm for 15 minutes. The upper aqueous phase was transferred to an RNeasy mini column and processed according to the manufacturer's protocol. Total RNA was pooled from each group (experimental or control group at each time point) and 50ng of RNA from pool was converted to cDNA

treatment_protocol: The ON of the left eye was crushed 0.5mm posterior from the globe for 4 seconds using the Nickell’s technique. For the microarray studies, five mice were used per time-point. After the ON tissues were harvested samples were all pooled for each experimental (left, n=5) and control eye (right, n=5) group and sent for microarray analysis

value: right optic nerve


title: Arabidopsis seedlings nontreated control, biological rep3

first: Zhenyu

last: Cheng

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, cRNA were hybridized to Affymetrix Arabidopsis ATH1 Genome microarray chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner with Affymetrix GeneChip operating software.

data_processing: The data were analyzed using the Robust Multi-array Average (RMA), with background correction, as implemented in the Bioconductor Project's 'affy' package, version 1.36.1.

source_name: nontreated control seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seedlings were grown in liquid MS medium (Murashige and Skoog basal medium with vitamins from Phytotechnology Laboratories supplemented with 0.5 g/L MES hydrate and 0.5% sucrose at pH 5.7) in 24-well assay plates. Plates were placed on grid-like shelves over water trays on a Floralight cart in a plant growth chamber for 10 days at 21°C with 75% relative humidity under 16 hours of daylight (65-70 μE·m−2·s−1).

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: MS medium in each well was replaced with fresh medium on Day 8. On Day 10, 20 nM of purified protease IV was added into each well and mixed by pipetting. The seedlings were treated for 1 hour before being harvested for RNA extraction.

value: ten-day old seedlings

tag: treated with

value: none (mock control)

value: whole seedling


title: Arabidopsis seedlings nontreated control, biological rep1


title: Arabidopsis seedlings nontreated control, biological rep2


title: rGRF3x35S:GIF1 A

source_name: Apices from rGRF3x35S:GIF1 plants

value: GRF3 and GIF1 overexpressor


title: Naïve control - left retina

value: BALB/cJ


title: rGRF3x35S:GIF1 B


title: 35S:GIF1 B

source_name: Apices from 35S:GIF1 plants

value: GIF1 overexpressor


title: 21 dpc_control - right optic nerve

source_name: Optic nerves harvested at 21 dpc

value: ONC of left eye


title: 14 dpc_control - right optic nerve

source_name: Optic nerves harvested at 14 dpc


title: 35S:GIF1 A


title: Arabidopsis seedlings protease IV-treated sample, biological rep3

description: Arabidopsis_protease IV-3

source_name: protease IV-treated seedlings

value: 20 nM purified protease IV for 1 hr


title: Arabidopsis seedlings protease IV-treated sample, biological rep2

description: Arabidopsis_protease IV-2


title: Arabidopsis seedlings protease IV-treated sample, biological rep1

description: Arabidopsis_protease IV-1


title: 21 dpc_crush - left optic nerve

value: left optic nerve

value: 21 dpc


title: 3 dpc_control - right optic nerve

source_name: Optic nerves harvested at 3 dpc


title: 14 dpc_crush - left optic nerve

value: 14 dpc


title: rGRF3 A


title: 7 dpc_crush - left optic nerve

source_name: Optic nerves harvested at 7 dpc

value: 7 dpc


title: PAXGene blood healthy person H6 t0

status: Public on Jun 16 2014

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

institute: Saarland University

description:
miRNA profiling
PAXGene blood healthy person H6 t0
H6 PAX t0

hyb_protocol: Hybridizations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using feature extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.

source_name: whole blood

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridization Kit

extract_protocol: Total RNA including small RNAs was isolated using miRNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.

tag: individual

tag: disease

value: healthy

value: female

tag: cell type

value: whole blood

tag: time


title: PAXGene blood healthy person H7 t0

description:
miRNA profiling
PAXGene blood healthy person H7 t0
H7 PAX t0


title: CD15 fraction healthy person H7 t0

description:
miRNA profiling
CD15 fraction healthy person H7 t0
H7 CD15+ t0

source_name: CD15 cells

value: CD15 cells


title: Col-0 A

source_name: Apices from wild-type plants

tag: ecotype background

value: Apices from 20 day-old plants growth in shortdays

tag: genotype/variation

value: Wild-type


title: 7 dpc_control - right optic nerve

value: right optic nerve


title: CD56 fraction healthy person H6 t0

description:
miRNA profiling
CD56 fraction healthy person H6 t0
H6 CD56+ t0

source_name: CD56 cells

value: CD56 cells


title: Col-0 B


title: Naïve control - right optic nerve

source_name: Optic nerves harvested from naïve mice

value: Naïve control

value: naÃ¯ve


title: Naïve control - left optic nerve

value: BALB/cJ


title: CD19 fraction healthy person H6 t0

description:
miRNA profiling
CD19 fraction healthy person H6 t0
H6 CD19+ t0

source_name: CD19 cells

value: CD19 cells


title: CD15 fraction healthy person H6 t0

description:
miRNA profiling
CD15 fraction healthy person H6 t0
H6 CD15+ t0


title: CD14 fraction healthy person H6 t0

description:
miRNA profiling
CD14 fraction healthy person H6 t0
H6 CD14+  t0

source_name: CD14 cells

value: CD14 cells


title: CD3 fraction healthy person H6 t0

description:
miRNA profiling
CD3 fraction healthy person H6 t0
H6 CD3+ t0

source_name: CD3 cells

value: CD3 cells


title: CD56 fraction healthy person H5 t0

description:
miRNA profiling
CD56 fraction healthy person H5 t0
H5 CD56+ t0

value: male


title: CD15 fraction healthy person H5 t0

description:
miRNA profiling
CD15 fraction healthy person H5 t0
H5 CD15+ t0


title: CD14 fraction healthy person H5 t0

description:
miRNA profiling
CD14 fraction healthy person H5 t0
H5 CD14+ t0


title: PAXGene blood healthy person H4 t0

description:
miRNA profiling
PAXGene blood healthy person H4 t0
H4 PAX t0


title: CD19 fraction healthy person H4 t0

description:
miRNA profiling
CD19 fraction healthy person H4 t0
H4 CD19+ t0


title: CD3 fraction healthy person H4 t0

description:
miRNA profiling
CD3 fraction healthy person H4 t0
H4 CD3+ t0


title: CD56 fraction healthy person H4 t0

description:
miRNA profiling
CD56 fraction healthy person H4 t0
H4 CD56+ t0


title: CD14 fraction healthy person H4 t0

description:
miRNA profiling
CD14 fraction healthy person H4 t0
H4 CD14+ t0


title: CD15 fraction healthy person H4 t0

description:
miRNA profiling
CD15 fraction healthy person H4 t0
H4 CD15+ t0


title: PAXGene blood healthy person H3 t2

description:
miRNA profiling
PAXGene blood healthy person H3 t2
H3 PAX t2


title: CD3 fraction healthy person H5 t0

description:
miRNA profiling
CD3 fraction healthy person H5 t0
H5 CD3+ t0


title: CD19 fraction healthy person H5 t0

description:
miRNA profiling
CD19 fraction healthy person H5 t0
H5 CD19+ t0


title: 3 dpc_crush - left optic nerve

description: gene expression data from optic nerve following ONC

value: ONC of left eye

value: left optic nerve

value: 3 dpc


title: Exosomes healthy person H3 t1

description:
miRNA profiling
Exosomes healthy person H3 t1
H3 Exos t1

source_name: Exosomes

value: healthy

value: Exosomes


title: Exosomes healthy person H3 t2

description:
miRNA profiling
Exosomes healthy person H3 t2
H3 Exos t2


title: PAXGene blood healthy person H3 t1

description:
miRNA profiling
PAXGene blood healthy person H3 t1
H3 PAX t1

value: whole blood


title: PAXGene blood healthy person H3 t0

description:
miRNA profiling
PAXGene blood healthy person H3 t0
H3 PAX t0


title: CD56 fraction healthy person H3 t0

description:
miRNA profiling
CD56 fraction healthy person H3 t0
H3 CD56+ t0


title: CD56 fraction healthy person H3 t1

description:
miRNA profiling
CD56 fraction healthy person H3 t1
H3 CD56 t1