title: 6_3_Control

description: Agilent Design ID (AMADID): 047718

source_name: Intestinal biospies

tag: patient number

value: Control 6

tag: biopsy location

value: Colon desendens

tag: diagnosis

value: Control

value: F


title: Shoot, control, pH 5.8, rep1

status: Public on Apr 10 2015

type: RNA

city: Mishima, Osaka

first: Jun

last: Murata

address: 1-1-1 Wakayamadai, Shimamoto

department: Bioorganic Research Institute

country: Japan

institute: Suntory Foundation for Life Sciences

description: Gene expression in control plant shoot for pH 5.8.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was used to hybridize Agilent-015241 Rice Gene Expression 4x44K Microarray slides.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) according to manufacturer's instructions.

data_processing: Feature Extraction Software 9.1 (Agilent) was used to analyze scanned images using default parameters.

molecule: total RNA

organism: Oryza sativa

source_name: rice shoot, control, pH 5.8

label_protocol: Cy3-labeled cRNA was prepared from 0.5 ug RNA using One-Color Low RNA Input Linear Amplification PLUS kit (Agilent, CA), and purified using RNeasy column purification (QIAGEN). NanoDrop ND-1000 Spectrophotometer was used to monitor dye incorporation and cRNA yield.

extract_protocol: RNeasy Plant Mini Kit (Qiagen) was used for RNA extraction. The RNA samples were subjected to on-column DNase I digestion according to the manufacturer's instruction. RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific, DE). The quality of RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, CA).

treatment_protocol: Rice seedlings were treated with DMA or EDTA at pH 5.8 or 8.0. The control experiment was no chelator.

tag: tissue

value: shoot

tag: treatment

value: control

tag: ph


title: insulin resistane low risk sample 9

city: Los Angeles

first: yong

last: zhang

state: CA

address: 650 Charles E. Young Drive South

department: school of dentistry

country: USA

institute: UCLA

description: Health, IR low risk

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

label: Biotin

organism: Homo sapiens

source_name: saliva supernatant

label_protocol: standard Affymetrix protocol

growth_protocol: Participants enrolled in this study were recruited in the overnight fasted state, then the collection and processing of glucose (fasting, 30, 60 and 120 minutes) and insulin from blood samples, hemoglobin A1c (HbA1c) , assessment of medical history, socio-demographic characteristics, lifestyle factors, blood pressure and anthropometric and body composition measurements were conducted. During baseline visit, participants were asked to refrain from eating, drinking and oral hygiene procedures for at least 1-hour prior to saliva collection.

extract_protocol: Total RNA was extracted from salia supernatant by using Qiagen RNeasy Mini kit

treatment_protocol: Based on the homeostasis model assessment of insulin resistance (HOMA-IR), using the formula [HOMA-IR= (fasting glucose*fasting insulin)/405], participants were divided into 2 groups: IR high risk group (HOMA-IR value ≥2.5) and IR low risk group (HOMA-IR value <2.5)

tag: risk

value: insulin resistance low risk

tag: disease state

value: Health, IR low risk

tag: sample type

value: saliva supernatant


title: insulin resistane low risk sample 8

description: Health, IR low risk


title: 5_2_iCD

city: Copenhagen

first: Aashiq

middle: H.

last: Mirza

state: Herlev

address: Herlev Ringvej 75

department: University of Copenhagen, Herlev Hospital

country: Denmark

institute: Center for non-coding RNA in Technology and Health

description: Agilent Design ID (AMADID): 047718

hyb_protocol: The labeled cRNA was hybridized to the Agilent Custom 8x60K format lncRNA expression microarray (AMADID 047718, based on Gencodev15 catalog of human long noncoding RNAs, probe length = 60 nt) according to the manufacturer's protocol.

scan_protocol: The arrays were washed, and scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3 μm resolution. Intensity data was extracted using the Feature Extraction software (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software  (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: 100 ng of total RNA was labeled using LowInputQuick Amp Labeling kit v6.5 (Agilent 5190-2305) following manufacturer instructions

growth_protocol: In total 96 colonic biopsy samples were collected from 45 subjects and stored in RNAlater solution (QIAGEN) until RNA extraction.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following manufacturer's instructions. RNA quility was assessed by analysis of rRNA band integrity on an Agilent 2100 Bioanalyzer RNA 6000 LabChip kit (Agilent Technologies).

value: Patient 5

value: Terminal Ileum

value: iCD

tag: Sex

value: M

tag: age


title: insulin resistane high risk sample 11

description: Health, IR high risk

value: insulin risistance high risk

value: Health, IR high risk


title: insulin resistane high risk sample 13

description: Health, IR high risk


title: Ascending aorta from fibulin-4 knockout pup, biological replicate 1

city: Saint Louis

first: Jessica

last: Wagenseil

state: MO

address: 1 Brookings Dr.  Box 1185

department: Mechanical Engineering and Materials Sciences

institute: Washington University

description:
Gene expression data from ascending aortic tissue from p0 pups
KOAA1

hyb_protocol: 5ng of cDNA were fragmented and hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 2.0 ST Array.  Affymetrix Gene 2.0 microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip 7G 3000 scanner.

data_processing: The gene array data was analyzed with the Affymetrix GeneChip Command Console and raw .CEL files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.

label: biotin

organism: Mus musculus

source_name: Mouse lacking fibulin-4 gene, p0, section of aorta from aortic valve to ductus arteriosis

label_protocol: Targets were labeled using Nugen Encore Biotin kit according to the standard NuGenOvationPico WTA System Amplification from 5ng of total RNA

extract_protocol: Total RNA was extracted according to manufacturer kit (Qiagen)

treatment_protocol: p0 pups were sacrificed and the tissues dissected and snap frozen. Mice were genotyped and like-gentoypes and like-tissue sections were pooled in groups of eight.

value: ascending aorta

tag: genotype

value: fibulin-4 knockout

tag: strain


title: Descending aorta from wild-type pup, biological replicate 2

description:
Gene expression data from descending aortic tissue from p0 pups
WTDA2

source_name: Control mouse, p0, section of aorta from vena cava to diaphragm

value: descending aorta

value: wild-type


title: 5_3_iCD

description: Agilent Design ID (AMADID): 047718


title: Root, EDTA, pH 8.0, rep1

description: Gene expression in EDTA-treated plant root at pH 8.0.

source_name: rice root, 30 µM of EDTA, pH 8.0

value: root

value: EDTA


title: insulin resistane high risk sample 12

description: Pre-diabetes, IR high risk

value: Pre-diabetes, IR high risk


title: insulin resistane low risk sample 10

description: Health, IR low risk


title: 5_8_iCD

description: Agilent Design ID (AMADID): 047718

value: Colon sigmoideum


title: Descending aorta from wild-type pup, biological replicate 1

description:
Gene expression data from descending aortic tissue from p0 pups
WTDA1


title: 5_6_iCD

description: Agilent Design ID (AMADID): 047718

value: Colon transversum


title: Root, control, pH 8.0, rep1

description: Gene expression in control plant root for pH 8.0.

source_name: rice root, control, pH 8.0

value: control


title: Descending aorta from fibulin-4 knockout pup, biological replicate 1

description:
Gene expression data from descending aortic tissue from p0 pups
KODA1

source_name: Mouse lacking fibulin-4 gene p0, section of aorta from vena cava to diaphragm


title: Root, EDTA, pH 5.8, rep1

description: Gene expression in EDTA-treated plant root at pH 5.8.

source_name: rice root, 30 µM of EDTA, pH 5.8


title: Root, DMA, pH 8.0, rep1

description: Gene expression in DMA-treated plant root at pH 8.0.

source_name: rice root, 30 µM of DMA, pH 8.0

value: DMA


title: Ascending aorta from fibulin-4 knockout pup, biological replicate 2

description:
Gene expression data from ascending aortic tissue from p0 pups
KOAA2


title: Ascending aorta from wild-type pup, biological replicate 2

description:
Gene expression data from ascending aortic tissue from p0 pups
WTAA2

source_name: Control mouse, p0, section of aorta from aortic valve to ductus arteriosis


title: 2_6_Control

description: Agilent Design ID (AMADID): 047718

value: Control 2

value: Rectum

value: Control


title: Ascending aorta from wild-type pup, biological replicate 1

description:
Gene expression data from ascending aortic tissue from p0 pups
WTAA1


title: insulin resistane high risk sample 9

description: Health, IR high risk

value: saliva supernatant


title: Root, DMA, pH 5.8, rep1

description: Gene expression in DMA-treated plant root at pH 5.8.

source_name: rice root, 30 µM of DMA, pH 5.8


title: insulin resistane high risk sample 10

description: Pre-diabetes, IR high risk

value: insulin risistance high risk


title: 2_4_Control

description: Agilent Design ID (AMADID): 047718

value: Colon desendens

value: M


title: Root, control, pH 5.8, rep1

description: Gene expression in control plant root for pH 5.8.

source_name: rice root, control, pH 5.8


title: insulin resistane low risk sample 7

description: Health, IR low risk

value: insulin resistance low risk

value: Health, IR low risk


title: 2_3_Control

description: Agilent Design ID (AMADID): 047718


title: insulin resistane high risk sample 8

description: Health, IR high risk

value: Health, IR high risk


title: 1_3_Control

description: Agilent Design ID (AMADID): 047718

value: Control 1


title: insulin resistane high risk sample 6

description: Pre-diabetes, IR high risk


title: 1_6_Control

description: Agilent Design ID (AMADID): 047718


title: Ly6D- CLP from mutant, rep 2

city: Boston

first: Vionnie

middle: W. C.

last: Yu

state: MA

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital/Harvard University

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to the Mouse430A microarray chip overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing:
Standard QA/QC analyses involved chip analysis with the assayQualityMetrics BioConductor package and found no significant quality issues with any of the chips, as determined by (among other methods) visualinspection, intensity distributions or RNA degradation plots.
The data was background corrected and normalized with RMA (Robust Multichip Average, described here: http://bioinformatics.oxfordjournals.org/content/19/2/185) using the BioConductor package.

source_name: OcnCre+;iDTR+/- mutant mice

label_protocol: The purified cDNA was fragmented through a chemical and enzymatic prosess and labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3’-hydroxyl end of the fragmented cDNA.

extract_protocol: RNA was extracted using the Trizol® (Invitrogen) according to the manufacturer’s instructions. Samples were further processed by the NuGen Ovation V2 laboratory Process in the microarray core facility of Dana-Farber Cancer Institute.  Briefly, first stand cDNA was prepared from total RNA using a DNA/RNA chimeric primer and a reverse transcriptase. The resulting double stranded cDNA with a unique heteroduplex at the 5’end of the antisense strand were amplified using SPIATM amplification, a repeated process of SPIATM DNA/RNA primer hybridization, DNA replication, strand displacement and RNA cleavage which resulted in a rapid accumulation of cDNA with sequence complementary to the original RNA. The SPIATM amplified cDNA was purified using the Zymo Research DNA Clean & ConcentratorTM system.

treatment_protocol:
Ly6D- CLPs were isolated from OcnCre;iDTR control or mutant mice by flow cytometry.
Both OcnCre+;iDTR+/- mutant and OcnCre-;iDTR+/- control mice were subjected to daily diptheria toxin injection for 4 weeks to induce endogenous Ocn+ cell deletion.  Next day following the last injection, Ly6D- CLPs were sorted from the bone marrow of 6-8 weeks adults using the FACSAria.

tag: cell type

value: Ly6D- CLPs

value: bone marrow stromal cells

value: 6-8 weeks old mice

tag: condition

value: Diphtheria toxin induced Ocn+ cell deletion for 4 weeks


title: 1_4_Control

description: Agilent Design ID (AMADID): 047718


title: Ly6D- CLP from mutant, rep 1


title: A549-luc-CDDP-4th_Rep 2

city: Guangzhou

first: junchao

last: Cai

address: zhongshan er road

country: China

institute: Sun-yat sen university

description: A549-luc cells cultured from parental tumor explants within mouse treated with fourth round of CDDP replicate 2, after 30 days inoculation.

hyb_protocol: Hybridization was performed in Shanghai Biochip Corporation (http://www.shbiochip.com/) following standard Agilent protocol.

scan_protocol: Scanning was performed in Shanghai Biochip Corporation (http://www.shbiochip.com/) following standard Agilent protocol.

data_processing: Data normalization and transformation were performed in GeneSpring GX 11 (Agilent) in Shanghai Biochip Corporation.

source_name: tumor-derived cultured cells from fourth round of CDDP treatment

label_protocol: Labeling was performed in Shanghai Biochip Corporation (http://www.shbiochip.com/) following standard Agilent protocol.

growth_protocol: The lung cancer cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using mirVanaTM miRNA isolation kit (Ambion, Austin, TX) following supplier’s protocol.

treatment_protocol: Mice bearing A549-luc xenografts were intraperitoneally injected with the first round of CDDP treatment (CDDP-1st for short) or control treatment (Ctrl-1st for short), and cells were isolated from the resultantly remaining tumors, primarily cultured and re-transplanted, followed by a second round of CDDP treatment (CDDP-2nd) or control treatment (Ctrl-2nd), and so on. Total RNA were extracted from tumor-derived cultured cells from Ctrl-4th and CDDP-4th treatment for miRNA array analysis.

value: cisplatin (CDDP)

value: chemoresistant metastatic lung cancer cell line


title: 7_5_niCD

description: Agilent Design ID (AMADID): 047718

value: Patient 7

value: Colon sigmoideum

value: niCD

value: F


title: insulin resistane high risk sample 5

description: Pre-diabetes, IR high risk

value: insulin risistance high risk

value: Pre-diabetes, IR high risk

value: saliva supernatant


title: 1_5_Control

description: Agilent Design ID (AMADID): 047718

value: Control

value: M


title: insulin resistane high risk sample 4

description: Pre-diabetes, IR high risk


title: Ly6D- CLP from mutant, rep 3


title: insulin resistane high risk sample 3

description: Pre-diabetes, IR high risk


title: Ly6D- CLP from control, rep 2

source_name: OcnCre-;iDTR+/- control mice


title: wt_4

city: Zurich

first: Marianna

last: Di Chiara

state: Zurich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

hyb_protocol: Hybridization, washing and staining were done on an Affymetrix gene chip processing platform at the FGCZ following in principal the GeneChip® Expression Analysis Technical Manual of Affymetrix (Appendix C & D).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.  data processing: The data were process with the Affymetrix Power Tools v1.10.2 using the RMA algorithm.

data_processing: Data were processed using Affymetrix Power Tools

source_name: wt

label_protocol: labeled cDNA was generated from 100 ng RNA by the Functional Genomic Center Zurich (FGCZ)

growth_protocol: TBC1D4 WT and TBC1D4 KO mice were crossed with transgenic (tg) PV-EGFPwt/tg mice expressing EGFP under control of the parvalbumin-promoter

extract_protocol: RNA was extracted from isolated DCTs by using a high pure RNA isolation kit

treatment_protocol: Male, 8 week old TBC1D4 WT x PV-EGFPwt/tg and TBC1D4 KO x PV-EGFPwt/tg were used to isolate (fluorescent) DCTs in a a large scale by complex object parametric analysis and sorting (COPAS)

value: male

tag: genotype/variation

value: TBC1D4 wild-type

value: kidney


title: insulin resistane high risk sample 7

description: Pre-diabetes, IR high risk


title: citrus leaf without Huanglongbing, mixed three biological reps

first: Meirong

last: Xu

address: Wushan rode 483, Tianhe

institute: South China Agricultural University

description: gene expression data from 3-year-old Citrus reticulata Blanco cv. jiaogan

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C used 1792 Hybridization and Stain Module for 3’IVT Arrays(Affymetrix,P/N 900720) on Genechip® Hybridization Oven 640. GeneChips were washed and stained in the Genechip® Fluidics Station.

scan_protocol: GeneChips were scanned using the Genechip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Citrus reticulata

source_name: 3-year-old citrus seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using MessageAmp™ Premier RNA Amplification Kit, Ambion, ＃1792, 1 Poly-A RNA Control Kit (Affymetrix, P/N 900433), and 1 Hybridization Control Kit (Affymetrix, P/N 900454)

growth_protocol: Plants were grown at screenhouse of South China Agricultural University, under natural light conditions.

extract_protocol: One-hundred milligram of leaf tissue was grounded by mortar and pestle in liquid nitrogen for RNA extraction. RNA manipulation was done according to SDS method with few modifications.

treatment_protocol: Each of the citrus plant was graft-inoculated with one sweet orange scions with or without “Ca. L. asiaticus” in Dectember, 2009.

value: mature leaf

value: not infected


title: A549-luc-CDDP-4th_Rep 1

description: A549-luc cells cultured from parental tumor explants within mouse treated with fourth round of CDDP replicate 1, after 30 days inoculation.


title: insulin resistane low risk sample 6

description: Health, IR low risk

value: insulin resistance low risk

value: Health, IR low risk


title: mCherry Osterix, rep 4

data_processing: Standard QA/QC analyses involved chip analysis with the assayQualityMetrics BioConductor package and found no significant quality issues with any of the chips, as determined by (among other methods) visual inspection, intensity distributions or RNA degradation plots. The data was background corrected and normalized with RMA (Robust Multichip Average, described here: http://bioinformatics.oxfordjournals.org/content/19/2/185) using the affy BioConductor package.

extract_protocol:
Osx-mCherry cells and Ocn-Topaz cells were isolated from the OsxCre-mCherry;OcnCre-Topaz double transgenic mice by flow cytometry.
RNA was extracted using the Trizol® (Invitrogen) according to the manufacturer’s instructions. Samples were further processed by the NuGen Ovation V2 laboratory Process in the microarray core facility of Dana-Farber Cancer Institute.  Briefly, first stand cDNA was prepared from total RNA using a DNA/RNA chimeric primer and a reverse transcriptase. The resulting double stranded cDNA with a unique heteroduplex at the 5’end of the antisense strand were amplified using SPIATM amplification, a repeated process of SPIATM DNA/RNA primer hybridization, DNA replication, strand displacement and RNA cleavage which resulted in a rapid accumulation of cDNA with sequence complementary to the original RNA. The SPIATM amplified cDNA was purified using the Zymo Research DNA Clean & ConcentratorTM system.

treatment_protocol: Osx, ++ and OC cells were sorted at 6 days post tamoxifen injection from 4-6 weeks adults using the FACSAria.

value: Osx+

value: bone marrow stromal cells

value: 4-6 weeks old mice

value: 6 days post-tamoxifen induction


title: mCherry Osterix, rep 3

source_name: OsxCre-mCherry;OcnCre-Topaz double transgenic mice


title: Ly6D- CLP from control, rep 3

value: Ly6D- CLPs

value: 6-8 weeks old mice

value: Diphtheria toxin induced Ocn+ cell deletion for 4 weeks


title: A549-luc-Ctrl-4th_Rep 2

description: A549-luc cells cultured from parental tumor explants within mouse treated with fourth round of control solvent replicate 2, after 30 days inoculation.

source_name: tumor-derived cultured cells from fourth round of control treatment

value: control solvent

value: chemosensitive non-metastatic lung cancer cell line


title: wt_3


title: wt_2


title: mCherry Osterix, rep 2


title: insulin resistane low risk sample 5

description: Health, IR low risk

source_name: saliva supernatant

value: saliva supernatant


title: A549-luc-Ctrl-4th_Rep 1

description: A549-luc cells cultured from parental tumor explants within mouse treated with fourth round of control solvent replicate 1, after 30 days inoculation.


title: citrus leaf with Huanglongbing, mixed three biological reps

description: gene expression data from 3-year-old Citrus reticulata Blanco cv. jiaogan with 2 years' Huanglongbing infection

source_name: 3-year-old citrus seedlings infected by Huanglongbing

value: infected


title: Ly6D- CLP from control, rep 1


title: wt_1

value: male

value: TBC1D4 wild-type


title: insulin resistane low risk sample 3

description: Pre-diabetes, IR low risk

value: Pre-diabetes, IR low risk


title: insulin resistane low risk sample 4

description: Pre-diabetes, IR low risk


title: control_array_batch2

status: Public on Apr 09 2015

type: genomic

city: Utrecht

first: Roel

last: Hermsen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Array done in batch2; this array was used already once and reused by removing the hybridized probe from the slide according to the manufactures’ instructions, using the NimbleGen Array Reuse Kit from Roche Nimblegen.

hyb_protocol: Hybridization was done according to Nimblegen standard aCGH protocol

scan_protocol: Arrays were scanned on a Agilent G2565CA scanner at resolution 2 μm, double pass.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.6 SegMNT data extraction. Log2 ratio data for analysis is found in the last column titled: "RATIO_CORRECTED"

molecule: genomic DNA

organism: Rattus norvegicus

source_name: hom196 ear

label_protocol: Labelling was done using standard Nimblegen protocol for aCGH

extract_protocol: DNA was extracted from 100 milligrams of tissue using Qiagen Genomic-tip DNA isolation kit

tag: p53 genotype animal

value: homozygous

value: ear


title: mCherry Osterix, rep 1


title: het95

source_name: het95 tumor

value: heterozygous

value: tumor

source_name: het95 ear


title: het125

source_name: het125 tumor

source_name: het125 ear


title: het202

source_name: het202 tumor

source_name: het202 ear


title: ko_3

source_name: ko

value: kidney


title: het144

source_name: het144 tumor

source_name: het144 ear


title: ko_4


title: Topaz Osteocalcin, rep 3

value: Ocn+

value: bone marrow stromal cells

value: 4-6 weeks old mice


title: insulin resistane high risk sample 2

description: Health, IR high risk

value: insulin risistance high risk

value: Health, IR high risk


title: insulin resistane high risk sample 1

description: Pre-diabetes, IR high risk

value: Pre-diabetes, IR high risk


title: het100

description: Array done in batch1; this array was new and not used before.

source_name: het100 tumor

source_name: het100 ear


title: het112

source_name: het112 tumor

source_name: het112 ear


title: het118

source_name: het118 tumor

source_name: het118 ear


title: insulin resistane low risk sample 1

description: Pre-diabetes, IR low risk

source_name: saliva supernatant

value: insulin resistance low risk


title: ko_1


title: Topaz Osteocalcin, rep 2

source_name: OsxCre-mCherry;OcnCre-Topaz double transgenic mice

value: 6 days post-tamoxifen induction


title: het97

source_name: het97 tumor

source_name: het97 ear


title: insulin resistane low risk sample 2

description: Health, IR low risk

value: Health, IR low risk

value: saliva supernatant


title: control_array_batch1

source_name: BN-Lx

value: BN-Lx/Cub

value: wildtype

value: liver

source_name: BN/NHsdmCWi

value: BN/NHsdmCWi


title: het82

source_name: het82 tumor

value: heterozygous

source_name: het82 ear

value: ear


title: ko_2

source_name: ko

value: male

value: kidney


title: het170

source_name: het170 tumor

value: tumor

source_name: het170 ear


title: het103

source_name: het103 tumor

source_name: het103 ear


title: Topaz Osteocalcin, rep 1

value: Ocn+

value: bone marrow stromal cells

value: 4-6 weeks old mice


title: hom201

source_name: hom201 tumor

value: homozygous

source_name: hom201 ear


title: het20

source_name: het20 tumor

source_name: het20 ear


title: het9

source_name: het9 tumor

source_name: het9 ear


title: het160

source_name: het160 tumor

source_name: het160 ear


title: hom225

source_name: hom225 tumor

source_name: hom225 ear


title: hom261

source_name: hom261 tumor

source_name: hom261 ear


title: het142

source_name: het142 tumor

source_name: het142 ear


title: hom247

source_name: hom247 tumor

source_name: hom247 ear


title: hom174

source_name: hom174 tumor

source_name: hom174 ear


title: hom223

source_name: hom223 tumor

source_name: hom223 ear


title: hom199

source_name: hom199 tumor

source_name: hom199 ear


title: hom164

source_name: hom164 tumor

source_name: hom164 ear


title: hom198

source_name: hom198 tumor

source_name: hom198 ear


title: hom196

source_name: hom196 tumor

source_name: hom196 ear


title: het153

source_name: het153 tumor

source_name: het153 ear


title: T84

city: Melbourne

first: Oliver

middle: M

last: Sieber

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Genomic DNA extracted from colorectal cancer cell lines was genotyped using Human610-Quad v1.0 Genotyping BeadChips (Illumina).

hyb_protocol: Standard Illumina protocols for Human 610w-Quad chip

data_processing:
Log R ratio (LRR) and B allele frequency (BAF) were generated using using GenomeStudio (Illumina). DNA copy-number assignment was performed using OncoSNPv2.1.
Series supplementary file matrix_processed.txt value definition: Genotype: AA,AB,BB up to a copy number of 6 (i.e. AAAAAA) or NC (no call). Copy number is for the absolute value and not relative to ploidy.

label: C-Bio and A-DNP

source_name: Human colorectal cancer

extract_protocol: AllPrep DNA/RNA Mini Kit (QUAGEN)

tag: cell line

tag: msi status

value: S

tag: cimp status

value: CIMP-


title: SW948

scan_protocol: Standard Illumina protocols for Human 610w-Quad chip


title: SW837

label_protocol: Standard Illumina protocols for Human 610w-Quad chip

value: CIMP+


title: SW480


title: treated A/J mice, biological rep 2

city: Barcelona

first: Sergi

last: Mas Herrero

state: Catalunya

address: Casanova 143

department: Pharmacology, School of Medicine

country: Spain

institute: University of Barcelona

data_processing: RMA processing algorithm. Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)

source_name: treated A/J mice with Risperidone 1 mg/Kg

growth_protocol: Male mice (7 to 8 weeks old) from two inbred strains, A/JOlaHsd (A/J) and DBA/2JRccHsd (DBA/2J) (Harlan Laboratories, Sant Feliu de Codines, Spain), were housed eight per cage under a 12 h dark/light cycle with free access to food and water.

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

treatment_protocol: Mice were injected i.p. (volume 0.25 mL) with risperidone (1.0 mg/kg) or saline once per day for three consecutive days.

value: A/J

tag: agent

value: risperidone

tag: tissue

value: striatum

value: 7 to 8 weeks old


title: SW48

value: U


title: untreated DBA2J mice, biological rep 1

hyb_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)

source_name: untreated DBA2J mice

value: untreated


title: treated A/J mice, biological rep 1

scan_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: untreated A/J mice, biological rep 3

source_name: untreated A/J mice

label_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: untreated DBA2J mice, biological rep 2


title: untreated A/J mice, biological rep 2


title: treated DBA2J mice, biological rep 1

source_name: treated DBA2J mice with Risperidone 1 mg/kg


title: treated A/J mice, biological rep 3


title: untreated DBA2J mice, biological rep 4


title: treated A/J mice, biological rep 4


title: treated DBA2J mice, biological rep 3


title: treated DBA2J mice, biological rep 4


title: G4-2 GMP

city: Houston

first: Ronald

last: Depinho

address: 1400 Pressler St

institute: University of Texas MD Anderson Cancer Center

description: 08_G4-2 GMP_(Mouse430_2)

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). The TGT intensity of each array was arbitrarily set to 100.

source_name: GMP from telomere dysfunctional  mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  5-10 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: strain background

value: Mainly C576BL/6 (mice were generated in-house (PMID:21113150)

value: mouse with short telomeres

value: G4/G5 TERTER/ER

tag: gender

value: bone marrow

value: FACs sorted granulocyte–macrophage progenitor (GMP) cells


title: untreated A/J mice, biological rep 1


title: treated DBA2J mice, biological rep 2


title: untreated DBA2J mice, biological rep 3


title: G4-1 GMP

description: 07_G4-1 GMP_(Mouse430_2)

value: male


title: G0-2 GMP

description: 06_G0-2 GMP_(Mouse430_2)

source_name: GMP from normal mice

value: normal mice

value: G0 TERTER/+


title: untreated A/J mice, biological rep 4


title: G4-2 CMP

description: 04_G4-2 CMP_(Mouse430_2)

source_name: CMP from telomere dysfunctional  mice

value: FACs sorted cells common myeloid progenitor (CMP) cells


title: G0-2 CMP

description: 02_G0-2 CMP_(Mouse430_2)

source_name: CMP from normal mice


title: SW620

value: S

value: CIMP-


title: G4-1 CMP

description: 03_G4-1 CMP_(Mouse430_2)


title: SW403


title: SW1116


title: RW2982


title: RKO

value: RKO

value: CIMP+


title: LS174T


title: SW1222


title: LOVO

value: LOVO


title: LIM2551


title: G0-1 GMP

description: 05_G0-1 GMP_(Mouse430_2)


title: LIM2405


title: G0-1 CMP

description: 01_G0-1 CMP_(Mouse430_2)


title: RW7213


title: KM12


title: LIM1899


title: LIM1215


title: HCT8


title: HCT116


title: HCC2998


title: PDAC xenograft from patient HN014-rep 1

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized to the Affymetrix HuGene 2.0 for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: RMA

source_name: PDAC

label_protocol: Total mRNA was RNase H reduced and labelled with the SuperScript One-Cycle cDNA Kit following manufacturer's instructions (Invitrogen).

growth_protocol: Each PDAC sample obtained from Endoscopic Ultrasound-Guided Fine-Needle Aspiration was mixed with 100 µl of Matrigel (BD Biosciences) and injected in the upper right flank in a nude mouse (Swiss Nude Mouse Crl: NU(lco)-Foxn1nu, Charles River Laboratories). Each sample derived from surgery resection was fragmented, mixed with 100 µl of Matrigel (BD Biosciences) and implanted with a trocar (10 Gauge, Innovative Research of America, Sarasota, FL) in the subcutaneous right upper flank of an anesthetized and disinfected mouse. When tumors reached 1 cm3, mice were sacrificed and tumors were removed and immediately drawn in cold guanidinium thiocyanate to perform total RNA extraction.

extract_protocol: Total RNA was extracted with cold guanidinium thiocyanate (4M) solution, followed by protein denaturation and RNAs extraction according to Chirgwin’s protocol . Total RNA was them purified using the RNeasy Mini kit with DNAse digestion (Qiagen, Valencia, CA) and resuspended in PCR-grade water. To ensure adequate quality, RNA was analysed with an Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA) in the Quebec Genomics Center Microarray core facility.

value: Pancreatic Ductal Adenocarcinoma

value: M

tag: tumor histology


title: HCA7

value: U


title: PDAC xenograft from patient AO-IPC-rep 2

value: F


title: Gp5D


title: PDAC xenograft from patient HN-01-rep 2


title: PDAC xenograft from patient E-NOR-rep 2


title: PDAC xenograft from patient HN014-rep 2


title: Gp2D


title: PDAC xenograft from patient AO-IPC-rep 1


title: PDAC xenograft from patient 01-030-rep 1


title: PDAC xenograft from patient Foie_8b1-rep 1


title: PDAC xenograft from patient 01-030-rep 2


title: HCT15


title: PDAC xenograft from patient HN-01-rep 1


title: PDAC xenograft from patient AH-IPC-rep 2


title: PDAC xenograft from patient AH-IPC-rep 1


title: DLD1


title: COLO678


title: PDAC xenograft from patient E-NOR-rep 1


title: PDAC xenograft from patient AD-IPC-rep 2


title: PDAC xenograft from patient L-IPC-rep 2


title: PDAC xenograft from patient AD-IPC-rep 1


title: COLO205


title: CACO2


title: C99


title: C84


title: C80


title: C125


title: PDAC xenograft from patient D-IPC-rep 2


title: C106


title: PDAC xenograft from patient J-IPC-rep 1


title: PDAC xenograft from patient J-IPC-rep 2


title: VACO10


title: SW1463


title: PDAC xenograft from patient D-IPC-rep 1


title: PDAC xenograft from patient B-Tim-rep 1


title: PDAC xenograft from patient B-Tim-rep 2


title: PDAC xenograft from patient C-Nor-rep 2


title: PDAC xenograft from patient L-IPC-rep 1


title: PDAC xenograft from patient C-Nor-rep 1


title: SW1417


title: PDAC xenograft from patient A-Nor-rep 2


title: SNU-C2B


title: SNU-283


title: SNU-175


title: VACO4S


title: PDAC xenograft from patient HN03-rep 2


title: NCI-H747


title: PDAC xenograft from patient HN03-rep 1


title: PDAC xenograft from patient H-Nor-rep 1


title: SNU-C1


title: NCI-H716


title: PDAC xenograft from patient 01.001-rep 1


title: PDAC xenograft from patient H-Nor-rep 2


title: PDAC xenograft from patient A-Nor-rep 1


title: LS513


title: LS411


title: LS180


title: SKCO-1


title: HT55


title: LIM2099


title: Native liver biopsy Poor_SK22

city: london

first: siamak

last: salehi

address: denmark hill

department: liver studies

country: United Kingdom

institute: kings college hospital

description:
Sample name: SK22
total RNA with miRNA enrichment
archived formalin fixed histology sample

hyb_protocol: After labeling, 21.5 ug of RNA was hybridized for 16 hr at 48°C on GeneChip miRNA 2.0  Arrays . GeneChips were washed and stained in the Affymetrix Genechip fluidis 450 station.

scan_protocol: Hybridized samples were scanned using Genechip scanner 3000 7G (Affymetrix)

data_processing: miRNA QC Tool v1.0.33.0 ,  algorithim  default  was used with the following settings:  Detection ( Background detection), Background adjustment (BC-CG Adjustment),  Normalization (Quantile), Other Process (Add small constant, CVS tab), Other Processes (Threshhold), Summarization ( Median Polish))

source_name: Native liver biopsy Poor

label_protocol: Total RNA containing miRNA was enriched using microcon YM-100 centrifugal  filter device ( Millipore Cat no: 42413,) according to the manufacturer's protocol. 100 ng of enriched RNA was labeled using Flashtag biotin RNA labeling kit ( Genisphere) according to protocol by Genisphere for labeling RNA for affymetrix Genechip RNA.

extract_protocol: High Pure FFPE RNA Micro Kit ( Roche Applied Sciences) was used to extract  total RNA from FFPE liver sections or slides according  to manufacturers instructions

treatment_protocol: FFPE sections and samples were processed using the FFPE RNA pure kit from Roche, following the manufacturer's protocol.

value: liver

value: Poor PNF


title: Native liver biopsy PNF_SK23

description:
Sample name: SK23
total RNA with miRNA enrichment
archived formalin fixed histology sample

source_name: Native liver biopsy PNF

value: PNF DCD


title: PDAC xenograft from patient 01.001-rep 2


title: Native liver biopsy PNF_SK21

description:
Sample name: SK21
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy PNF_SK25

description:
Sample name: SK25
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy Good_SK24

description:
Sample name: SK24
total RNA with miRNA enrichment
archived formalin fixed histology sample

source_name: Native liver biopsy Good

value: Good DCD


title: HT115


title: Native liver biopsy Poor_SK16

description:
Sample name: SK16
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy Poor_SK17

description:
Sample name: SK17
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy Poor_SK15

description:
Sample name: SK15
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: HRA19


title: PDAC xenograft from patient Foie_8b1-rep 2


title: HDC90


title: Native liver biopsy Good_SK19

description:
Sample name: SK19
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: HT29


title: Native liver biopsy Poor_SK18

description:
Sample name: SK18
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: HDC87


title: Native liver biopsy PNF_SK12

description:
Sample name: SK12
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: HDC82


title: Native liver biopsy PNF_SK11

description:
Sample name: SK11
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: HDC54


title: Native liver biopsy Poor_SK10

description:
Sample name: SK10
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: HCA46


title: HDC101


title: Native liver biopsy PNF_SK20

description:
Sample name: SK20
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: CX-1


title: Native liver biopsy PNF_SK13

description:
Sample name: SK13
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy Good_5A

description:
Sample name: 5A
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: GD2 BBz - Donor 3

city: Bethesda

first: Adrienne

last: Long

state: Maryland

address: 10 Center Dr.

department: POB

institute: NIH/NCI

hyb_protocol: not provided

scan_protocol: not provided

label_protocol: Samples were processed according to Affymetrix manufacturer's guidelines and in accordance with the microarray core facility NCI Frederick.

growth_protocol: PBMCs activated with aCD3/CD28 beads and grown in IL2

extract_protocol: not provided

treatment_protocol: Transduced with CD19-28z, CD19-BBz, GD2-28z or GD2 BBz CARs or untransduced controls

tag: car

value: GD2 BBz

tag: donor

value: blood

value: T cells


title: GD2 BBz - Donor 2


title: GD2 28z - Donor 3

value: GD2 28z


title: COLO320-DM

description: Genomic DNA extracted from colorectal cancer cell lines was genotyped using Human610-Quad v1.0 Genotyping BeadChips (Illumina).

value: S


title: Native liver biopsy Good_2A

description:
Sample name: 2A
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy Good_3A

description:
Sample name: 3A
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: GD2 BBz - Donor 1


title: COLO201


title: GD2 28z - Donor 2


title: CD19 BBz - Donor 3

value: CD19 BBz


title: GD2 28z - Donor 1


title: CoCM-1

value: CIMP-


title: Native liver biopsy Poor_9A

description:
Sample name: 9A
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy Poor_8A

description:
Sample name: 8A
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Native liver biopsy Good_1A

description:
Sample name: 1A
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: Primary_myoblasts_untreated_biological_replicate_2

first: Patrizia

last: Pessina

address: C/ Dr. Aiguader 88

institute: University Pompeu Fabra

description: Gene expression in untreated cells

hyb_protocol: After fragmentation, 600 ng of labeled cDNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent). The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Primary myoblasts, untreated, biological replicate 2

label_protocol: Total cDNA from each sample was labeled with Cy3-UTP and purified using the SureTag Complete DNA Labeling Kit (Agilent).

growth_protocol: FACS-sorted primary myoblasts were culture in DMEM supplemented with 20% FBS, L-glutamine and penicillin/streptomycin

extract_protocol: RNA isolation  was performed with the RNeasy Micro kit

treatment_protocol: primary myoblasts were treated (or not) for 4 days with TGFb

value: skeletal muscle

value: male

tag: age


title: Native liver biopsy Poor_SK14

description:
Sample name: SK14
total RNA with miRNA enrichment
archived formalin fixed histology sample


title: CD19 BBz - Donor 1


title: C70


title: CD19 28z - Donor 3


title: C32


title: CCK81


title: CD19 28z - Donor 2


title: C10


title: Mock - Donor 3

value: Mock


title: CD19 BBz - Donor 2


title: Primary_myoblasts_TGFb treated_biological_replicate_3

description: Gene expression after 4 days of TGFb treatment

source_name: Primary myoblasts, TGFb treated, biological replicate 3


title: Primary_myoblasts_TGFb treated_biological_replicate_1

source_name: Primary myoblasts, TGFb treated, biological replicate 1


title: Primary_myoblasts_untreated_biological_replicate_1

description: Gene expression in untreated cells

source_name: Primary myoblasts, untreated, biological replicate 1


title: CD19 28z - Donor 1


title: Primary_myoblasts_untreated_biological_replicate_3

description: Gene expression in untreated cells

source_name: Primary myoblasts, untreated, biological replicate 3


title: Primary_myoblasts_TGFb treated_biological_replicate_2

source_name: Primary myoblasts, TGFb treated, biological replicate 2


title: P5424_rep2

city: Marseille - cedex 09

first: Aurélien

last: Griffon

address: 163, Avenue de Luminy - case 928

country: France

institute: TAGC - Inserm U1090

description: Gene expression of P5424 cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: P5424 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RPMI1640, supplement with 10% fetal bovine serum and 0.1 mM 2-mercaptoethanol

extract_protocol: Total RNA was isolated using the Trizol (Life Technologies) according to manufacturer's recommendation. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genotype

value: Rag2 and P53 knockout

tag: treatment


title: Mock - Donor 2

tag: cell type


title: C135

source_name: Human colorectal cancer

value: U

value: CIMP+


title: P5424_rep1

description: Gene expression of P5424 cell line


title: C4-2B-MDVR_no treatment

city: Sacramento

first: allen

last: Gao

state: California

address: 4645 2nd Ave Research 3

institute: UC Davis

description: Gene expression data from docetaxel resistant TaxR cells

hyb_protocol: 2.5 ug of fragmented and labeled DNA target were hybridized to the Affymetrix Genechip Human Geneome U133 Plus 2.0 arrays using using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes then centrifuge at max speed for 1 minute . • Transfer 80μl of hyb solution to each array, then tape holes. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.0 software.  Probe summarization and calculation of normalized expression signals from Affymetrix CEL files was performed with the RMA16 algorithm (Irizarry et al., 2003).

source_name: Enzalutamide resistant prostate cancer cell line C4-2B-MDVR, without any treatment

label_protocol: 100ng of total RNA were amplified using the Ambion WT Expression Kit.  Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Both were cultured in RPMI-1640 medium containing 10% complete fetal bovine serum (FBS) 100 units/mL penicillin and 0.1 mg/mL streptomycin and maintained at 37C in a humidified incubator with 5% CO2.

treatment_protocol: No treatment on either cell lines.

value: In vitro prostate cancer cell line


title: C4-2B_no treatment

description: Gene expression data from docetaxel sensitive C4-2B cells

source_name: Enzalutamide sensitive prostate cancer cell line C4-2B, without any treatment


title: iDcLcn1-1 Monocyte-derived dendritic cells

status: Public on Apr 08 2015

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

description: Monocyte-derived dendritic cells treared with lipocalin Lcn-1. Monocytes were isolated with the Monocyte isolation kit II (Milteny Biotec, Bergisch Gladbach, Germany), supplemented with 50 µg/ml gentamicin, 2 mM L-glutamine (Sigma Chemicals, St Louis, MO), 10% fetal calf serum (Biological Industries or Seromed Biochrom, Berlin, Germany), 800 U/ml GM-CSF (specific activity 1.1 x 106 U/mg; Leukomax; Novartis, Basel, Switzerland) and 20 U/ml IL-4 (Strathmann, Hamburg, Germany). Culture medium was renewed every other day by removing 1 ml medium and substituting with 1.5 ml fresh medium containing 1600 U/ml GM-CSF and 20 U/ml IL-4. On day 6, cells were cultured for 2 additional days with 10 µg/ml recombinant lipocalin Lcn-1.

hyb_protocol: Target samples were hybridized to Human Gene 1.0 ST v2 microarrays according to the manufacturer's protocols.The microarrays were washed and stained in an Affymetrix fluidic station 450.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data were preprocessed using a modified version of the GC-RMA method. For transcript probe set definition a custom CDF package (hugene10stv173, defining probe sets for transcripts from Ensemble core database version 73) was used.

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

growth_protocol: 2 x 106 monocytes isolated with the Monocyte isolation kit II (Milteny Biotec, Bergisch Gladbach, Germany) per well were plated in 6-well tissue culture plates in 3 ml complete culture medium (RPMI-1640 [PAN]; Biotech GmbH, Aidenbach, Germany), supplemented with 50 µg/ml gentamicin, 2 mM L-glutamine (Sigma Chemicals, St Louis, MO), 10% fetal calf serum (Biological Industries or Seromed Biochrom, Berlin, Germany), 800 U/ml GM-CSF (specific activity 1.1 x 106 U/mg; Leukomax; Novartis, Basel, Switzerland) and 20 U/ml IL-4 (Strathmann, Hamburg, Germany). Culture medium was renewed every other day by removing 1 ml medium and substituting with 1.5 ml fresh medium containing 1600 U/ml GM-CSF and 20 U/ml IL-4.

extract_protocol: RNA was isolated using TRIzol reagent (Invitrogen)

treatment_protocol: On day 6, cells were cultured for 2 additional days with or without 10 µg/ml recombinant lipocalins or a defined cytokine cocktail consisting of TNFα (10 ng/ml; kindly provided by Dr G. R. Adolf, Bender, Vienna, Austria), IL-1β (2 ng/ml; PeproTech EC LTD, London, England), IL-6 (1000 U/ml; PeproTech) and PGE2 (1 µg/ml, Prostaglandin E2; Pharmacia & Upjohn SA, Buurs, Belgium) as maturation stimulus

value: lipocalin Lcn1


title: iDcCanf1-1 Monocyte-derived dendritic cells

description: Monocyte-derived dendritic cells treared with lipocalin Can f 1. Monocytes were isolated with the Monocyte isolation kit II (Milteny Biotec, Bergisch Gladbach, Germany), supplemented with 50 µg/ml gentamicin, 2 mM L-glutamine (Sigma Chemicals, St Louis, MO), 10% fetal calf serum (Biological Industries or Seromed Biochrom, Berlin, Germany), 800 U/ml GM-CSF (specific activity 1.1 x 106 U/mg; Leukomax; Novartis, Basel, Switzerland) and 20 U/ml IL-4 (Strathmann, Hamburg, Germany). Culture medium was renewed every other day by removing 1 ml medium and substituting with 1.5 ml fresh medium containing 1600 U/ml GM-CSF and 20 U/ml IL-4. On day 6, cells were cultured for 2 additional days with 10 µg/ml recombinant lipocalin Can f 1.

value: lipocalin Canf1


title: conventional iTreg

city: Chuncheon, Gangwon-Do

first: Kwon Ik

last: Oh

address: 1 Hallymdaehak-gil

department: Pathology

country: South Korea

institute: Hallym University College of Medicine

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Mouse Ref-8 expression v.2 bead array for 16~18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). Array probes were transformed by logarithm and normalized by quantile method.

source_name: cultured cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: For iTreg cell generation, FACS−sorted naïve CD4+ T cells (CD4+GFP−CD44low) were stimulated by anti-CD3/CD28 (1 micro-g/ml, each), rIL2 (15 ng/ml) and rTGF-b (10 ng/ml) in the presence or absence of vitamin C (10 micro-g/ml) for 5~6 d and then GFP+CD25+ iTreg cells were re-sorted.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), purified using RNeasy columns (Qiagen) according to the manufacturers’ protocol. After clean-up procedures, RNA samples were quantified, and stored at -80°C until use.

treatment_protocol: Sorted naive CD4+ T cells were cultured under iTreg condition in the presence or absence of vitamin C (10 micro-g/ml) for 5~6 d

tag: strain

value: Foxp3-GFP transgenic (B6.Cg-Foxp3tm2Tch/J) mice

value: GFP+ iTreg cells generated from FACS-sorted naïve CD4+ T cells cultured under iTreg condition for 5-6 days


title: d1_A2_N24b_naivelike

city: Lausanne

first: Silvia

last: Fuertes Marraco

address: Avenue Pierre-Decker 4

department: Ludwig Center for Cancer Research

institute: University of Lausanne

hyb_protocol: Cy3-labelled cDNA were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 8x60K v2 using Agilent's recommended hybridization chamber and oven.

scan_protocol: The slides were scanned using Agilent's Microarray Scanner System (Agilent Technologies)

data_processing: The scanned images were analyzed with the Agilent Feature Extraction Software. Raw intensity values were background corrected (normexp method) and quantile normalized between arrays using the limma R package (version 3.20.8). Probes that were not expressed well above the background in any of the samples were excluded. Replicate probes were averaged, and control probes were excluded.

source_name: PBMC

label_protocol: Cy3-labelled cDNA was prepared from 250 ng of cDNA according to the protocol of Miltenyi Biotec.

extract_protocol: Total RNA was extracted from 1'000 cells and processed using the SuperAmp Preparation kit (Miltenyi Biotec) according to the manufacturer's protocol. Quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Donors vaccinated with YF-17D; PBMC ex-vivo (cryopreserved)


title: iDcCanf1-2 Monocyte-derived dendritic cells


title: d2_total_effector


title: Mock - Donor 1

value: blood


title: d6_total_effector


title: d4_total_Tscm


title: vitamin C treated iTreg

value: GFP+ iTreg cells generated from FACS-sorted naïve CD4+ T cells cultured under iTreg condition plus vitamin C for 5-6 days


title: naïve CD4+ T cells

source_name: lymphnode and spleen

value: FACS sorted CD4+CD8-GFP-CD44low naïve CD4+ T cells (ex vivo)


title: d8_A2_N24b_naivelike


title: d7_total_effector


title: d8_total_Tscm


title: d5_total_naive


title: d2_total_naive


title: d3_A2_N24b_naivelike


title: d7_total_cm


title: d8_total_cm


title: d5_total_cm


title: d7_total_Tscm


title: d4_A2_N24b_naivelike


title: d3_total_cm


title: iDcLcn1-2 Monocyte-derived dendritic cells


title: d4_total_naive


title: natural Treg

value: FACS sorted CD4+CD8-GFP+ natural Treg cells (ex vivo)


title: d1_total_naive


title: d6_total_Tscm


title: d3_total_effector


title: Native liver biopsy Good_4A

description:
Sample name: 4A
total RNA with miRNA enrichment
archived formalin fixed histology sample

value: liver

tag: condition

value: Good DCD


title: d2_total_cm


title: d7_total_naive


title: d5_total_effector


title: d1_total_Tscm


title: WT vs. Brpf1-deficient P4 brain 1

city: Montreal

first: Xiang-Jiao

last: Yang

address: 1160 Pine Ave W

department: Medicine

institute: McGill University

description: Pair 1

hyb_protocol: 825 ng each of  Cy3-labelled (WT) and Cy5-labelled (MUT) aRNA samples were co-hybridised in duplicate on Agilent whole mouse genome arrays (catalogue number G4852A; Agilent Technologies).

scan_protocol: The microarray slides were washed according to the manufacturer’s instructions and scanned using an Agilent dual-laser scanner.  Feature extraction was performed using Agilent Feature Extraction software (version 9.5.3.1).

data_processing: Limma package (Smyth, 2004) was used to normalize and determine the modulated genes from microarray data. Signal background correction was carried out using normexp method and offset = 50 as suggested by Limma. To determine the modulated genes between a mutant and its wild type, we applied the two-‐channel normalization. Within-‐array normalization was carried out using loess method while between-‐array normalization was performed using a quantile method (Li et al., 2010). Empirical Bayes statistics was applied to determine the differential expression of the genes. The data from the three pairs were averaged to generate the normalized file (Gene list B Aug 26 2014.txt, attached).

source_name: Wild-type P4 pup

label_protocol: 350 ng of total RNA was subjected to a single round of amplification using the Amino Allyl MessageAmpTM II aRNA kit (catalogue number AM1753; Ambion/Life Technologies,  Burlington, Ontario, Canada) according to the manufacturere's instructions, and the amplified product was labelled using a CyDye Post-Labeling Reactive Dye Pack (GE Healthcare Life Sciences, Baie d'Urfé, Quebec, Canada ).

growth_protocol: The pups were sacrificed at postnatal day 4.

extract_protocol: RNA was isolated from P4 brain dorsal cortex. RNA quality was assessed using a Bioanalyzer microfluidics workstation (Agilent Technologies, Mississaugo, Ontario, Canada) and quantitated using a NanoDrop spectrophotometer (Thermo Scientific, Wilminton , DE).

treatment_protocol: There was no treatment applied to the pups.

value: Brain dorsal cortex

tag: genotype/variation

value: Wild-type

source_name: P4 Brpf1-deficient pup


title: d8_total_effector


title: d5_A2_N24b_naivelike


title: P7_N5

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

institute: AIT

hyb_protocol: Labelled cRNA was hybridised onto 4x44k Agilent whole human genome microarrays overnight and washed according to manufacturers instructions.

scan_protocol: Chips were scanned using an Agilent scanner (G2505C) with 3 micron resolution

data_processing: 20bit tiff images were analysed in Agilent Feature extraction software (v10.5.1.1) and raw data extracted in text format. Except Background substraction no further preprocessing of the data was applied.

source_name: pericytes

label_protocol: Extracted total RNA was reverse transcribed and labelled by in vitro transcription (Agilent QuickAmp, according to manufacturers instructions).

extract_protocol: RNeasy

tag: blood flow

tag: arterial density

tag: capillary density


title: HEK293T_non-silencingsiRNA_rep2

city: West Haven

first: Sarah

middle: A

last: Slavoff

state: CT

address: 600 West Campus Drive, MIC 319A

department: Chemistry

institute: Yale University

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip HuGene 2.0 ST Array for 16 hours at 45C, then washed and stained on the Affymetrix Fluidics Station according to the manufacturer's instructions.

scan_protocol: The GeneChips were scanned on a GeneChip Scanner 3000 with Autoloader.

data_processing: The data were processed with RMA method (oligo package in R Bioconductor).

source_name: HEK293T cells, non-silencing siRNA transfected, actinomycin D (1 ug/mL) 4 hr

label_protocol: Biotinylated cRNA was prepared using the Ambion Whole Transcript Expression Kit (Affymetrix).

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% fetal bovine serum, penicillin and streptomycin in a 5% CO2 atmosphere to 50% confluency.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions. Each sample was digested with RNase-free DNase I (NEB) for 1 hour to remove genomic DNA contamination, then column cleanup was performed using the RNeasy kit.

treatment_protocol: Cells were transfected with siRNA (Qiagen) targeting each experimental gene or a control siRNA that does not hybridize to any human genes (non-silencing) using Dharmafect 1 according to the manufacturer's instructions. 48 hours post-transfection, cells were treated with 1 ug/mL actinomycin D for 4 hours.

tag: cell line

tag: sirna

value: non-silencing

value: actinomycin D (1 ug/mL) for 4 hr


title: P7_21.10


title: d4_total_cm


title: HEK293T_non-silencingsiRNA_rep3


title: WT vs. Brpf1-deficient P4 brain 2

description: Pair 2

tag: tissue


title: d3_total_Tscm


title: HEK293T_GAPDHsiRNA_rep1

source_name: HEK293T cells, GAPDH siRNA transfected, actinomycin D (1 ug/mL) 4 hr

value: GAPDH


title: HEK293T_non-silencingsiRNA_rep1


title: d6_total_cm


title: WT vs. Brpf1-deficient P4 brain 3

description: Pair 3


title: P7_22.10


title: HEK293T_GAPDHsiRNA_rep3


title: P7_23.08


title: d1_total_cm


title: d2_total_Tscm


title: d1_total_effector


title: pad2.1_cd_6_rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Transcriptomic profiling of Arabidopsis thaliana in response to combined stress treatment under altered GSH conditions.

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5242).

scan_protocol: Scanned on an Agilent scanner and Images were quantified using Agilent Feature Extraction Software version 11.5

data_processing: The normalization was done using GeneSpring GX 12 Software. 75th Percentile Shift Normalization

organism: Arabidopsis thaliana

source_name: leaf tissue_cd_6

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop.

extract_protocol: Trizol-RNA extraction

value: leaf

tag: genetic background


title: HEK293T_GAPDHsiRNA_rep2


title: HEK293T_DcpSsiRNA_rep3

source_name: HEK293T cells, DcpS siRNA transfected, actinomycin D (1 ug/mL) 4 hr

value: DcpS


title: Pad2.1_cd_6_rep1


title: P7_10.02


title: 409-shRNA2

city: Dallas

first: Diego

middle: H

last: Castrillon

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array analysis was performed using Illumina GenomeStudio 2011 Software v2011.1

source_name: Immortalized endometrial cells transfected with 409-shRNA2

label_protocol: not provided

growth_protocol: Stable cell lines were grown in DMEM F:12 media supplemented with 10% FBS.  RNA was harvested from each cell line 48 hours later.

extract_protocol: Total mRNA was isolated from EM cells using the RNeasy Mini Kit (Qiagen, cat#74104) per the manufacturer’s protocol.

value: Immortalized endometrial cells


title: HEK293T_DcpSsiRNA_rep2


title: Col-0_cd_6_rep2

value: wild type


title: non-target reference control (NT)

source_name: Immortalized endometrial cells transfected with non-target reference control (NT)


title: d3_total_naive


title: 408-shRNA1

source_name: Immortalized endometrial cells transfected with 408-shRNA1


title: Col-0_cd_6_rep1


title: HEK293T_Dcp2siRNA_rep3

source_name: HEK293T cells, Dcp2 siRNA transfected, actinomycin D (1 ug/mL) 4 hr


title: HEK293T_Dcp2siRNA_rep2


title: d6_A2_N24b_naivelike


title: HEK293T_Dcp2siRNA_rep1


title: d2_A2_N24b_naivelike


title: HEK293T_DcpSsiRNA_rep1


title: d8_total_naive


title: HEK293T_LOC550643siRNA_rep2

source_name: HEK293T cells, LOC550643 siRNA transfected, actinomycin D (1 ug/mL) 4 hr


title: Macrophage-control-6

city: Oxford

first: Christopher

last: O'Callaghan

state: Oxfordshire

address: Roosevelt Drive

department: Nuffield Department of Medicine

institute: University of Oxford

hyb_protocol: Biotinylated cRNA was hybridized to a single Illumina HumanHT-12 V4 BeadCHIP at 58 degrees C for 18 hours.

scan_protocol: The BeadCHIP was scnned using the Illumina Iscanner and data pre-processed using the Illumina Bead Studio to correct for local background effects, remove outlier beads, compute average bead signal and SD for each probe and gene and calculation of detection P-values using negative controls present on the array.

data_processing: The matrix of non-normalized values includes Bead Studio Output and detection P values output from the 'scan protocol'. Data were then processed using the LUMI pipeline in R. Data were subjected to VST transformation and robust spline normalization.

source_name: CD14+ derived macrophages - control buffer

label_protocol: Total RNA was reverse tanscribed, amplified and biotinylated using the Illumina TotalPrep-96 RNA Amplification Kit(# 4393543 Ambion Inc., Austin, TX).

growth_protocol: Purified CD14 positive peripheral blood monocytes were cultured for 7 days with 50ng/ml macrophage colony stimulating factor.

extract_protocol: Primary human macrophages and foam cells were lyzed in the TRIZOL reagent and total RNA was extracted using the Invitrogen RNA PLUS extraction kit according to the manufacturers protocol (LifeTechnologies, Paisley UK). The integrity of the total RNA was analyzed on an Agilent Bioanalyzer 2100 (Agilent Technologies, Boeblingen, Germany).

treatment_protocol: For foam cell formation (after 7 days) macrophages were treated with oxLDL (50mcg/ml, enodtoxin free, Copper oxidized). Control macrophages were treated with a matching buffer without oxLDL. Treatment duration - 48 hours.

tag: background

value: European

value: Macrophage

tag: agent

value: control buffer


title: d4_total_effector

tag: donor


title: d6_total_naive


title: HEK293T_LOC550643siRNA_rep3


title: Macrophage-control-5


title: Frozen paraganglioma

city: MADRID

first: ALBERTO

middle: CASCÓN

last: SORIANO

state: MADRID

address: C/MELCHOR FERNÁNDEZ ALMAGRO Nº3

department: HUMAN GENETICS

institute: CENTRO NACIONAL DE INVESTIGACIONES ONCOLÓGICAS

hyb_protocol: Microarray: Human WHG 44K (Agilent microarray design ID 014850, P/N G4112F). Microarray sequences and annotations are listed in sheet '014850_AllAnnotations_20110819'.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing: The data were normalized using the method normexp in order to eliminate the background (Herrero et al.,Nucleic Acids Research, 2003) and limma library by Bioconductor ( Performing loess for intra-array correction and quantiles for inter-array correction)[Smyth et al., Bioinformatics, 2005]. Merged replicates (median) with GEPAS package (Herrero J et al., Nucleic Acids Research, 2003).

source_name: RNA extracted from human paraganglioma

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.

growth_protocol: Tissue preserved frozen in OCT previous to RNA extraction

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Amplified RNA - MMLV-RT.

treatment_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 7,3 to 9,4 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

tag: age

value: 55 years old

value: Paraganglioma primary tumor

source_name: Universal Human Reference RNA (Stratagene)

value: Pool of 10 cell lines (Adenocarcinoma, mammary gland Hepatoblastoma, liver Adenocarcinoma, cervix Embryonal carcinoma, testis Glioblastoma, brain Melanoma Liposarcoma Histiocytic lymphoma; macrophase; histocyte Lymphoblastic leukemiaPlasmacytoma; myeloma; B lymphocyte )


title: d5_total_Tscm

source_name: PBMC


title: U373_in-direct_co-culture_rep3

city: Piran

first: Ana

last: Rotter

address: Fornace 41

department: Marine Biology Station

country: Slovenia

institute: National Institute of BIology

description: replicate 3

hyb_protocol: Labelled samples were hybridized to HumanWG-6 v3 Expression BeadChip (Illumina) - by standard Illumina protocol.

data_processing: data was background subtracted during microarray scanning and later vsn normalized in R using the vsn library.

label: Illumina TotalPrep RNA Amplification kit (Ambion)

source_name: glioma cells

label_protocol: The isolated RNA samples of U87MG and U373 cells were further labelled with Illumina TotalPrep RNA Amplification Kit (Ambion) according to manufacturer's instructions.

growth_protocol: U87MG and U373 cells were grown and maintained in DMEM supplemented with 10% FBS, NEAA, P/S, L-Glu and Na-Pyr. The monocultures and indirect co-cultures were set up in duplicates using six-well Transwell inserts (Costar, Corning Inc.) with 0.4 um pore size. In the bottom chamber the U87MG cells were plated at the density of 105 cells in 2 ml, whereas the U373 cells were always plated in the insert at the same density in 1 ml of media. Cells were left to adhere  for 3h, before being put together for 72h. For monocultures the cells were plated accordingly in the bottom or in the insert, also provided with 3 ml of media.

extract_protocol: Total RNA was isolated from three biological replicates of monocultured and cocultured U87MG and U373 cells using Trizol reagent (Invitrogen Limited, UK) following the manufacturer's instructions. RNA was column purified with RNAeasy Mini Kit (Qiagen, UK) and integrity confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: None.

tag: sample type

value: co-culture

tag: cell line vendor

value: ATTC


title: Macrophage-oxLDL-5

source_name: CD14+ derived macrophages - oxLDL

tag: cell type

value: oxLDL


title: Macrophage-control-3


title: Macrophage-control-4


title: Day2 + bFGF + 4OHT

city: Tokyo

first: Shigeru

last: Saito

address: 6, Yonban-cho Chiyoda-ku

department: Data Science Lab

institute: OPT HOLDING, INC

description: Gene expression of SSEA-1 positive cells at cultured day 2treat with 4OHT

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014868_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit (one-color) (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured Knockout DMEM (Invitrogen) supplemented with 15% KSR (Invitrogen),　2 mM glutamine, 1 mM non-essential amino acids, 2-β-mercaptoethanol, LIF, except for EGCs induction contained bFGF.

extract_protocol: RNA was prepared using the RNeasy (QIAGEN, Venlo, Netherlands) according to the manufacturer's instruction. Quality of RNA was measured with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The chemical compounds were PD325901 (1μM), CHIR99021 (3μM), and A83-01 (250nM). In the case of AKT activation, 4-hydroxytamoxifen (Sigma) was added at 100nM concentration.


title: U87MG_in-direct_co-culture_rep 3

description: replicate 3


title: Macrophage-oxLDL-6


title: Macrophage-oxLDL-3


title: Day2 + bFGF + A83

description: Gene expression of SSEA-1 positive cells at cultured day 2 treat with A83


title: d7_A2_N24b_naivelike


title: Day2 + bFGF + GSK

description: Gene expression of SSEA-1 positive cells at cultured day 2 terat with GSKi


title: HEK293T_LOC550643siRNA_rep1

tag: treatment


title: Macrophage-oxLDL-2

value: Nepalese


title: Day2 + bFGF + 2i+A83 + 4OHT

description: Gene expression of SSEA-1 positive cells at cultured day 2 treat with 2i A83 4OHT


title: U373_monoculture_rep 3

description: replicate 3

value: monoculture


title: U87MG_monoculture_rep 3

description: replicate 3


title: Macrophage-control-2


title: Day2 + bFGF

description: Gene expression of SSEA-1 positive cells at cultured day 2


title: 3mM_2h

city: bunkyou-ku

first: Takeshi

last: Funakoshi

state: Tokyo

address: 1-5-45 yushima

department: forensic medicine

institute: Tokyo medical and dental university

hyb_protocol: standard agilent technologies protocol using Gene Expression Hybridization kit (Agilent Technologies)

scan_protocol: Whole Human Genome oligo DNA microarray was scanned using an DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Feature Extraction software (version 9.5.3.1, Agilent Technologies).

data_processing: The expression values were normalized using Percentile Shift Normalization with recomended setting (75th percentile) using GeneSpring GX software.

source_name: 3mM norephedrine, 2h

label_protocol: cRNA was generated and labeled with Cy3 using Quick Amp labeling kit (Agilent Technologies).

growth_protocol: SH-SY5Y human neuroblastoma cells were grown in a medium (1:1 mixture of Ham’s F12 medium and Modified Eagle’s Medium) supplemented with 10% fetal calf serum at 37oC in a humidified atmosphere of 5% CO2. For the induction of neuronal differentiation, retinoic acid was added to the medium at a concentration of 10 μM and further incubated for four days. Differentiation medium was changed every two days.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA).  Double-stranded cDNA was synthesized from extracted total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

value: neuroblastoma cells


title: Day2 + bFGF + MEK

description: Gene expression of SSEA-1 positive cells at cultured day 2 terat with MEKi


title: U373_in-direct_co-culture_rep2

description: replicate 2


title: Macrophage-oxLDL-1


title: Macrophage-control-1


title: 3mM_6h

source_name: 3mM norephedrine, 6h


title: U87MG_in-direct_co-culture_rep 2

description: replicate 2


title: EBRT cH3 EF1a Blimp-IRES-GFP day2

description: Gene expression of GFP positive cells


title: U87MG_monoculture_rep 2

description: replicate 2


title: KO4(Tfh)

city: Indianapolis

first: Alexander

last: Dent

state: IN

address: 950 W. Walnut St. R2 302, Walther Oncology Center

institute: Alexander Dent

hyb_protocol: Labeled DNA were hybridized for 17 hr at 45C on Mouse Gene 1.0 St Genechips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned using Affymetrix GeneChip® Scanner 3000 7G

data_processing: CEL files were imported into Partek Genomics Suite (Partek, Inc., St. Louis, Mo). RMA (robust multi-array average) signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish (Irizarry, 2003). Summarized signals for each probe set were log2 transformed.

source_name: Naïve CD4 T cell

label_protocol: Biotinylated DNA were prepared according to the Affymetrix standard WT protocol using 100ng of total RNA (not pretreated with Ribominus (Invitrogen))

extract_protocol: standard RNA isolation method-- Qiagen Rneasy

treatment_protocol: Naïve CD4 T cells were stimulated with anti-CD3, anti-CD28, anti-IL-4, anti-IFNg, anti-TGFb Abs plus IL6 and IL21 for 24 hours prior to RNA extraction

value: Follicular helper T (Tfh) cells

tag: genotype

value: T cell-specific conditional Bcl6-/-


title: KO3(Tfh)


title: U373_monoculture_rep 2

description: replicate 2


title: U87MG_in-direct_co-culture_rep 1

description: replicate 1


title: EBRTcH3 Nanos3

description: Gene expression of GFP positive cells


title: KO2(Tfh)


title: KO1(Tfh)


title: EBRTcH3 Dnd

description: Gene expression of GFP positive cells


title: U373_in-direct_co-culture_rep1

description: replicate 1


title: U87MG_monoculture_rep 1

description: replicate 1


title: EBRTcH3 Nanos2

description: Gene expression of GFP positive cells


title: U373_monoculture_rep 1

description: replicate 1


title: EBRTcH3 Prdm14

description: Gene expression of GFP positive cells


title: WT3(Tfh)

value: Wild type


title: 3mM_0h

source_name: 3mM norephedrine, 0h


title: EGCs

description: Gene expression of SSEA-1 positive cells


title: Total RNA, negative control siRNA

city: Edmonton

first: Luiz

middle: Filipe

last: Lisboa

state: AB

address: 6-020 Katz bldg

department: Medical Microbiology and Immunology

institute: University of Alberta

description: MRC-5 transfected with negative control siRNA from which total RNA was harvested

hyb_protocol: Hybridization was performed by Alberta Transplant Applied Genomics Centre (see atagc.med.ualberta.ca)

scan_protocol: Scan protocol was determined by Alberta Transplant Applied Genomics Centre (see atagc.med.ualberta.ca)

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package

source_name: MRC-5 ATCC CCL-171

label_protocol: Labeling was performed by Alberta Transplant Applied Genomics Centre (see atagc.med.ualberta.ca)

growth_protocol: MRC-5 cells grown for 48 hours post-transfection in EMEM 10% FBS at 37 degrees Celsius in humidified 5% CO2 atmosphere

extract_protocol: Manual RNA extraction utilizing miRNeasy mini kit (Qiagen)

treatment_protocol: Reverse transfection with 50 nM of hcmv-miR-UL22A-5p miScript mimic or AllStars Negative Control siRNA (Qiagen) using Lipofectamine RNAiMAX in serum-free medium (in Transfecting Stealth RNAi or siRNA into NIH 3T3 Cells Using Lipofectamine RNAiMAX, Invitrogen, Part no. 25-0906W, Rev. Date: 27Jan2006)

value: lung

value: fibroblast

tag: gender

value: male

value: 14 weeks gestation


title: EBRTcH3 Vasa

description: Gene expression of GFP positive cells


title: WT2(Tfh)


title: Normal-4

city: La Jolla

first: Lana

last: Schaffer

state: CA

address: 10550 North Torrey Pines Road

department: DNA Array Core

institute: TSRI

description: 0.4ug/ml HC and 20pM T3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v3 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: 0.4ug/ml HC and 20pM T3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA using MessageAmp™ II aRNA Kit from Ambion

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

value: Engineered Human Dermal matrix

value: unknown


title: Normal-3

description: 0.4ug/ml HC and 20pM T3


title: WT1(Tfh)


title: WT4(Tfh)


title: Total RNA, hcmv-miR-UL22A-5 siRNA

description: MRC-5 transfected with hcmv-miR-UL22A-5p from which total RNA was harvested


title: RISC RNA, negative control siRNA

description: MRC-5 transfected with negative control siRNA from which RISC RNA was harvested


title: KO3(Tf0)

treatment_protocol: Naïve CD4 T cells were stimulated with anti-CD3 and anti-CD28 Abs  for 24 hours prior to RNA extraction

value: Naïve CD4 T (Tf0) cells


title: Day6 + bFGF + 2i+A83

description: Gene expression of SSEA-1 positive cells at cultured day 6


title: KO2(Tf0)


title: EBRTcH3

description: Gene expression of ESCs

value: blastocyst


title: RISC RNA, hcmv-miR-UL22A-5p siRNA

description: MRC-5 transfected with hcmv-miR-UL22A-5p from which RISC RNA was harvested


title: HCx500_02nMT3-1

description: 200ug/ml HC and 0.2nM T3

source_name: 200ug/ml HC and 0.2nM T3


title: Normal-1

description: 0.4ug/ml HC and 20pM T3


title: KO4(Tf0)


title: Day2 + bFGF + 2i+A83


title: WT3(Tf0)


title: WT4(Tf0)


title: Day1 + bFGF

description: Gene expression of SSEA-1 positive cells at cultured day 1


title: Day3 + bFGF + 2i+A83

description: Gene expression of SSEA-1 positive cells at cultured day 3


title: Day10

description: Gene expression of SSEA-1 positive cells at cultured day 10


title: WT2(Tf0)


title: Normal-2

description: 0.4ug/ml HC and 20pM T3


title: ESCs


title: WT1(Tf0)


title: Rapa_BY007_T1

status: Public on Apr 07 2015

city: Zurich

first: Uwe

last: Sauer

address: Auguste-Piccard-Hof 1

department: Institute of Molecular Systems Biology

institute: ETH Zurich

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before rapamycin treatment, of experiment BY007.

hyb_protocol: Biotin-labeled cRNA samples were fragmented randomly to 35-200 bp at 94°C in fragmentation buffer (Affymetrix Inc., P/N 900371) and suspended in 100ml of hybridization mix (Affymetrix Inc., P/N 900720), containing a hybridization control and control oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip Yeast Genome 2.0 arrays for16h at 45°C.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.) was used to determine the fluorescent intensity emitted by the labeled target.

data_processing: Affymetrix CEL files were processed using R (version 2.10.0) and the Bioconductor affy package. Probe intensities were normalized for background by using the robust multiarray average method (RMA), using only perfect match (PM) probes. Normalization was performed using the qsplines algorithm. Gene expression values were calculated from the PM probes using the expression index calculation method (Li and Wong, 2001).

organism: Saccharomyces cerevisiae

source_name: Rapamycin, -10 min, BY007

label_protocol: Total RNA samples were reverse-transcribed with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using the Sample Cleanup Module (Affymetrix Inc.,P/N 900371). The purified double-stranded cDNAs were in vitro transcribed with biotin labeled nucleotides using the IVT Labeling Kit (Affymetrix Inc., P/N 900449).

growth_protocol: Batch fermentor with defined minimal medium, 20 g/L of glucose as carbon source, 1 g/L of glutamine as nitrogen source, 30°C, 1000 rpm, pH5. At around OD600=1, when cells were still growing exponentially on glutamine, a pulse of rapamycin was instantaneously added to the fermentor to a final concentration of 400 microgram/L.

extract_protocol: Extraction as explained in mechanical disruption protocol of the RNeasy Mini Kit (50), Qiagen.

treatment_protocol: Culture broth (20 mL) was directly harvested and quickly quenched into a tube containing (1:1 v/v) methanol pre-cooled at -40 °C, and pelleted by centrifugation. Pellets were washed once with 10 ml ice-cold water.

tag: strain/background

tag: genotype/variation

value: wildtype

value: rapamycin

tag: time after shift (minutes)

tag: experiment


title: HCx500_02nMT3-3

description: 200ug/ml HC and 0.2nM T3


title: Rapa_BY007_T3

description: Gene expression of wild-type YSBN6 7 minutes after rapamycin treatment, of experiment BY007.

source_name: Rapamycin, 7 min, BY007


title: Rapa_BY006_T6

description: Gene expression of wild-type YSBN6 24 minutes after rapamycin treatment, of experiment BY006.

source_name: Rapamycin, 24 min, BY006


title: Rapa_BY006_T3

description: Gene expression of wild-type YSBN6 7 minutes after rapamycin treatment, of experiment BY006.

source_name: Rapamycin, 7 min, BY006


title: Rapa_BY005_T6

description: Gene expression of wild-type YSBN6 24 minutes after rapamycin treatment, of experiment BY005.

source_name: Rapamycin, 24 min, BY005


title: Rapa_BY006_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before rapamycin treatment, of experiment BY006.

source_name: Rapamycin, -10 min, BY006


title: EBRT cH3 EF1a IRES-GFP day2

description: Gene expression of GFP positive cells


title: PGC


title: Rapa_BY005_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before rapamycin treatment, of experiment BY005.

source_name: Rapamycin, -10 min, BY005


title: HCx500_02nMT3-2

description: 200ug/ml HC and 0.2nM T3


title: Gln2Pro_BY009_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before glutamine depletion, of experiment BY009.

source_name: Gln2Pro, -10 min, BY009

growth_protocol: Batch fermentor with defined minimal medium, 20g/L of glucose as carbon source, 500 mg/L of glutamine and 250 mg/L of proline as nitrogen sources, 30°C, 300 rpm, pH5. At appropriate intervals, the concentration of glutamine in the broth was monitored by using at-line direct flow injection MS analysis on an Agilent LC-qTOF system, allowing readouts within less than 2 minutes after sampling. The time at which glutamine was not detected anymore by direct flow injection MS is referred to as the time of the shift.

value: nutritional downshift from glutamine to proline


title: Rapa_BY007_T6

description: Gene expression of wild-type YSBN6 24 minutes after rapamycin treatment, of experiment BY007.

source_name: Rapamycin, 24 min, BY007


title: Gln2Pro_BY010_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before glutamine depletion, of experiment BY010.

source_name: Gln2Pro, -10 min, BY010


title: Gln2Pro_BY010_T3

description: Gene expression of wild-type YSBN6 7 minutes after glutamine depletion, of experiment BY010.

source_name: Gln2Pro, 7 min, BY010


title: Gln2Pro_BY010_T6

description: Gene expression of wild-type YSBN6 24 minutes after glutamine depletion, of experiment BY010.

source_name: Gln2Pro, 24 min, BY010


title: Macrophage-oxLDL-4

source_name: CD14+ derived macrophages - oxLDL

value: European

value: Macrophage

value: oxLDL


title: Gln2Pro_BY013_T3

description: Gene expression of wild-type YSBN6 7 minutes after glutamine depletion, of experiment BY013.

source_name: Gln2Pro, 7 min, BY013


title: Gln2Pro_BY013_T5

description: Gene expression of wild-type YSBN6 14 minutes after glutamine depletion, of experiment BY013.

source_name: Gln2Pro, 14 min, BY013


title: Gln2Pro_BY013_T4

description: Gene expression of wild-type YSBN6 10 minutes after glutamine depletion, of experiment BY013.

source_name: Gln2Pro, 10 min, BY013


title: Rapa_BY005_T2

description: Gene expression of wild-type YSBN6 3 minutes after rapamycin treatment, of experiment BY005.

source_name: Rapamycin, 3 min, BY005


title: Rapa_BY005_T3

description: Gene expression of wild-type YSBN6 7 minutes after rapamycin treatment, of experiment BY005.

source_name: Rapamycin, 7 min, BY005


title: Rapa_BY005_T8

description: Gene expression of wild-type YSBN6 120 minutes after rapamycin treatment, of experiment BY005.

source_name: Rapamycin, 120 min, BY005


title: Gln2Pro_BY009_T6

description: Gene expression of wild-type YSBN6 24 minutes after glutamine depletion, of experiment BY009.

source_name: Gln2Pro, 24 min, BY009


title: Rapa_BY005_T7

description: Gene expression of wild-type YSBN6 56 minutes after rapamycin treatment, of experiment BY005.

source_name: Rapamycin, 56 min, BY005


title: Gln2Pro_BY013_T2

description: Gene expression of wild-type YSBN6 3 minutes after glutamine depletion, of experiment BY013.

source_name: Gln2Pro, 3 min, BY013


title: Rapa_BY005_T5

description: Gene expression of wild-type YSBN6 14 minutes after rapamycin treatment, of experiment BY005.

source_name: Rapamycin, 14 min, BY005


title: Rapa_BY005_T4

description: Gene expression of wild-type YSBN6 10 minutes after rapamycin treatment, of experiment BY005.

source_name: Rapamycin, 10 min, BY005


title: Gln2Pro_BY009_T3

description: Gene expression of wild-type YSBN6 7 minutes after glutamine depletion, of experiment BY009.

source_name: Gln2Pro, 7 min, BY009


title: Gln2Pro_BY013_T0

description: Gene expression of wild-type YSBN6 at steady-state 5 minutes before glutamine depletion, of experiment BY013.

source_name: Gln2Pro, -5 min, BY013


title: Gln2Pro_BY013_T6

description: Gene expression of wild-type YSBN6 24 minutes after glutamine depletion, of experiment BY013.

source_name: Gln2Pro, 24 min, BY013


title: Gln2Pro_BY013_T7

description: Gene expression of wild-type YSBN6 56 minutes after glutamine depletion, of experiment BY013.

source_name: Gln2Pro, 56 min, BY013


title: Gln2Pro_BY013_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before glutamine depletion, of experiment BY013.

source_name: Gln2Pro, -10 min, BY013


title: Gln2Pro_BY013_T8

description: Gene expression of wild-type YSBN6 120 minutes after glutamine depletion, of experiment BY013.

source_name: Gln2Pro, 120 min, BY013


title: Pro2Gln_BY012_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before the addition of glutamine, of experiment BY012.

hyb_protocol: Biotin-labeled cRNA samples were fragmented randomly to 35-200 bp at 94°C in fragmentation buffer (Affymetrix Inc., P/N 900371) and suspended in 100ml of hybridization mix (Affymetrix Inc., P/N 900720), containing a hybridization control and control oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip Yeast Genome 2.0 arrays for 16h at 45°C.

source_name: Pro2Gln, -10 min, BY012

growth_protocol: Batch fermentor with defined minimal medium, 20 g/L of glucose as carbon source, 200 mg/L of proline as nitrogen source, 30°C, 1000 rpm, pH5. At around OD600=1, when cells were still growing exponentially on proline, a pulse of glutamine was instantaneously added to the fermentor to a final concentration of 400 mg/L.

value: nutritional upshift from proline to glutamine


title: Pro2Gln_BY008_T5

description: Gene expression of wild-type YSBN6 14 minutes after the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, 14 min, BY008


title: Pro2Gln_BY008_T6

description: Gene expression of wild-type YSBN6 24 minutes after the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, 24 min, BY008


title: Pro2Gln_BY003_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before the addition of glutamine, of experiment BY003.

source_name: Pro2Gln, -10 min, BY003


title: Pro2Gln_BY008_T7

description: Gene expression of wild-type YSBN6 56 minutes after the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, 56 min, BY008


title: Pro2Gln_BY003_T6

description: Gene expression of wild-type YSBN6 24 minutes after the addition of glutamine, of experiment BY003.

source_name: Pro2Gln, 24 min, BY003


title: Pro2Gln_BY012_T6

description: Gene expression of wild-type YSBN6 24 minutes after the addition of glutamine, of experiment BY012.

source_name: Pro2Gln, 24 min, BY012


title: Pro2Gln_BY008_T8

description: Gene expression of wild-type YSBN6 120 minutes after the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, 120 min, BY008


title: Pro2Gln_BY003_T3

description: Gene expression of wild-type YSBN6 7 minutes after the addition of glutamine, of experiment BY003.

source_name: Pro2Gln, 7 min, BY003


title: Pro2Gln_BY008_T4

description: Gene expression of wild-type YSBN6 10 minutes after the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, 10 min, BY008


title: Pro2Gln_BY008_T2

description: Gene expression of wild-type YSBN6 3 minutes after the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, 3 min, BY008


title: KO1(Tf0)

source_name: Naïve CD4 T cell

value: T cell-specific conditional Bcl6-/-


title: Pro2Gln_BY012_T3

description: Gene expression of wild-type YSBN6 7 minutes after the addition of glutamine, of experiment BY012.

source_name: Pro2Gln, 7 min, BY012


title: Pro2Gln_BY008_T3

description: Gene expression of wild-type YSBN6 7 minutes after the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, 7 min, BY008


title: Postnatal day 11 dorsal subventricular zone tissue replicate 2

first: Kaz

last: Azim

address: Brain Research Institute

institute: Univ of Zurich

description: Gene expression of P11 dorsal subventricular zone tissue

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Mouse Genome 430-2.0 Array (Affymetrix) as per manufacturer guidelines. Affymetrix chips were incubated at 45°C for 16 hours with biotin-labelled cRNA probes. Following this, these were washed and stained using a streptavidin-phycoerythrin conjugate antibody with an amplification step as described in Affymetrix protocol.

scan_protocol: Chips were scanned on a GC3000 scanner (Affymetrix).

data_processing: Microarray data were preprocessed (background subtraction, normalization, and summarization) via robust multi-chip analysis using the Partek® Genomic Suite software package version 6.6.

source_name: Later stages of postnatal forebrain development of the subventricular zone at P11

label_protocol: 400 ng cRNA was reverse transcribed for obtaining biotinylated cRNAs  generated from double-strand cDNAs using an in vitro transcription labelling kit (Affymetrix).

extract_protocol: For the case of the whole SVZ microdomains, microdissected samples were snap frozen in PrepProtect (Miltenyi Biotech), stored in -80 and pooled. Thawed sampled were spun at 2000 g to remove storage stabilizer. For the case FACsed NSCs or early progenitor, following microdissection, tissues were pooled in HBSS (Gibco/Invitrogen) and dissociated using a trypsin-based kit following manufacturer's guidelines (Miltenyl Biotec). NSCs were further immunostained for Prominin1 (Prom1; 1:100, ebiosciences) for 15 mins. Facsed cells were sorted directly into lysis buffer. Tissues/cells were homogenized in RNA lysis buffer containing β-mercaptoethanol, then subsequentlypassed through Qiashredder columns (Qiagen) to obtain lysates. RNAeasy Minikit (Qiagen) containing DNAase treatment as per manufacturer's instructions. RNA quality was assed via a Bioanalyzer. 200 ngs of total RNA was amplified using the Ambion MEGAscript T7 kit and following manufacturers guidelines.

tag: strain

tag: Stage


title: Pro2Gln_BY008_T1

description: Gene expression of wild-type YSBN6 at steady-state 10 minutes before the addition of glutamine, of experiment BY008.

source_name: Pro2Gln, -10 min, BY008


title: Postnatal day 11 lateral subventricular zone  tissue replicate 2

description: Gene expression of P11 lateral subventricular zone tissue


title: Postnatal day 11 lateral subventricular zone  tissue replicate 1