title: MycOFF treated with water at 16 hours, biological rep3

city: Coventry

first: Michael

last: Khan

address: Gibbet Hill Road

department: Life Sciences

country: United Kingdom

institute: University of Warwick

hyb_protocol: 10µg double-amplified biotin-labelled cRNA were hybridised to Affymetrix MOE430 2.0 GeneChips (Affymetrix, Santa Clara, CA) together with pre-labelled hybridisation controls as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further processing was performed by GCRMA normalization.
After the quality control step, the following 8 samples out of 60 showing poor reproducibility were excluded from our further study: GSM930242, GSM930247, GSM930251, GSM930263, GSM930264, GSM930289, GSM930291, GSM930298

source_name: c-Myc-unactivated_pancreatic islets_vehicle (water)_16 hrs

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

growth_protocol: Pelengaris S, Khan M, Evan G (2002) Suppression of Myc-induced apoptosis in beta cells exposes multiple innate oncogenic properties of Myc sufficient to trigger immediate carcinogenic progression. Cell 109: 321-334

extract_protocol: Fresh frozen pancreas sections were cut to a thickness of 15 µm, bound to a MMI MembraneSlide (Molecular Machines and Industries, Rockledge, FL) and fixed in ice-cold 100 % ethanol for 2 minutes. The SL µCut laser capture microdissection system (Molecular Machines and Industries, Rockledge, FL) was used to isolate islets from surrounding exocrine tissue. Isolated islets were collected on the lid of a MMI IsolationCap (Molecular Machines and Industries, Rockledge, FL) and RNA was homogenised in a solution of RLT buffer (Qiagen, Valencia, CA), a guanidine-isothiocyanate-containing lysis buffer, with β-mercaptoethanol as described in the RNA Microkit protocol. Total RNA was isolated from homogenised pancreata lysates using the Qiagen Microkit (Qiagen, Valencia, CA) for small sample RNA preparation, incorporating a DNase I treatment step. RNA integrity was analysed using an Agilent 2100 Bioanalyser (Agilent, Santa Clara, CA) and RNA was quantified using an Ambion Nanodrop spectrophotometer (Ambion, Foster City, CA).

treatment_protocol: All mice were housed and treated in accordance with protocols and regulations sanctioned by the Home Office under the Animals Act of 1986. Mice used throughout studies were adults, aged 3 months at the start of studies. Activation of MYCERTAM was achieved through administration of 1mg of 4 hydroxytamoxifen (4OHT; Sigma-Aldrich, St. Louis, MO) by daily intraperitoneal injection. To assess the effect of exendin-4 on MYCER-induced hyperglycaemia, mice were given either twice-daily subcutaneous (sc) injections of exendin-4 (50ug/kg dissolved in 5mls water), or equivalent volumes of water vehicle, starting 2 days prior to 4OHT injections.

tag: strain background

value: pIns-MYCERTAM transgenic

value: male

value: 8-12 weeks

value: pancreatic islets

tag: treated with

value: peanut oil (vehicle for 4OHT)

value: water (vehicle for exendin-4)


title: CA1-transformed subiculum and retrosplenial cortex of D6/Zbtb20S mice, rep2

status: Public on Apr 11 2014

type: RNA

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA and loess normalization using the limma package in R.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CA1-transformed subiculum and retrosplenial cortex, D6/Zbtb20S

label_protocol: Ambion MessageAmp3.

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. Each RNA sample represents a pool of RNA obtained from dissected tissues of seven animals.

tag: strain/background

tag: genotype

value: D6/Zbtb20S transgenic

tag: tissue

tag: age

value: postnatal day 1


title: MycOFF treated with water at 8 hours, biological rep2

source_name: c-Myc-unactivated_pancreatic islets_vehicle (water)_8 hrs

tag: genotype/variation

tag: gender


title: MycOFF treated with water at 32 hours, biological rep2

source_name: c-Myc-unactivated_pancreatic islets_vehicle (water)_32 hrs


title: MycOFF treated with water at 32 hours, biological rep1


title: MycOFF treated with water at 4 hours, biological rep3

source_name: c-Myc-unactivated_pancreatic islets_vehicle (water)_4 hrs


title: MycOFF treated with water at 8 hours, biological rep3


title: Wildtype subiculum and retrosplenial cortex, rep2

source_name: subiculum and retrosplenial cortex, wildtype

value: wildtype

value: subiculum and retrosplenial cortex


title: MycOFF treated with exenatide at 72 hours, biological rep2

value: exendin-4 (50ug/kg dissolved in 5mls water)


title: MycOFF treated with water at 72 hours, biological rep2

source_name: c-Myc-unactivated_pancreatic islets_vehicle (water)_72 hrs


title: MycOFF treated with water at 16 hours, biological rep2


title: MycOFF treated with exenatide at 72 hours, biological rep3


title: MycOFF treated with water at 72 hours, biological rep1


title: MycOFF treated with water at 4 hours, biological rep2


title: MycOFF treated with water at 16 hours, biological rep1


title: MycOFF treated with water at 8 hours, biological rep1


title: MycOFF treated with water at 4 hours, biological rep1


title: MycOFF treated with water at 72 hours, biological rep3


title: MycOFF treated with exenatide at 72 hours, biological rep1


title: MycOFF treated with water at 32 hours, biological rep3


title: MycOFF treated with exenatide at 16 hours, biological rep1


title: MycOFF treated with exenatide at 32 hours, biological rep1


title: MycOFF treated with exenatide at 32 hours, biological rep3


title: MycOFF treated with exenatide at 16 hours, biological rep3


title: MycOFF treated with exenatide at 16 hours, biological rep2


title: MycOFF treated with exenatide at 8 hours, biological rep3


title: MycOFF treated with exenatide at 32 hours, biological rep2


title: MycOFF treated with exenatide at 8 hours, biological rep1


title: MycON treated with water at 72 hours, biological rep3

source_name: c-Myc-activated_pancreatic islets_vehicle (water)_72 hrs

value: 1mg of 4 hydroxytamoxifen (4OHT)


title: MycOFF treated with exenatide at 4 hours, biological rep3


title: MycON treated with water at 32 hours, biological rep3

source_name: c-Myc-activated_pancreatic islets_vehicle (water)_32 hrs


title: MycON treated with water at 72 hours, biological rep2


title: MycOFF treated with exenatide at 8 hours, biological rep2


title: MycON treated with water at 8 hours, biological rep3

source_name: c-Myc-activated_pancreatic islets_vehicle (water)_8 hrs


title: MycON treated with water at 16 hours, biological rep1

source_name: c-Myc-activated_pancreatic islets_vehicle (water)_16 hrs


title: MycON treated with water at 72 hours, biological rep1


title: MycOFF treated with exenatide at 4 hours, biological rep1


title: MycON treated with water at 32 hours, biological rep2


title: MycON treated with water at 4 hours, biological rep2

source_name: c-Myc-activated_pancreatic islets_vehicle (water)_4 hrs


title: MycON treated with water at 16 hours, biological rep2


title: MycON treated with water at 4 hours, biological rep3


title: MycON treated with water at 32 hours, biological rep1


title: MycON treated with exenatide at 72 hours, biological rep2


title: MycOFF treated with exenatide at 4 hours, biological rep2


title: MycON treated with water at 4 hours, biological rep1


title: MycON treated with exenatide at 72 hours, biological rep3


title: MycON treated with water at 16 hours, biological rep3


title: MycON treated with water at 8 hours, biological rep2


title: MycON treated with exenatide at 72 hours, biological rep1


title: MycON treated with exenatide at 16 hours, biological rep2


title: MycON treated with exenatide at 32 hours, biological rep2


title: MycON treated with exenatide at 32 hours, biological rep1


title: MycON treated with exenatide at 16 hours, biological rep3


title: MycON treated with exenatide at 8 hours, biological rep3


title: MycON treated with exenatide at 32 hours, biological rep3


title: MycON treated with exenatide at 8 hours, biological rep1


title: MycON treated with exenatide at 8 hours, biological rep2


title: MycON treated with exenatide at 4 hours, biological rep3


title: MycON treated with exenatide at 16 hours, biological rep1


title: RatHpctx primary neuron CAT+ADDL treated replicate 2 of 2

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

country: USA

institute: Karmanos Cancer Institute & Wayne State University

hyb_protocol: Whole-genome expression was measured by a 2-color microarray approach using Agilent SurePrint G3 Rat GE 8X60K arrays (Agilent Technologies)

scan_protocol: GE2_1105_Oct12 protocol and Agilent SureScan System

data_processing: Data quality were assessed and data were processed with Agilent Feature Extraction software (version 11.5) producing expression data measures including Log10 Ratio expression levels (background subtracted, lowess normalizd), LogRatioError and PValueLogRatio.

organism: Rattus norvegicus

source_name: CATSKL+ADDL treated RatHpctx primary neuron

label_protocol: Labeling reaction used the Low Input Quick Amp Labeling Kit from Agilent Technologies, Inc. following the recommended protocol to produce cRNA for a two-color microarray experiment

growth_protocol: Primary neurons were plated and incubated under normal cell culture conditions for 5-7 days to differentiate.  Media was changed every 3-4 days

extract_protocol: Total RNA was isolated from cell pellets using an RNeasy Midi Kit from Qiagen.  Quantity and quality of all mRNA samples was determined by analysis with the NanoDrop 1000, Agilent Bioanalyzer and the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After 7 days in vitro, neurons were treated with the following on days 8 and 9:  pre-treated with 1 uM CAT-SKL for 24 hours, and post-treated with 1 uM ADDL for an additional 24 hours, or pre-treated with 1 uM ADDL for 24 hours and then post-treated with 1 uM CAT-SKL for an additional 24 hours, or 1 uM CAT-SKL or ADDL alone for 24 hours

value: Primary Rat E18 coritical/hippocampal neurons

value: CAT+ADDL

source_name: vehicle treated Primary neuron

value: Primary neuron

value: vehicle (control)


title: MycON treated with exenatide at 4 hours, biological rep2


title: RatHpctx primary neuron ADDL treated replicate 2 of 2

source_name: ADDL treated RatHpctx primary neuron

value: ADDL


title: RatHpctx primary neuron ADDL+CAT treated replicate 2 of 2

source_name: ADDL+CATSKL treated RatHpctx primary neuron

value: ADDL+CAT


title: RatHpctx primary neuron CAT+ADDL treated replicate 1 of 2


title: RatHpctx primary neuron CATSKL treated replicate 2 of 2

source_name: CATSKL treated RatHpctx primary neuron

value: CATSKL


title: muscle_rfi_pr13

city: College Station

first: Robert

middle: Neil

last: Vaughn

state: TX

address: 0965 Agronomy

department: Soil and Crop Sciences

institute: Texas A&M University

description: Biological replicate 13 of 16: high vs. low rfi

hyb_protocol: RNA was hybridized to Agilent bovine 4x44K slides according to the hybridization procedures in the QuickAmp Labeling kit manual.  Hybridized slides were also washed and dried according to that protocol.

scan_protocol: Slides were scanned on an Axon GenePix Personal 4100A scanner.  Data were quantified in GenePix Pro v.6.0.

data_processing: Agilent GeneSpring software (v 10.0.02) was used for background subtraction and LOWESS normalization.

organism: Bos indicus x Bos taurus

source_name: Longissimus cervicis, excised ~45 min post-exsanguination

label_protocol:
1.  Samples from steers with high residual feed efficiency were paired randomly with samples from steers with low residual feed efficiency.  Four samples were randomly chosen to be labeled with Cy3 and four with Cy5; the other member of each pair was labeled with the opposite dye.
2.  RNA (2.5 μg/sample) was labeled with the Agilent two-color QuickAmp Labeling Kit, according to the manufacturer's protocol.

extract_protocol:
1.  RNA was extracted once with TRI Reagent and bromochloropropane (Molecular Research Center) according to the manufacturer's protocol, once with TRI Reagent and BCP in a 2:1 ratio, and once with BCP alone (again according to the manufacturer's protocol).  RNA was precipitated with isopropanol, washed with ethanol, dried, and resuspended in nuclease-free water.
2.  RNA was quantified on a NanoDrop ND-1000 spectrophotometer.  RNA quality was assayed on an Agilent 2100 Bioanalyzer.
3.  RNA was purified on Qiagen RNeasy columns using their RNA cleanup protocol, and Dnase-treated with Ambion's DNA-free kit.

value: steer

value: approx. 18 months

tag: efficiency

value: Low


title: muscle_rfi_pr16

description: Biological replicate 16 of 16: high vs. low rfi


title: muscle_rfi_pr11

description: Biological replicate 11 of 16: high vs. low rfi

value: High


title: MycON treated with exenatide at 4 hours, biological rep1

value: pIns-MYCERTAM transgenic

value: male

value: 8-12 weeks

value: pancreatic islets


title: muscle_rfi_pr12

description: Biological replicate 12 of 16: high vs. low rfi


title: RatHpctx primary neuron ADDL treated replicate 1 of 2


title: GzmBKO_HSC 1

city: Macclesfield

first: Larissa

middle: S

last: Carnevalli

state: Cheshire

address: Mereside, Alderley Park

institute: Astrazeneca

description: replicate 1, 8294816095_D

hyb_protocol: Standard Illumina hybridiation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: hematopoiteic stem cells

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) is used to generate single-stranded cDNA from small input amounts of 2.5ng RNA. Labeled cRNA were prepared according to Nugene Encore BiotinIL Module.

growth_protocol: sorted HSCs by flow cytometry

extract_protocol: Total mRNA was extracted from sorted HSCs and isolated using Arcturus PicoPure (Applied Biosystems).

value: female

tag: strain

value: 12 weeks

value: GzmB-/-


title: muscle_rfi_pr14

description: Biological replicate 14 of 16: high vs. low rfi


title: muscle_rfi_pr15

description: Biological replicate 15 of 16: high vs. low rfi


title: RatHpctx primary neuron ADDL+CAT treated replicate 1 of 2

description: ADDL+CATSKL_1 LogRatio

value: Primary Rat E18 coritical/hippocampal neurons


title: WT_HSC 2

description: replicate 2, 8294816095_B

value: wild type


title: muscle_rfi_pr9

description: Biological replicate 9 of 16: high vs. low rfi


title: muscle_rfi_pr8

description: Biological replicate 8 of 16: high vs. low rfi


title: WT_HSC 3

description: replicate 3, 8294816095_C


title: GzmBKO_HSC 3

description: replicate 3, 8294816095_F


title: RatHpctx primary neuron CATSKL treated replicate 1 of 2

value: Primary neuron

value: vehicle (control)


title: GzmBKO_HSC 2

description: replicate 2, 8294816095_E


title: muscle_rfi_pr10

description: Biological replicate 10 of 16: high vs. low rfi


title: WT_HSC 1

description: replicate 1, 8294816095_A


title: E13 hepatoblasts 2

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai University

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the Agilent instructions. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software according to the Agilent instructions.

source_name: E13 hepatoblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA according to the Agilent instructions.

extract_protocol: RNA was extracted using RNeasy Micro Kit (Qiagen; Venlo, The Netherlands).

value: liver

tag: cell type

value: hepatoblasts

tag: Stage

value: embryonic day 13


title: Adult hepatocytes 2

source_name: Adult hepatocytes

value: hepatocytes

value: 8 weeks old


title: Adult hepatocytes 1


title: muscle_rfi_pr6

description: Biological replicate 6 of 16: high vs. low rfi

value: steer

value: approx. 18 months

value: Low


title: SF539 PARK2 siRNA#1 replicate 2

city: New York

first: Yongxing

last: Gong

state: NY

address: 1275 York Avenue

institute: Momerial Sloan-Kettering Cancer Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: data was normalized and analyzed using partek software and R packages. Specifically log2 transformation was used for data normalization.

label: Biotin

organism: Homo sapiens

source_name: SF539 GBM cell line

label_protocol: Affymetrix protocol

growth_protocol: SNB19 cells were cultured in DMEM media supplemented with 10% FBS and penicillin-streptomycin at 37 °C in 5% CO2. SF539 cells were grown in MEM media with 10% FBX and penicillin-streptomycin at 37 °C in 5% CO2

extract_protocol: Total RNA was extracted by using Rneasy Plus Mini Kit (Qiagen). RNA quality was determined with the Nanodrop Spectrophotometer (Thermo).

treatment_protocol: siRNAs were transfected into cells in antibiotic-free medium using Lipofectamine RNAiMAX , medium was changed after 4–6 h and cells were harvested after 48 hours .

tag: cell line

tag: transfection

value: PARK2 siRNA#1


title: LNCaP empty vector transfectant

city: Kyoto

first: Atsushi

last: Maeno

address: Skyo-ku Shogoin Kawahara-cho 54

department: Urology

institute: Kyoto University Facalty of Medicine

hyb_protocol: Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes and centrifuge at maximum speed for 1 minute. Hybridization buffer and washing protocol was followed by the protocol supplied by affymetrix Inc..

scan_protocol: GeneChip®Scanner 3000 7G was used for scanning. Images were quantified using GeneChip® Command Console® Software.

data_processing: The raw data was processed using GeneSpring GX Version11.5.1. Summarization Algorithm was RMA16. Confidence level was All. Do not perform baseline transformation. Genes in the matrix table were down-regulated in LNCaP miR-582-5p in comparison to LNCaP EV by >2-fold .

source_name: LNCaP empty vector transfectant

label_protocol: cDNA  was labeled with biotin using the GeneChip® WT Terminal Labeling Kit.

extract_protocol: Total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocols.

value: empty vector transfectant


title: SF539 PARK2 siRNA#2 replicate 1

value: PARK2 siRNA#2


title: muscle_rfi_pr7

description: Biological replicate 7 of 16: high vs. low rfi

value: High


title: SF539 PARK2 siRNA#2 replicate 2


title: LNCaP miR-582-5p transfectant

source_name: LNCaP miR-582-5p transfectant

value: miR-582-5p transfectant


title: muscle_rfi_pr3

description: Biological replicate 3 of 16: high vs. low rfi


title: MycON treated with water at 8 hours, biological rep1

value: pIns-MYCERTAM transgenic

value: male

value: 8-12 weeks

value: pancreatic islets

value: 1mg of 4 hydroxytamoxifen (4OHT)

value: water (vehicle for exendin-4)


title: SF539 PARK2 siRNA#1 replicate 1


title: muscle_rfi_pr1

description: Biological replicate 1 of 16: high vs. low rfi


title: SF539 scramble siRNA replicate 2

value: Scramble siRNA


title: SF539 scramble siRNA replicate 1


title: muscle_rfi_pr5

description: Biological replicate 5 of 16: high vs. low rfi


title: muscle_rfi_pr2

description: Biological replicate 2 of 16: high vs. low rfi


title: muscle_rfi_pr4

description: Biological replicate 4 of 16: high vs. low rfi


title: E13 hepatoblasts 1

value: liver

value: hepatoblasts

value: embryonic day 13


title: SNB19 PARK2 siRNA#1 replicate 2

source_name: SNB19 GBM cell line


title: RptorKO CSC Technical Rep.1

status: Public on Apr 10 2014

city: Palo Alto

first: Joseph

middle: T

last: Rodgers

state: CA

address: 3801 Miranda Ave

institute: Stanford University

description: Gene expression data from Rptr KO, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 2.5 days post injury

hyb_protocol: Fragmented biotin-labeled single stranded DNA was hybridized to Affymetrix Mouse Gene 1.0  Array according to the standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymertix Expression Console software using Affymetrix default RMA analysis settings

source_name: FACS purified YFP+ muscle stem cells, harvest immediately after isolation

label_protocol: Biotinylated single stranded cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: Cells were FACS-purified from hindlimb muscle of uninjured or injured mice as indicated  and were NOT cultured after isolation

extract_protocol: Trizol extraction of total RNA followed by Qiagen Rneasy Plus cleanup was performed according to the manufacturer's instructions

treatment_protocol: No treatment

value: mixed C57BL6

value: 3-5 months old

tag: treatment

value: BaCl2 muscle injury

value: hindlimb muscle contralateral to BaCl2 muscle injury

value: CSC

tag: time

value: 2.5 days post injury


title: RptorKO CSC Technical Rep.2


title: SNB19 scramble siRNA replicate 1


title: SNB19 PARK2 siRNA#2 replicate 1

value: PARK2 siRNA#2


title: cMetKO CSC Technical Rep.2

description: Gene expression data from cMet KO, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 2.5 days post injury

value: C57BL6 mixed FVB


title: cMetKO CSC Technical Rep.1


title: SNB19 scramble siRNA replicate 2


title: SNB19 PARK2 siRNA#2 replicate 2


title: SNB19 PARK2 siRNA#1 replicate 1

value: PARK2 siRNA#1


title: cMetKO QSC Technical Rep.2

description: Gene expression data from cMet KO, YFP+ muscle stem cells isolated from a noninjured animal

value: noninjured

value: hindlimb muscle

value: QSC

value: control


title: TSC1KO QSC Technical Rep.2

description: Gene expression data from TSC1 KO, YFP+ muscle stem cells isolated from a noninjured animal


title: WTGFP CSC Biological Rep.2 Technical Rep.1

description: Gene expression data from WT, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 2.5 days post injury


title: WTGFP CSC 28DPI Technical Rep.1

description: Gene expression data from WT, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 28 days post injury

value: 28 days post injury


title: cMetKO QSC Technical Rep.1


title: TSC1KO QSC Technical Rep.1


title: RptorKO QSC Technical Rep.2

description: Gene expression data from Rptr KO, YFP+ muscle stem cells isolated from a noninjured animal


title: RptorKO QSC Technical Rep.1


title: WTGFP CSC 28DPI Technical Rep.2


title: WTGFP CSC Biological Rep.3 Technical Rep.1


title: WTGFP QSC Biological Rep.2 Technical Rep.1

description: Gene expression data from WT, YFP+ muscle stem cells isolated from a noninjured animal


title: WTGFP QSC Biological Rep.2 Technical Rep.2


title: Normal2

city: Goyang

first: Hark

middle: Kyun

last: Kim

address: 323 Ilsanro

department: Biomolecular Function Research Branch

country: South Korea

institute: National Cancer Center

description: Normal gastric mucosa

hyb_protocol: See Affymetrix protocol

scan_protocol: See Affymetrix protocol

data_processing: RMA summarized in R.

source_name: Normal gastric mucosa

label_protocol: See Affymetrix protocol

extract_protocol: All prep kit (Qiagen)

tag: tissue type

value: Normal gastric mucosa


title: WTGFP CSC Biological Rep.1 Technical Rep.1


title: GC3

description: Gastric adenocarcinoma

source_name: Gastric adenocarcinoma

value: Gastric adenocarcinoma


title: WTGFP QSC Biological Rep.1 Technical Rep.1


title: Normal4

description: Normal gastric mucosa


title: GC4

description: Gastric adenocarcinoma


title: WTGFP QSC Biological Rep.1 Technical Rep.2


title: Normal3

description: Normal gastric mucosa


title: WTGFP CSC Biological Rep.1 Technical Rep.2


title: WTGFP QSC Biological Rep.3 Technical Rep.1


title: 4P_60min_rep2

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description: replicate 2 of 2

hyb_protocol: 600ng of each cRNA was fragmented and hybridized as per manufacturers instructions (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90050_GeneExpression_TwoColor_6.6.pdf).

scan_protocol: Slides were scanned on an Agilent G2505C scanner with ChipScan software version A.8.4.1.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1) using default normalization settings.

organism: Saccharomyces cerevisiae

source_name: MW836a, mid-log

label_protocol: RNA was subjected to amplification and labeling using the Agilent Low Input Quick Amp Labeling Kit protocol (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90050_GeneExpression_TwoColor_6.6.pdf) with minor modifications. Briefly, cRNA was amplified by in vitro transcription with amino-allyl UTP (3:2 ratio for amino-ally UTP: UTP) overnight at 37°C. Then, cRNA was purified using RNA Clean and Concentrator columns (Zymo Research) and labeled with Cy3 or Cy5 (GE healthcare) at room temperature for 90 minutes in the dark.

growth_protocol: Cells were arrested in G1 phase with alpha-factor for 2 hours, released from the arrest, and samples collected at 15 minute intervals.

extract_protocol: Total RNA was extracted using an acid-phenol prep as previously described (Schmitt et al, 1990; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC330876/)

value: HCM1 TOS4 YOX1 YHP1

tag: time point

value: mid-log

source_name: YBL289, alpha-factor arrest-release, 60 minutes

value: hcm1-15A-3HA tos4-9A-3FLAG yox1-9A-3V5 yhp1-13A-13MYC

value: 60 minutes


title: 4P_0min_rep2

description: replicate 2 of 2

source_name: YBL289, alpha-factor arrest-release, 0 minutes

value: 0 minutes


title: 4P_15min_rep2

description: replicate 2 of 2

source_name: YBL289, alpha-factor arrest-release, 15 minutes

value: 15 minutes


title: 4P_105min_rep2

description: replicate 2 of 2

source_name: YBL289, alpha-factor arrest-release, 105 minutes

value: 105 minutes


title: GC2

description: Gastric adenocarcinoma


title: 4P_75min_rep2

description: replicate 2 of 2

source_name: YBL289, alpha-factor arrest-release, 75 minutes

value: 75 minutes


title: 4P_90min_rep2

description: replicate 2 of 2

source_name: YBL289, alpha-factor arrest-release, 90 minutes

value: 90 minutes


title: 4P_30min_rep2

description: replicate 2 of 2

source_name: YBL289, alpha-factor arrest-release, 30 minutes

value: 30 minutes


title: WT_90min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 90 minutes

value: HCM1-3HA TOS4-3FLAG YOX1-3V5 YHP1-13MYC


title: GC1

description: Gastric adenocarcinoma


title: WT_105min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 105 minutes


title: WT_45min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 45 minutes

value: 45 minutes


title: WT_75min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 75 minutes


title: WT_0min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 0 minutes


title: WT_60min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 60 minutes


title: 4P_45min_rep2

description: replicate 2 of 2

source_name: YBL289, alpha-factor arrest-release, 45 minutes


title: 4P_90min_rep1

description: replicate 1 of 2


title: WT_15min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 15 minutes


title: 4P_75min_rep1

description: replicate 1 of 2


title: WT_30min_rep2

description: replicate 2 of 2

source_name: YBL320, alpha-factor arrest-release, 30 minutes


title: 4P_105min_rep1

description: replicate 1 of 2

source_name: MW836a, mid-log


title: Normal1

description: Normal gastric mucosa

source_name: Normal gastric mucosa


title: 4P_45min_rep1

description: replicate 1 of 2


title: 4P_0min_rep1

description: replicate 1 of 2

source_name: YBL289, alpha-factor arrest-release, 0 minutes


title: 4P_30min_rep1

description: replicate 1 of 2


title: 4P_60min_rep1

description: replicate 1 of 2

source_name: YBL289, alpha-factor arrest-release, 60 minutes


title: 4P_15min_rep1

description: replicate 1 of 2

source_name: YBL289, alpha-factor arrest-release, 15 minutes


title: WT_105min_rep1

description: replicate 1 of 2


title: WT_75min_rep1

description: replicate 1 of 2


title: WT_30min_rep1

description: replicate 1 of 2


title: WT_60min_rep1

description: replicate 1 of 2


title: WT_15min_rep1

description: replicate 1 of 2


title: WT_0min_rep1

description: replicate 1 of 2


title: WT_45min_rep1

description: replicate 1 of 2


title: WT_90min_rep1

description: replicate 1 of 2


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Female Hippocampus 3938

city: Philadelphia

first: David

middle: William

last: Anderson

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy & Cell Biology

institute: Thomas Jefferson University

description: Gene expression in female Sprague Dawley rat hippocampus following 750ppm lead exposure during postnatal development

hyb_protocol: standard Affymetrix protocol

scan_protocol: Chips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Raw gene expression data was normalized using RMA in Partek Genomics Suit.

source_name: Hippocampus

label_protocol: standard Affymetrix protocol

extract_protocol: Tissue was extracted using Qiagen miRNeasy kits according to the manufacturers protocol on a Qiagen Qiacube Automated Extraction system.  Following extraction samples underwent QA/QC checks using a GE NanoVue Spectrophotometer and were then run on an Agilent Bioanalyzer 2100 for RNA integerity.

treatment_protocol: Animals received either perinatal or postnatal exposure to control chow, control chow containing 250ppm lead-acetate or control chow containing 750ppm lead acetate.  Perinatal exposure consisted of the dams being placed on lead food for 10 days pior to breeding and remaining on this food until weening, at which time the weaned pups were placed on control food until the end of the experiment at PND55.  Postnatal animals only received lead-containgin food from brith through to PND 45, then were placed on control food until PND 55. Animals were euthanized and hippocampii immediately dissected and flash frozen.  Samples were then stored at -80 degrees C until processed.

value: Female

tag: developmental period

value: Postnatal

value: 750ppm lead

value: Sprague Dawley

value: hippocampus


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Female Hippocampus 3937


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Male Hippocampus 3933

description: Gene expression in male Sprague Dawley rat hippocampus following 750ppm lead exposure during postnatal development

value: Male


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Male Hippocampus 3934


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Female Hippocampus 3936


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Female Hippocampus 3960

description: Gene expression in female Sprague Dawley rat hippocampus following 750ppm lead exposure during perinatal development

value: Perinatal


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Female Hippocampus 3796

description: Gene expression in female Sprague Dawley rat hippocampus following 250ppm lead exposure during postnatal development

value: 250ppm lead


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Female Hippocampus 3962


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Male Hippocampus 3931


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Male Hippocampus 3956

description: Gene expression in male Sprague Dawley rat hippocampus following 750ppm lead exposure during perinatal development


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Male Hippocampus 3957


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Female Hippocampus 3935


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Female Hippocampus 3961


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Female Hippocampus 3793


title: Sprague Dawley Postnatal 750ppm Lead-Exposed Male Hippocampus 3932


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Male Hippocampus 3958


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Male Hippocampus 3955


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Female Hippocampus 3794


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Male Hippocampus 3789

description: Gene expression in male Sprague Dawley rat hippocampus following 250ppm lead exposure during postnatal development


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Female Hippocampus 4050

description: Gene expression in female Sprague Dawley rat hippocampus following 250ppm lead exposure during perinatal development


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Female Hippocampus 4051


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Female Hippocampus 4052


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Male Hippocampus 4049

description: Gene expression in male Sprague Dawley rat hippocampus following 250ppm lead exposure during perinatal development


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Male Hippocampus 3791


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Female Hippocampus 4053


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Male Hippocampus 3792


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Male Hippocampus 3790


title: Sprague Dawley Perinatal 750ppm Lead-Exposed Female Hippocampus 3959


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Male Hippocampus 4048


title: Long Evans Postnatal 750ppm Lead-Exposed Female Hippocampus 2823

description: Gene expression in female Long Evans rat hippocampus following 750ppm lead exposure during postnatal development

value: Long Evans


title: Sprague Dawley Control Female Hippocampus 3976

description: Gene expression in female Sprague Dawley rat hippocampus

value: Control

value: 0ppm lead (Control)


title: Sprague Dawley Postnatal 250ppm Lead-Exposed Female Hippocampus 3795


title: Long Evans Postnatal 750ppm Lead-Exposed Male Hippocampus 2845

description: Gene expression in male Long Evans rat hippocampus following 750ppm lead exposure during postnatal development


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Male Hippocampus 4046


title: Long Evans Perinatal 750ppm Lead-Exposed Male Hippocampus 3447

description: Gene expression in male Long Evans rat hippocampus following 750ppm lead exposure during perinatal development


title: Long Evans Postnatal 750ppm Lead-Exposed Male Hippocampus 2846


title: Sprague Dawley Perinatal 250ppm Lead-Exposed Male Hippocampus 4047


title: Sprague Dawley Control Male Hippocampus 3973

description: Gene expression in male Sprague Dawley rat hippocampus


title: Sprague Dawley Control Female Hippocampus 3975


title: Long Evans Postnatal 750ppm Lead-Exposed Female Hippocampus 2824


title: Long Evans Perinatal 750ppm Lead-Exposed Male Hippocampus 3446


title: Long Evans Postnatal 750ppm Lead-Exposed Female Hippocampus 2822


title: Sprague Dawley Control Female Hippocampus 3978


title: Long Evans Perinatal 750ppm Lead-Exposed Female Hippocampus 1981

description: Gene expression in female Long Evans rat hippocampus following 750ppm lead exposure during perinatal development


title: Long Evans Perinatal 750ppm Lead-Exposed Female Hippocampus 1979


title: Long Evans Postnatal 750ppm Lead-Exposed Female Hippocampus 2821


title: Long Evans Postnatal 750ppm Lead-Exposed Male Hippocampus 2848


title: Long Evans Postnatal 750ppm Lead-Exposed Male Hippocampus 2847


title: Sprague Dawley Control Female Hippocampus 3977


title: Long Evans Perinatal 750ppm Lead-Exposed Female Hippocampus 1978


title: Sprague Dawley Control Male Hippocampus 3971


title: Long Evans Perinatal 750ppm Lead-Exposed Male Hippocampus 3445


title: Long Evans Perinatal 750ppm Lead-Exposed Female Hippocampus 1980


title: Sprague Dawley Control Male Hippocampus 3974


title: Long Evans Postnatal 250ppm Lead-Exposed Female Hippocampus 2844

description: Gene expression in female Long Evans rat hippocampus following 250ppm lead exposure during postnatal development


title: Long Evans Perinatal 750ppm Lead-Exposed Male Hippocampus 3444


title: Long Evans Postnatal 250ppm Lead-Exposed Female Hippocampus 2843


title: Long Evans Postnatal 250ppm Lead-Exposed Female Hippocampus 2842


title: Long Evans Postnatal 250ppm Lead-Exposed Female Hippocampus 2841


title: Long Evans Postnatal 250ppm Lead-Exposed Male Hippocampus 2873

description: Gene expression in male Long Evans rat hippocampus following 250ppm lead exposure during postnatal development


title: Long Evans Postnatal 250ppm Lead-Exposed Male Hippocampus 2875


title: Long Evans Postnatal 250ppm Lead-Exposed Male Hippocampus 2874


title: Long Evans Perinatal 250ppm Lead-Exposed Female Hippocampus 2857

description: Gene expression in female Long Evans rat hippocampus following 250ppm lead exposure during perinatal development


title: Long Evans Perinatal 250ppm Lead-Exposed Male Hippocampus 2867

description: Gene expression in male Long Evans rat hippocampus following 250ppm lead exposure during perinatal development


title: Long Evans Postnatal 250ppm Lead-Exposed Male Hippocampus 2876


title: Long Evans Control Female Hippocampus 1976

description: Gene expression in female Long Evans rat hippocampus


title: Long Evans Perinatal 250ppm Lead-Exposed Female Hippocampus 2859


title: Long Evans Perinatal 250ppm Lead-Exposed Female Hippocampus 2860


title: Long Evans Perinatal 250ppm Lead-Exposed Male Hippocampus 2868


title: Long Evans Perinatal 250ppm Lead-Exposed Male Hippocampus 2866


title: Long Evans Control Female Hippocampus 1977


title: Long Evans Control Female Hippocampus 1974


title: Long Evans Perinatal 250ppm Lead-Exposed Female Hippocampus 2858


title: Long Evans Perinatal 250ppm Lead-Exposed Male Hippocampus 2865


title: Long Evans Control Female Hippocampus 1975


title: Fischer Postnatal 750ppm Lead-Exposed Male Hippocampus 3164

description: Gene expression in male Fischer rat hippocampus following 750ppm lead exposure during postnatal development

value: Fischer


title: Fischer Postnatal 750ppm Lead-Exposed Male Hippocampus 3162


title: Fischer Postnatal 750ppm Lead-Exposed Female Hippocampus 3165

description: Gene expression in female Fischer rat hippocampus following 750ppm lead exposure during postnatal development


title: Fischer Postnatal 750ppm Lead-Exposed Male Hippocampus 3163


title: Fischer Postnatal 750ppm Lead-Exposed Female Hippocampus 3167


title: Fischer Postnatal 750ppm Lead-Exposed Male Hippocampus 3161


title: Long Evans Control Male Hippocampus 1972

description: Gene expression in male Long Evans rat hippocampus


title: Fischer Postnatal 750ppm Lead-Exposed Female Hippocampus 3168


title: Long Evans Control Male Hippocampus 1970


title: Fischer Perinatal 750ppm Lead-Exposed Female Hippocampus 3365

description: Gene expression in female Fischer rat hippocampus following 750ppm lead exposure during perinatal development


title: Long Evans Control Male Hippocampus 1971


title: Long Evans Control Male Hippocampus 1973


title: Fischer Perinatal 750ppm Lead-Exposed Male Hippocampus 3360

description: Gene expression in male Fischer rat hippocampus following 750ppm lead exposure during perinatal development


title: Fischer Postnatal 750ppm Lead-Exposed Female Hippocampus 3166


title: Fischer Perinatal 750ppm Lead-Exposed Female Hippocampus 3364


title: Fischer Postnatal 250ppm Lead-Exposed Female Hippocampus 3196

description: Gene expression in female Fischer rat hippocampus following 250ppm lead exposure during postnatal development


title: Fischer Postnatal 250ppm Lead-Exposed Female Hippocampus 3199


title: Fischer Postnatal 250ppm Lead-Exposed Male Hippocampus 3190

description: Gene expression in male Fischer rat hippocampus following 250ppm lead exposure during postnatal development


title: Fischer Perinatal 750ppm Lead-Exposed Male Hippocampus 3358


title: Fischer Perinatal 750ppm Lead-Exposed Female Hippocampus 3363


title: Fischer Postnatal 250ppm Lead-Exposed Male Hippocampus 3188


title: Fischer Perinatal 750ppm Lead-Exposed Female Hippocampus 3362


title: Fischer Perinatal 750ppm Lead-Exposed Male Hippocampus 3361


title: Fischer Postnatal 250ppm Lead-Exposed Female Hippocampus 3197


title: Fischer Postnatal 250ppm Lead-Exposed Male Hippocampus 3191


title: Fischer Postnatal 250ppm Lead-Exposed Male Hippocampus 3189


title: Fischer Perinatal 750ppm Lead-Exposed Male Hippocampus 3359


title: Fischer Perinatal 250ppm Lead-Exposed Female Hippocampus 3376

description: Gene expression in female Fischer rat hippocampus following 250ppm lead exposure during perinatal development


title: Fischer Perinatal 250ppm Lead-Exposed Female Hippocampus 3375


title: Fischer Perinatal 250ppm Lead-Exposed Female Hippocampus 3374


title: Fischer Postnatal 250ppm Lead-Exposed Female Hippocampus 3198


title: Fischer Control Female Hippocampus 3228

description: Gene expression in female Fischer rat hippocampus


title: Fischer Perinatal 250ppm Lead-Exposed Female Hippocampus 3373


title: Fischer Perinatal 250ppm Lead-Exposed Male Hippocampus 3371

description: Gene expression in male Fischer rat hippocampus following 250ppm lead exposure during perinatal development


title: Fischer Perinatal 250ppm Lead-Exposed Male Hippocampus 3369


title: Fischer Control Female Hippocampus 3226


title: Fischer Control Female Hippocampus 3225


title: Fischer Control Female Hippocampus 3227


title: Fischer Control Male Hippocampus 3222

description: Gene expression in male Fischer rat hippocampus


title: Fischer Control Male Hippocampus 3221


title: Fischer Perinatal 250ppm Lead-Exposed Male Hippocampus 3370


title: Fischer Control Male Hippocampus 3219


title: Fischer Perinatal 250ppm Lead-Exposed Male Hippocampus 3368


title: Day 3 post MRSA wild type infection and linezolid treated sample 2

city: Chicago

first: Jiwang

last: Chen

state: IL

address: 840 S Wood Street

institute: University of Illinois at Chicago

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Quantile normalized using Bioconductor lumi package

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: 3 d

value: lung

value: male

tag: infection

value: MRSA LAC

value: linezolid


title: Day 3 post MRSA wild type infection and linezolid treated sample 1


title: Day 3 post MRSA wild type infection and linezolid treated sample 4


title: Fischer Control Male Hippocampus 3220


title: Day 3 post PBS mock sample 2

description: Day 3 post PBS mock

source_name: Day 3 post PBS mock

value: mock


title: Day 1 post MRSA wild type infection and linezolid treated sample 3

value: 1 d


title: Day 3 post PBS mock and linezolid treated sample 2


title: Day 1 post MRSA wild type infection and linezolid treated sample 1


title: Day 1 post MRSA wild type infection and linezolid treated sample 4


title: Day 3 post PBS mock sample 4

description: Day 3 post PBS mock


title: Day 3 post PBS mock and linezolid treated sample 4


title: Day 1 post PBS mock and linezolid treated sample 4


title: Day 3 post PBS mock sample 1

description: Day 3 post PBS mock


title: Day 3 post PBS mock and linezolid treated sample 3


title: Day 1 post PBS mock and linezolid treated sample 3


title: Day 3 post PBS mock sample 3

description: Day 3 post PBS mock


title: Day 3 post PBS mock and linezolid treated sample 1


title: Day 3 post MRSA wild type infection and linezolid treated sample 3


title: Normal Pituitary cDNA SAGE Library

type: SAGE

anchor: NlaIII

city: Ribeirao Preto

first: Leandro

middle: Machado

last: Colli

state: SP

address: Av Bandeirantes 3900

department: Department of Internal Medicine

country: Brazil

institute: School of Medicine of Ribeirao Preto

data_processing: Raw SAGE tags

source_name: Normal Pituitary

extract_protocol: TRIzol® Reagent

value: pituitary

tag: source

value: pool from 3 normal individuals who died from accidental death


title: Non Secreting Pituitary Tumor cDNA SAGE Library

source_name: Non Secreting Pituitary Tumor

tag: tissue

value: pool from three non secreting pituitary tumor patients


title: Day 1 post MRSA wild type infection and linezolid treated sample 2


title: Day 1 post PBS mock and linezolid treated sample 1


title: Secreting-GH Pituitary Tumor cDNA SAGE Library

source_name: Secreting-GH Pituitary Tumors

value: pool from five secreting-GH pituitary tumor patients


title: Day 1 post PBS mock and linezolid treated sample 2


title: Secreting-ACTH Pituitary Tumors cDNA SAGE Library

source_name: Secreting-ACTH Pituitary Tumors

value: pool from two secreting-ACTH pituitary tumor patients


title: Day 1 post PBS mock sample 3

description: Day 1 post PBS mock

source_name: Day 1 post PBS mock


title: Day 1 post PBS mock sample 4

description: Day 1 post PBS mock


title: PBMC-1_rep2

city: Cambridge

first: Yegor

last: Smurnyy

address: 250 Massachusetts Ave

institute: Novartis Institutes for Biomedical Research

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: CEL files were loaded into GeneSpring v 11.5 and the data were analyzed using the guided workflow. Reported values are log2 GC-RMA values

source_name: Peripheral blood mononuclear cells sample 1, biological replicate 2

growth_protocol: KBM7 cells were grown in IMDM medium according to the standard BL2 tissue culture practices

extract_protocol: Total RNA was isolated from 5 million of cultured cells using the Qiagen kit

treatment_protocol: Single cell clones were established by FACS sorting into 96 well plates and subsequent outgrowth for 2 weeks. Ploidy of clones was cofirmed by FACS

value: peripheral blood mononuclear cells (PBMC)

tag: ploidy

value: Diploid


title: Day 1 post PBS mock sample 2

description: Day 1 post PBS mock


title: KBM7-diploid-9_rep1

source_name: Diploid clone of KBM7 cell line, clone number 9, biological replicate 1

value: myeloid leukemia


title: KBM7-diploid-9_rep2

source_name: Diploid clone of KBM7 cell line, clone number 9, biological replicate 2


title: Day 1 post PBS mock sample 1

description: Day 1 post PBS mock


title: KBM7-diploid-7_rep2

source_name: Diploid clone of KBM7 cell line, clone number 7, biological replicate 2


title: KBM7-diploid-8_rep2

source_name: Diploid clone of KBM7 cell line, clone number 8, biological replicate 2


title: KBM7-diploid-10_rep1

source_name: Diploid clone of KBM7 cell line, clone number 10, biological replicate 1


title: KBM7-diploid-7_rep1

source_name: Diploid clone of KBM7 cell line, clone number 7, biological replicate 1


title: KBM7-diploid-10_rep2

source_name: Diploid clone of KBM7 cell line, clone number 10, biological replicate 2


title: PBMC-1_rep1

source_name: Peripheral blood mononuclear cells sample 1, biological replicate 1


title: PBMC-2_rep2

source_name: Peripheral blood mononuclear cells sample 2, biological replicate 2


title: KBM7-diploid-8_rep1

source_name: Diploid clone of KBM7 cell line, clone number 8, biological replicate 1


title: Winner, rep 1

city: Lisboa

first: José Miguel

last: Simões

address: Rua Jardim do Tabaco 34

department: Eco-Ethology Research Unit

country: Portugal

institute: ISPA - Instituto Universitário

hyb_protocol: 15 µg of fragmented aRNA was used in a 250-µl hybridization cocktail containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0004; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G. Scanned arrays were analyzed first with Affymetrix Expression Console software to obtain Absent/Present calls and to assure that all quality parameters were in the recommended range.

data_processing: Subsequent analysis was carried out with Partek Genomics Suite 6.6. A contrast analysis between the reference group (Isolation) and the target groups (winner, loser, and mirror) were performed using a two-way ANOVA for clustering the groups. For all the gene lists, genes were considered differentially expressed under a false discovery rate of 10% at a minimal fold change of 1.1.

organism: Danio rerio

source_name: winners of a real opponent fight_brain

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Zebrafish Genome Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: All subjects used in this experiment were wild-type (AB) zebrafish (Danio rerio) acquired from Zebrafish International Resource Center (ZIRC). Prior to the experiment, animals were quarantined in 40L tanks (50x30x35cm) in a balanced sex ratio (1:1) for a period of two weeks.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: In our study we used a modified version of an already established and reliable behavioural paradigm (see Oliveira et al., 2011) to study the influence of an acute agonistic interaction on the neurogenomic state of the adult zebrafish brain. In the present study, fish were isolated five days prior to the interaction. To control for the outcome perception experienced by fighting dyads, two other groups were used, an isolation group and a mirror directed aggression group. Mirror image stimulation has been known to elicit aggressive responses in fish, which do not recognize their own image and behave as in the presence of an intruder.

value: AB

tag: genotype/variation

value: wild type

tag: phenotype regarding social experience

value: winners of a real opponent fight (W)

value: whole brain


title: Winner, rep 2


title: Winner, rep 3


title: Mirror, rep 3

source_name: mirror fighters_brain

value: mirror fighters (M)


title: KBM7-diploid-6_rep2

source_name: Diploid clone of KBM7 cell line, clone number 6, biological replicate 2


title: KBM7-diploid-5_rep2

source_name: Diploid clone of KBM7 cell line, clone number 5, biological replicate 2


title: KBM7-diploid-3_rep1

source_name: Diploid clone of KBM7 cell line, clone number 3, biological replicate 1


title: Mirror, rep 2


title: KBM7-diploid-4_rep2

source_name: Diploid clone of KBM7 cell line, clone number 4, biological replicate 2


title: KBM7-diploid-6_rep1

source_name: Diploid clone of KBM7 cell line, clone number 6, biological replicate 1


title: KBM7-diploid-3_rep2

source_name: Diploid clone of KBM7 cell line, clone number 3, biological replicate 2


title: KBM7-diploid-5_rep1

source_name: Diploid clone of KBM7 cell line, clone number 5, biological replicate 1


title: KBM7-diploid-4_rep1

source_name: Diploid clone of KBM7 cell line, clone number 4, biological replicate 1


title: KBM7-diploid-2_rep1

source_name: Diploid clone of KBM7 cell line, clone number 2, biological replicate 1


title: KBM7-diploid-2_rep2

source_name: Diploid clone of KBM7 cell line, clone number 2, biological replicate 2


title: KBM7-haploid-7_rep1

source_name: Haploid clone of KBM7 cell line, clone number 7, biological replicate 1

value: Haploid


title: KBM7-diploid-1_rep2

source_name: Diploid clone of KBM7 cell line, clone number 1, biological replicate 2


title: Mirror, rep 1


title: Isolation, rep 2

source_name: socially isolated fish_brain

value: socially isolated fish (I)


title: Loser, rep 2

source_name: losers of a real opponent fight_brain

value: losers of a real opponent fight  (L)


title: KBM7-haploid-6_rep1

source_name: Haploid clone of KBM7 cell line, clone number 6, biological replicate 1


title: KBM7-haploid-6_rep2

source_name: Haploid clone of KBM7 cell line, clone number 6, biological replicate 2


title: Isolation, rep 3


title: KBM7-haploid-4_rep2

source_name: Haploid clone of KBM7 cell line, clone number 4, biological replicate 2


title: Loser, rep 1


title: KBM7-diploid-1_rep1

source_name: Diploid clone of KBM7 cell line, clone number 1, biological replicate 1


title: KBM7-haploid-5_rep2

source_name: Haploid clone of KBM7 cell line, clone number 5, biological replicate 2


title: Loser, rep 3


title: KBM7-haploid-5_rep1

source_name: Haploid clone of KBM7 cell line, clone number 5, biological replicate 1


title: KBM7-haploid-7_rep2

source_name: Haploid clone of KBM7 cell line, clone number 7, biological replicate 2


title: Isolation, rep 1


title: KBM7-haploid-4_rep1

source_name: Haploid clone of KBM7 cell line, clone number 4, biological replicate 1


title: KBM7-haploid-1_rep2

source_name: Haploid clone of KBM7 cell line, clone number 1, biological replicate 2


title: KBM7-haploid-3_rep1

source_name: Haploid clone of KBM7 cell line, clone number 3, biological replicate 1


title: KBM7-haploid-2_rep2

source_name: Haploid clone of KBM7 cell line, clone number 2, biological replicate 2


title: KBM7-haploid-2_rep1

source_name: Haploid clone of KBM7 cell line, clone number 2, biological replicate 1


title: KBM7-haploid-1_rep1

source_name: Haploid clone of KBM7 cell line, clone number 1, biological replicate 1


title: KBM7-haploid-3_rep2

source_name: Haploid clone of KBM7 cell line, clone number 3, biological replicate 2


title: AbP subject 35

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using Robust Spline Normalization (RSN) from lumi package

source_name: Peripheral Blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TargetAmp-Nano labeling kit as per the manufacturer’s instructions

extract_protocol: Peripheral blood (2.5 ml) was immediately preserved in the PaxGene RNA tubes. After 2 hours at room temperature, the tubes were frozen at -80°C freezers and total RNA was extracted within a few weeks using a Qiagen kit specially developed for the PaxGene RNA tubes. RNA quality and quantity was determined using NanoDrop ND-1000.  Extracted RNA was stored in -80°C freezers until use.

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: progressed to type 1 diabetes (t1d) by cut-off date

value: no

tag: date of first positive abp

tag: total number of autoantibodies positive

tag: time between abp first diagnosis and either diagnosis for progressors or cut-off for non-progressors (years)

tag: cut-off time


title: JD1203.Lu

city: Iowa City

first: Qin

last: Huang

address: 5-509 Bowen Science Bldg

department: Molecular  Physiology and Biophysics

institute: University of Iowa

description: A TEM4-18 cell line that was isolated from lung after intravenous injection in mouse. These cells are derived from ATCC PC-3 cells and termed JD1203.Lu. This cell line expresses luciferase.

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

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.    MAS 5    MAS 5    MAS 5

source_name: JD549.Ki cell line

label_protocol: According to Affymetrix protocol

growth_protocol: DMEM/F12 with 10% FBS

extract_protocol: We used TRIzol reagent and RNeasy cleanup kit. We followed both protocols according to manufacturer's instructions. RNA quality was assessed using the Agilent Model 2100 Bioanalyzer (Agilent Technologies). Five micrograms of total RNA was processed for use on the microarray.

tag: cell line


title: GS694.LAd

description: A JD549.Ki cell line that was isolated from left adrenal after intravenous injection in mouse. These cells are derived from ATCC PC-3 cells and termed JD549.Ki. This cell line expresses luciferase.

source_name: GS694.LAd cell line


title: GS683.LALN

description: A TEM4-18 cell line that was isolated from left axillary lymph node after intravenous injection in mouse. These cells are derived from ATCC PC-3 cells and termed GS683.LALN. This cell line expresses luciferase.

source_name: GS683.LALN cell line


title: AbP subject 36

tag: cell type


title: AbP subject 27

value: yes

tag: t1d diagnosis date


title: AbP subject 31


title: GS672.Ug

description: A PC-3 cell line that was isolated from urogenital after intravenous injection in mouse. These cells are derived from ATCC PC-3 cells and termed GS672.Ug. This cell line expresses luciferase.

source_name: GS672.Ug cell line


title: AbP subject 33


title: AbP subject 23


title: AbP subject 30


title: AbP subject 34


title: TEM4-18, rep 2

description: A PC-3 cell line that was isolated after transendothelial migration across human microvascular endothelial cells from the lung. These cells are derived from ATCC PC-3 cells and termed TEM4-18. This cell line expresses luciferase.

source_name: TEM4-18 cell line, replicate 2


title: siliques-21dap-biological-rep1

city: Minneapolis

first: Kevin

middle: A

last: Silverstein

state: MN

address: 599 Walter Library, 117 Pleasant St SE

department: Minnesota Supercomuting Institute

institute: Universtiy of Minnesota

description: Gene expression data from 21 dap siliques.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on to the AtMtDEFL custom Array. GeneChips were washed and stained using the MAUI 12-bay hybridization system.

scan_protocol: GeneChips were scanned using the MAUI 12-bay hybridization system.

data_processing: Microarray normalizations and initial analyses were performed in R using custom scripts that made use of Bioconductor routines. To implement the Stable-genes Based Quantile (SBQ) normalization (Sato et al., 2007), we first combined expression data from all 11 probes within a probe set into a single expression measure using the Bioconductor expression command, using RMA-style background correction and median polish probe summarization.  These summarized values were output from R and used as input to the SBQ perl script (Sato et al., 2007).For statistical analysis, SBQ normalized signal intensity values were Log2 transformed and statistical analysis was based on a t-test or ANOVA (P<0.05) with Benjamini and Hochberg false discovery rate multiple testing correction (Benjamini and Hochberg, 1995), and the corrected p values were designated as q values.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana dde2-1 mutant siliques were harvested 21 days after pollination.

label_protocol: Biotinylated cRNA was prepared using the two-cycle target Affymetrix labeling protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001.)

growth_protocol: Plant were grown in a growth chamber (Conviron) at 21 degree temperature with a light cycle of 16h light and 8h darkness.

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

treatment_protocol: Pollinations were conducted manually between 9:00-11:00am GMT. Siliques were harvested at 1, 4, 6, 12 and 21 days after pollination, frozen in liquid nitrogen and stored at -80 degrees until processing.

tag: genotype

tag: treatment

value: pollinated

tag: treatment-time

value: 21 days after pollination

value: siliques


title: siliques-21dap-biological-rep3


title: AbP subject 32


title: AbP subject 21


title: AbP subject 28


title: PBMC-2_rep1

source_name: Peripheral blood mononuclear cells sample 2, biological replicate 1

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

value: peripheral blood mononuclear cells (PBMC)


title: siliques-12dap-biological-rep3

description: Gene expression data from 12 dap siliques.

source_name: Arabidopsis thaliana dde2-1 mutant siliques were harvested 12 days after pollination.

value: 12 days after pollination


title: GS689.Li

description: A JD549.Ki cell line that was isolated from liver after intravenous injection in mouse. These cells are derived from ATCC PC-3 cells and termed . This cell line expresses luciferase.

source_name: GS689.Li cell line


title: AbP subject 24


title: AbP subject 25


title: AbP subject 26


title: siliques-21dap-biological-rep2


title: TEM4-18, rep 1

source_name: TEM4-18 cell line, replicate 1


title: AbP subject 22


title: AbP subject 19


title: siliques-12dap-biological-rep2


title: siliques-12dap-biological-rep1


title: AbP subject 29


title: siliques-6dap-biological-rep3

description: Gene expression data from 6 dap siliques.

source_name: Arabidopsis thaliana dde2-1 mutant siliques were harvested 6 days after pollination.

value: 6 days after pollination


title: siliques-6dap-biological-rep2


title: siliques-6dap-biological-rep1


title: siliques-1dap-biological-rep3

description: Gene expression data from 1 dap siliques.

source_name: Arabidopsis thaliana dde2-1 mutant siliques were harvested 1 day after pollination.

value: 1 day after pollination


title: siliques-3dap-biological-rep2

description: Gene expression data from 3 dap siliques.

source_name: Arabidopsis thaliana dde2-1 mutant siliques were harvested 3 days after pollination.

value: 3 days after pollination


title: siliques-3dap-biological-rep1


title: siliques-3dap-biological-rep3


title: AbP subject 20


title: AbP subject 16


title: siliques-1dap-biological-rep1


title: AbP subject 18


title: siliques-1dap-biological-rep2


title: AbP subject 17


title: AbP subject 13


title: AbP subject 14


title: pistils-0dap-biological-rep3

description: Gene expression data from 0 dap pistils used as control for pollinated siliques at various stages of development.

source_name: Arabidopsis thaliana dde2-1 mutant pistils were harvested to serve as timepoint 0 dap.

value: 0 days after pollination

value: pistils


title: AbP subject 15


title: pistils-0dap-biological-rep2


title: pistils-0dap-biological-rep1


title: AbP subject 11


title: AbP subject 10


title: AbP subject 12


title: AbP subject 6


title: AbP subject 9


title: AbP subject 5


title: AbP subject 7


title: AbP subject 8


title: AbP subject 3


title: AbP subject 4


title: AbP subject 2


title: AbP subject 1


title: line J2731-7 days-control conditions, biological rep2

city: Adelaide

first: aurelie

last: evrard

address: Hartley Grove, Urrbrae

country: Australia

institute: ACPFG

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on ATH1 GeneChip. GeneChips were washed with Gene Chip Fluidics Station 450.

scan_protocol: Chips were scanned with GeneChip Scanner 3000 (Affymetrix, USA).

data_processing: Background correction and Robust Multi-array Average (RMA) normalization were performed within the “R” program using “affy” and limma packages.

source_name: pericycle cells, protoplasted, FACS sorted

label_protocol: cDNA was labeled and sheared using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN technologies, USA).

growth_protocol: Sterilised Arabidopsis seeds germinated and grown for 5 or 7 days in 1/4X MS basal salt mixture, 1 X Gamborg’s B5 vitamin solution, 0.5% sucrose, 0.05% MES, pH 5.7 (with 10 M KOH).

extract_protocol: Roots were protoplasted for 30min in (400 mM mannitol, 20 mM MES hydrate, 20 mM KCl, 1.25% Cellulase R10, 0.3% Macerozyme R10. Adjust pH to 5.7 with 1 M Tris pH 8. Heat 10 min in 60 °C water bath, cool to room temperature while stirring. Add 10 mM CaCl2 , 0.1% BSA and 1.79 µl of β-mercapoethanol), RNA was extracted using a kit (RNeasy Micro kit, Qiagen).

treatment_protocol: Salt treatment day 6: Same composition as growth solution supplemented with 25 mM NaCl and 0.22 mM CaCl2 (see Note 2), pH 5.7 (with 10 M KOH); Salt treatment day 7: Same composition as growth solution supplemented with 50 mM NaCl and 0.375 mM CaCl2, pH 5.7 (with 10 M KOH).

value: pericycle cells

tag: growth conditions

value: 7 days control condition

tag: line


title: line J2731-5 days control conditions+ 2 days salt conditions, biological rep3

value: 5 days control condition + 2 days salt condition


title: Replicative/Young

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Young

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: TIG-3 cells were cultured in DME supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using TRIzol according to the manufacturer's instructions.

value: Human lung embryonic fibroblast

tag: passage

value: early passage

source_name: Replicative

value: late passage


title: line J2731-5 days control conditions+ 2 days salt conditions, biological rep2


title: Wild-type

first: Jay

last: Johnson

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

scan_protocol: GeneChips were scanned using an Axon GenePix array scanner.

data_processing: Raw intensity values were background-corrected and RMA-transformed (Robust Multi-array Average; RMAExpress 1.0.4) to produce natural scale expression sets.

label_protocol: Biotinylated cRNA were prepared by in vitro transcription, according to standard protocols and using 5 ug total RNA.

growth_protocol: Cells were struck onto YPAD solid media from frozen stocks or dissection plates, and allowed to grow at 30C for 48 hrs before colonies were inoculated into liquid synthetic complete (SC) medium. After an additional 48 hrs of growth, aliquots were transferred into fresh SC medium at a concentration of ~2 x 10^5 cells/ml and grown at 30C. Samples were harvested for RNA extraction after three days of growth.

extract_protocol: Following centrifugation, cells were mechanically disrupted using glass beads in combination with a Mini-BeadBeater 16 cell disruptor (Biospec; Bartlesvile, OK), total RNA was purified using the RNeasy Mini kit (Qiagen; Valencia, CA, USA).

value: Wild-type

tag: age

value: Day 3


title: line J2731-7 days-control conditions, biological rep1


title: line J2731-5 days control conditions+ 2 days salt conditions, biological rep1


title: rtg3Δ met15Δ

source_name: rtg3Δ met15Δ_3days

tag: genotype/variation

value: rtg3Δ met15Δ


title: line J1551-5 days control conditions+ 2 days salt conditions, biological rep3

source_name: cortex cells, protoplasted, FACS sorted

value: cortex cells


title: met15Δ


title: line J1551-5 days control conditions+ 2 days salt conditions, biological rep2


title: 981E5_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin

first: Ren

last: Shimamoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Dept. of Reprogramming Science

institute: Center for iPS Cell Research and Application (CiRA)

description: SAMPLE 12

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: Data were analyzed with GeneSpring GX 11. The parameters for normalization are as follows: Data transformation: Normalize to 75th percentile

label_protocol: Agilent standard protocol

growth_protocol: iPS cells were cultured in DMEM supplemented with 20% FBS, 0.1 mM non-essential amino acids, 2 mM L-glutamine, 50 U/ml penicillin-streptomycin, 0.11 mM 2-mercaptoethanol, LIF and 2 μg/mL puromycin on gelatin coated dishes.

extract_protocol: Total RNA was isolated with Trizol

value: iPS cell

value: Aid disrupted, Nanog-GFP

tag: strain

tag: gender

value: male


title: 981E4_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 11


title: 979B3_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 8

value: Nanog-GFP


title: 979F3_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 6


title: 979B4_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 9


title: 981E1_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 10


title: line J1551-7 days-control conditions, biological rep1


title: line J1551-5 days control conditions+ 2 days salt conditions, biological rep1


title: 979B1_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 7


title: 979F1_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 4


title: line J1551-7 days-control conditions, biological rep3


title: line J1551-7 days-control conditions, biological rep2


title: 979F2_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 5


title: OHT(+)/OHT(-)

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

source_name: OHT(-)

growth_protocol: TIG-3 ER-p16 cells were cultured in DME supplemented with 10% fetal bovine serum.

treatment_protocol: TIG-3 ER-p16 cells were cultured for 7 days  with or without 4-hydroxytamoxifen (4-OHT).

value: primary normal human diploid fibroblasts expressing a 4-hydroxytamoxifen(4-OHT) regulatable form of human p16

value: TIG-3 ER-p16

value: OHT(-)

source_name: OHT(+)

value: OHT(+)


title: SL3 mutant Cell_rep2_Cy5, Control H37RV_rep1_Cy3

city: New Delhi

first: Sachin

middle: Kumar

last: Samuchiwal

address: Aruna Asaf Ali Marg,

department: Recombinant Gene Products Group

country: India

institute: International Centre for Genetic Engineering and Biotechnology (ICGEB)

description: Biological replicate 2 of 2 for Control H37Rv H37Rv cells harvested after 10 days of in vitro culture. Biological replicate 2 of 2 for SL3 H37RvControl H37Rv cells harvested after 10 days of in vitro culture.

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040). To evaluate the effect of formamide on the specificity of annealing of the GC-rich targets, the purified cRNA (600ng) was fragmented with fragmentation blocking mix in the presence or absence of Formamide (7%) by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into the hybridization chamber, samples were placed in the hybridization oven ( G2545A-Agilent) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed accordingly as provided by Agilent Technologies.

scan_protocol: The array was scanned on an Agilent  G2505C scanner by deafault otption. The Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. All data analysis has been done on Genespring GX 12.6 software using single color array technology for AMAID:033693. The all red and green single called seprately in Genespring tool and grouped according to experiment condtion (RV & SL).

organism: Mycobacterium tuberculosis

source_name: H37Rv M.tb Cell

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

growth_protocol: H37Rv M.tb cells were cultured in vitro cultures in 7H9 media supplemented with 10% ADC (albumin, dextrose and catalase) for 10 days at temperature 37C and 180 rpm shaking

extract_protocol: Total RNA was extracted using phenol extraction method and M.tb cells were lysed using acid washed glass beads and heating at 65C with intermittent vigorous vortexing

treatment_protocol: Electro-competent cells were prepared with wild type H37Rv M.tb cells and electroporated with 2ug of constitutively expressing SL3pVV16 plasmid DNA containing kanamycin resistance. clones were confirmed by PCR and RT-PCR. Then Mutant H37Rv/SL3 cells were cultured in vitro cultures in 7H9 media supplemented with 10% ADC (albumin, dextrose and catalase) for 10 days at temperature 37C and 180 rpm shaking with 25ug/ml kanamycin

value: H37Rv virulent Lab strain

tag: culture

value: In vitro growing culture day 10

source_name: H37Rv M.tb SL3 expressing Mutant

value: 7H9 medium in vitro culture pellet at day 10


title: 967B6_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 3


title: SL3 mutant Cell_rep1_Cy5, Control H37RV_rep1_Cy3

description: Biological replicate 1 of 2 for Control H37Rv cells harvested after 10 days of in vitro culture. Biological replicate 1 of 2 for SL3 H37RvControl H37Rv cells harvested after 10 days of in vitro culture.


title: DP1-KD/Control-KD

source_name: Control-KD

treatment_protocol: TIG-3 cells were subjected to infection with retrovirus encoding DP1-shRNA or control-shRNA.

value: Human lung embryonic fibroblast

tag: infection

value: control-shRNA


title: 967B2_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 1


title: PBL-SMG-vs-PBL-CK

city: Harbin

first: Lijun

last: Wei

address: No 92 Western Dazhi street

country: China

institute: Harbin Institute of Technology

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

scan_protocol: Images were quantified using LuxScan 3.0 software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. LuxScan 3.0 software and CBC Analyzer were used.

source_name: PBL under simulated microgravity for 72 hours

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

growth_protocol: The control PBL cells are cultured under 1g condition. 2.0E6 cells of each sample are mixed to establish a PBL cell pool after harvested.

treatment_protocol: The PBL cells are harvested after they are kept under simulated microgravity for 72 hours. 2.0E6 cells of each sample are mixed to establish a PBL cell pool.

tag: tissue

value: blood

source_name: PBL untreated control


first: Gen

last: Kondoh

state: Kyoto

address: 53 Syogoin-Kawahara-cho, Sakyo-ku

department: Institute for Frontier Medical Sciences

institute: Kyoto University

description: RNA source: 3. pool of 10 females in estrous mated with normal male.

scan_protocol: We used Agilent DNA Microarray Scanner (G2505B) using one color scan setting.

data_processing: We used Agilent Feature Extraction Ver.9.5.3 for data analysis.  Background was subtracted and Processed Signal intensities were spatially detrended. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse utero-tubular junction (UTJ)

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM Oligo-dT primer at 70°C for 10 min, reversed transcribed at 42°C for 1 h in the presence of MMTV-RT, and then produced cRNA with T7 RNA polymerase with 100 µM NTP and 25 µM Cy3-labeled CTP.

treatment_protocol: Total RNA samples were prepared from uterotubular junction tissues of ten CD-1 females with three different statuses: 1. estrous without mating.2. estrous mated with vasectomized males. 3. estrous mated with normal males.

value: adult

value: females

tag: mating

value: yes with normal male


title: 967B4_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin

description: SAMPLE 2

value: iPS cell


description: RNA source: 2. pool of 10  females in estrous mated with vasectomized male.

value: yes with vasectomized male


title: SGE1 Overexpression C

status: Public on Apr 09 2014

city: Peoria

first: Daren

middle: W.

last: Brown

address: 1815 N. University St.

department: Bacterial Foodborn Pathogens and Mycology Research

institute: USDA-ARS

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
GMT272 30C

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

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, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Fusarium verticillioides

source_name: mycelia harvested 30 minutes after addition of inducer (xylose) after 18 hrs of growth in a liquid medium

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: RNA was prepared from cultures grown in SYP medium (100 mM sorbitol, 0.25% peptone and 0.075% yeast extract) at 28°C and 200 rpm.

extract_protocol: Mycelia were harvested 30 minutes after addition of D-xylose by vacuum filtration and flash frozen in liquid nitrogen.  Total RNA was extracted from mycelia using the RNeasy Plant Mini kit (Qiagen Inc., Valencia, CA).

treatment_protocol: Xylose was added 18 hrs after culture initiation.

value: SGE1 overexpression

value: mycelia


title: sge1 mutant C

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
SGE1 30C

value: sge1 mutant


title: sge1 mutant B

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
SGE1 30B


title: Wild-type B

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
M3125 30B

value: wild-type


title: sge1 mutant A

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
SGE1 30A


title: TIG3-Ras/TIG3-Vector

treatment_protocol: TIG-3 cells were subjected to infection with retrovirus encoding RasV12 or empty vector.

tag: cell line

tag: transduction

value: empty vector


title: Wild-type C

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
M3125 30C


title: SA3_12

city: Frankfurt

first: Peter

last: Mombaerts

address: Max-von-Laue-Str. 3

country: Germany

institute: Max Planck Research Unit for Neurogenetics

description: SAMPLE 24

hyb_protocol: Total RNA 1µg per sample was hybridized with CodeSet Chanel at 65°C for 18 hours.

scan_protocol: Hybridized RNA transcripts were imaged at 1155 fields of view per sample and processed using the nCounter Digital Analyzer.

data_processing: Raw counts were collected in XLS files and provided as 'non_normalized.txt' (linked as a series supplementary file). The first normalization was with respect to the geometric mean of the positive control spike counts. The second normalization was with respect to the geometric mean of five reference genes; Ano2, Cnga4, Gnai2, Omp, and Trpc2. Then a Background correction was done by subtracting the mean + 2*SD (standard deviation) of the negative control counts. Count values  <1 were fixed to background level. We define a gene as informative if the median of the normalized NanoString counts in wild-type control mice is ≥100. These processing steps were applied separately to the 21d and 8w old mice as those consisted of 2 independent NanoString cartridges. Note that our definition of informative gene implies that fewer genes appear in the final normalized data (in each sample data table).

label: NanoString capture/reporter probes

extract_protocol: The vomeronasal organ was dissected out from the base of the nasal septum of a mouse and placed in RNAlater Reagent (Qiagen). The bony capsule of the vomeronasal organ was removed, and whole vomeronasal mucosa dissected out. Tissue samples were lysed in RNA Lysis Buffer using a TissueLyser LT (Qiagen). Total RNA was extracted according to protocol of RNeasy Micro kit (Qiagen). Genomic DNA digestion was performed using on-column RNase-Free DNaseI (Qiagen).

tag: background strain

value: at least seven backcrosses from 129SvEv to C57BL/J

tag: strain name

value: C57BL/6 for ΔH2MvΔ-A

value: Wild-type

value: 8 weeks

value: female

value: Whole vomeronasal mucosa


title: SA3_11

description: SAMPLE 23


title: females in estrous no mating

city: Kyoto

description: RNA source: 1. pool of 10 females control

value: no


title: SGE1 Overexpression B

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
GMT272 30B


title: Wild-type A

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
M3125 30A


title: SA3_10

description: SAMPLE 22


title: BAT, Prdm16 Knockout vs WT, Aged Mice rep4

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Aged_rep4

hyb_protocol: Labeled samples were purified using the RNeasy Kit (Qiagen) and hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array

scan_protocol: After hybridization the arrays were washed and scanned with the Agilent DNA Microarray Scanner G2565B. Median intensities of each array element were captured with Agilent Feature Extraction.

data_processing: Median feature intensities were normalized by the print tip loess method in LIMMA (Smyth GK, et al. Bioinformatics 2005). Analysis for calling differentially expressed genes were performed by SAM (Tusher VG, et al. PNAS 2001).

source_name: Wildtype BAT, 11-month-old

label_protocol: 200ng of total RNA from each knockout and wiletype BAT (n = 4 per group) were amplified and labeled with Cy3 or Cy5 using Low Input Quick Amp Labeling Kit, two-color (Agilent, #5190-2306) with a dye swap experimental design.

growth_protocol: All mice used in this study were either 6-week-old or 11-month-old.

extract_protocol: Total RNA was extracted by TRIzol (Invitrogen) followed by purification using PureLink RNA columns (Invitrogen), then assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Brown Adipose Tissue

value: WT

source_name: Prdm16 Knockout BAT, 11-month-old

value: Prdm16 KO


title: SA3_09

description: SAMPLE 21

value: ΔH2MvΔ-C (B6-N7)

value: Homozygous


title: SA3_08

description: SAMPLE 20


title: BAT, Prdm16 Knockout vs WT, Young Mice rep1

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Young_rep1

source_name: Wildtype BAT, 6-week-old

source_name: Prdm16 Knockout BAT, 6-week-old


title: SA3_06

description: SAMPLE 18

value: male


title: SA3_05

description: SAMPLE 17


title: SA3_07

description: SAMPLE 19


title: SA3_01

description: SAMPLE 13


title: SA3_03

description: SAMPLE 15


title: SA3_02

description: SAMPLE 14


title: BAT, Prdm16 Knockout vs WT, Young Mice rep4

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Young_rep4


title: BAT, Prdm16 Knockout vs WT, Aged Mice rep3

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Aged_rep3


title: BAT, Prdm16 Knockout vs WT, Young Mice rep2

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Young_rep2


title: SA3_04

description: SAMPLE 16


title: SA4_11

description: SAMPLE 11

value: 129SvEv - inbred

value: 21 days


title: BAT, Prdm16 Knockout vs WT, Aged Mice rep1

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Aged_rep1


title: SA4_10

description: SAMPLE 10


title: SGE1 Overexpression A

description:
Total RNA was extracted.  cDNA was labeled and hybridized to array following NimbleGen protocols.
GMT272 30A

value: SGE1 overexpression

value: mycelia


title: SA4_12

description: SAMPLE 12


title: BAT, Prdm16 Knockout vs WT, Aged Mice rep2

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Aged_rep2


title: SA4_08

description: SAMPLE 8


title: SA4_09

description: SAMPLE 9


title: SA4_03

description: SAMPLE 3

value: 129SvEv WT for ΔH2MvΔ-C


title: SA4_04

description: SAMPLE 4


title: BAT, Prdm16 Knockout vs WT, Young Mice rep3

description:
Comparison of total RNA from Prdm16 knockout and wildtype BAT
Prdm16KO_Young_rep3


title: SA4_06

description: SAMPLE 6


title: SA4_07

description: SAMPLE 7


title: SA4_05

description: SAMPLE 5


title: SA4_02

description: SAMPLE 2


title: SA4_01

description: SAMPLE 1


title: Liver_Female_HighEggProduction_rep4

city: Riverside

first: Jordan

last: Crago

address: Science Lab 1

institute: University California-Riverside

description: Gene expression after 28d reproduction cycle

hyb_protocol: Agilent's Gene Expression Hybridization Kit and Wash Buffer Kit (Agilent, Carlsad, CA) were used to hybridize and wash arrays per manufacturer's instructions. Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 019597 custom fathead minnow 60mer  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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned at 5 μm resolution using an Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc., Sunnyvale, CA, USA)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent, Carlsbad, CA) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. and LOWESS normalization and analysis were performed using GeneSpring v.11 (Agilent). The criterion for conducting the analysis was a 2-way ANOVA using gender (male vs. female) and reproductive success (high vs. low total reproductive success from a stream) as components of this analysis. A Benjamini-Hochberg false discovery test was performed to correct for false discovery.  Gene probes needed to have greater than a 2-fold change or less than -2-fold changGene probes needed to have greater than a 2-fold change and be statistically significantly different (p < 0.05) after multiple test correction was performed. to be included in the analysis.

organism: Pimephales promelas

source_name: Pooled Liver of 6 females set in cages for 21-d, High Reproduction Stream

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Agilent's One-Color Low Quick AmpLabelling Linear Amplification kit (Agilent, Carlsbad, CA) 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.

extract_protocol: RNA was extracted from liver samples using TriZol reagent (Invitrogen, Carlsbad, CA), following the instructions provided by the manufacturer. Samples were cleaned to remove any solvent contamination by precipitating RNA with a 1M NaCl aqueous solution, and washing the precipitate with ethanol. RNA was then dissolved in 40µL of water, and stored at -80 °C. RNA concentrations (ng/µL) were measured using a Nanodrop spectrophotometer (Thermo Fischer Scientific, Wilmington, DE). RNA degradation was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Degraded RNA samples were excluded from this study.

treatment_protocol: For the original study, cages of 6 reproductive pairs of FHM were placed in 6 streams across eastern Wisconsin during July and August of 2006-2007. Sites were selected to represent a full range of urban influence and coordinated with the US Geological.  Survey National Water-Quality Assessment Program Effects of Urbanization on Stream Ecosystems (EUSE) study. One reproductive pair was placed in each one of six breeding cages within a flow-through chamber constructed of polycarbonate plastic. A removable PVC spawning substrate was fastened to the bottom of each cage to allow for breeding. Cages were monitored daily to feed fish, remove and count eggs, and to assess fish condition. After 21 d, fish were collected and euthanized. Liver and blood plasma were collected and stored in 1.5 mL tubes at -80 °C.

value: Liver


title: Liver_Female_HighEggProduction_rep3


title: Liver_Male_HighEggProduction_rep4

source_name: Pooled Liver of 6 males set in cages for 21-d, High Reproduction Stream


title: Liver_Male_HighEggProduction_rep3


title: Liver_Female_HighEggProduction_rep2


title: A2EN cells_Mock infected_repl2

city: Durham

first: Raphael

middle: H

last: Valdivia

state: NC

address: 207 Research drive, Jones bldg 272

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridization was achieved in Affymetrix  GeneChip hybridization oven 645 according to standard Affymetrix GeneChip protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip protocol

data_processing: The data were analyzed with Partek Genomic Suite 6.6 using Affymetrix default analysis settings, quantile normalization and RMA background correction.

label: Biotin-UTP

source_name: Mock infected human A2EN cells

label_protocol: Hybridization targets were prepared with MessageAmp Premier RNA Amplification Kit from total RNA

growth_protocol: Human endocervical epithelial A2EN cells were maintained in keratinocyte-SFM medium supplemented with 10 % FBS, 0.5 ng/mL human recombinant epidermal growth factor and 50 μg/mL bovine pituitary extract.

extract_protocol: Samples were collected using QIAGEN RNeasy Plus Mini Kit as described by the manufacturer.

treatment_protocol: A2EN cells were infected with different strains of Chlamydia trachomatis at an MOI of 10 by spinning at 3000 rpm for 30 min at 10 degree and shift to 37 degree incubator for 4 hours.

tag: cell type

value: Human endocervical epithelial cells

tag: infected with

value: none (mock)

tag: time point

value: 4 hr post infection


title: Liver_Female_LowEggProduction_rep1

source_name: Pooled Liver of 6 females set in cages for 21-d, Low Reproduction Stream

value: female


title: Zs-Mac-Donor2 Control

city: Toronto

first: Muhammad

middle: Atif

last: Zahoor

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GeneChip Operating Software (GCOS) were used for processing scanning data. Normalization was performed using the RMA method.

source_name: Healthy Donor 2

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

growth_protocol: Human PBMC were obtained using a standard Ficoll (Pharmacia ) gradient for heparinized blood extracted from two healthy individuals. CD14+ cells were isolated by positive selection using anti-human CD14+ magnetic beads (Miltenyi). Primary monocyte derived macrophages (MDMs) were generated by culturing CD14+ cells in RPMI (Sigma) medium supplemented with 10% FBS, 5% human AB serum, antibiotics and GlutaMax (Gibco) in the presence of recombinant human M-CSF (PeproTech).

extract_protocol: MDMs were washed three times with ice cold 1 x PBS, and total RNA was extracted using and RNeasy Mini Kit with DNase digestion, according to the manufacturer’s instructions (QIAgen).

treatment_protocol: MDMs were infected with adenovirus Vpr or ZsGreen1 at an MOI of 100. The cells were harvested for RNA extraction at 48 h post infection.

value: Monocyte Derived Macrophages (MDMs)

value: ZsGreen1 (control)

tag: individual

value: healthy donor 2


title: Liver_Female_HighEggProduction_rep1


title: AGS cells_solvent_24h_rep1

city: Beijing

first: tiantian

last: she

address: 52 Fucheng Road

department: Biochemistry and Molecular Biology

institute: Peking University Cancer Hospital & Institute

description: RMA expression value derived from Expression Console software; transcript analysis

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

source_name: human gastric cancer AGS cells,solvent,24h

label_protocol: Total RNA were amplified, labeled and purified by using Ambion  WT Expression Kit(Cat#411973， Ambion, US) and GeneChip  WT Terminal Labeling Kit (Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

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

treatment_protocol: Cells were treated by solvent or SW for 24h before the RNA extraction

tag: Sex

tag: diagnosis

value: gastric cancer

value: AGS


title: Vpr-Mac-Donor1

source_name: Healthy Donor 1

value: HIV-1 Vpr

value: healthy donor 1


title: Twist_DMSO

city: Cambridge

first: Yu-xiong

last: Feng

address: 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: Standard Affymetrix HG-U133 Plus2 arrays were hybridized with purified RNA samples.

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

data_processing: Raw CEL files were generated by Affymetrix GCOS 1.2 software, and the present/absent calls were defined with global scaling to target value of 500. By R software, the CEL files were normalized to a median-intensity array, and model-based expression values were calculated using PM/MM difference model.

source_name: HMLE_Twist cells treated with DMSO

label_protocol: All of the subsequent experimental procedures, including labeling, hybridization and scanning, were processed according to the standard Affymetrix protocols.

growth_protocol: HMLE cells were generated and maintained in a 1:1 mixture of DMEM + 10% FBS, insulin (10 μg/ml), hydrocortisone (0.5μg/ml), EGF (10 ng/ml) and MEGM

extract_protocol: Total RNA were extracted using Qiagen RNeasy kit, and the integrity and quality of the RNA met the quality requirements for Human Genome U133 Plus 2.0 arrays (Affymetrix, Inc., Santa Clara, CA) recommended by the company.

treatment_protocol: HMLE_ctrl and HMLE_Twist cells were treated with solvent control (DMSO), 5 µM or 10 µM of Cmp302 for 6 hours

value: HMLE

value: pBabe-Twist retrovirus

tag: treatment

value: DMSO


title: Zs-Mac-Donor1 Control


title: Liver_Female_LowEggProduction_rep2

tag: age