title: ICN1 T-ALL TAM

description:
F3_TAM
Leukemic bone marrow.
Cell suspension.


title: ICN1 T-ALL 3 1.4 TAM

status: Public on Aug 09 2014

type: RNA

city: Orsay

first: Jacques

last: GHYSDAEL

address: Centre Universitaire, Bat 110

country: France

institute: Institut Curie

description:
F3.1-4_TAM
Leukemic bone marrow.
Cell suspension.

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45oC, 60 rpm on Mouse GeneChip® 430 2.0 arrays. The chips were then washed and stained in the GeneChip® Fluidics Station 450 using the FS450_0004 script.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.

data_processing: The data was normalized using RMA.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: bone marrow, leukemic cells, tamoxifen

label_protocol: Biotinylated cRNA targets were prepared from 200 ng of total RNA using the MessageAmp™ Premier RNA Amplification Kit from Ambion, according to the Instruction Manual # 4386269 Revision B, 18 September 2007.

growth_protocol: Bone collection on ice; bone crushing and bone marrow hematopoietic cells collected by flushing; leukemic cells (>50% of total BM cells) were flow cytometry sorted by virtue of expression of a GFP or similar marker.

extract_protocol: Total RNA was isolated using the RNeasy kit from QIAGEN.

treatment_protocol: Mouse ICN1-induced T-ALL were generated that include a ROSCreERT2 transgene and 2 copies of a CnB1 floxed alleles. Cohorts of secondary recipient mice were injected with these T-ALL cells, and when becoming leukemic, divided into 2 subgroups. Group 1 was treated with Tamoxifen (TAM), resulting in CnB1 gene deletion and inactivation of calcineurin. Group 2 was treated with carrier solvent (corn OIL), thus maintaining CnB1 and calcineurin activity.

tag: cell type

value: ICN1-induced T-ALL leukemic cells

tag: genotype/variation

value: ROSCreERT2 transgene and 2 copies of CnB1 floxed alleles

tag: treatment

value: tamoxifen

tag: calcineurin gene cnb1 deleted

value: yes


title: SS133

city: Bordeaux

first: céline

last: brulard

address: 229 cours de l'argonne

institute: Institut Bergonié

hyb_protocol: Gene expression analysis was carried out using Agilent Whole human 44K Genome Oligo Array (G4845A; Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s protocol.

scan_protocol: the scan was performed according to manufacturer’s recommendations with scanning resolution of 5µm

data_processing: For each series all microarrays were simultaneously normalized using the Quantile algorithm.

organism: Homo sapiens

source_name: lower leg right

label_protocol: RNA was labeled according to manufacturer’s protocol.

extract_protocol: Total RNA were extracted from frozen tumor samples using the miRNeasy® Mini Kit (Qiagen) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Frozen tissue

tag: cinsarc group

tag: fusion transcrit

tag: metastasis

value: no

tag: time

tag: age group

value: pediatric


title: ICN1 T-ALL 204 TAM

description:
204_TAM
Leukemic bone marrow.
Cell suspension.


title: ICN1 T-ALL 3 OIL

description:
F3_OIL
Leukemic bone marrow.
Cell suspension.

source_name: bone marrow, leukemic cells, oil control

value: corn oil


title: ICN1 T-ALL 3 2.3 OIL

description:
F3.2-3_OIL
Leukemic bone marrow.
Cell suspension.


title: SS036

hyb_protocol: Gene expression analysis was carried out using Agilent Whole human 44K Genome Oligo Array (G4112F; Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s protocol.

source_name: member


title: SS034

source_name: head and neck


title: ICN1 T-ALL 3 1.1 OIL

description:
F3.1-1_OIL
Leukemic bone marrow.
Cell suspension.


title: ICN1 T-ALL 206 TAM

description:
206_TAM
Leukemic bone marrow.
Cell suspension.


title: SS128

source_name: tibia

value: adult


title: SS132

source_name: ankle right


title: SS032


title: SS131

source_name: femur left


title: SS038


title: SS031


title: SS033

source_name: trunk


title: SS130


title: SS035


title: ICN1 T-ALL 206 OIL

description:
206_OIL
Leukemic bone marrow.
Cell suspension.


title: SS127

source_name: ribs left


title: SS030


title: SS029


title: ICN1 T-ALL 204 OIL

description:
204_OIL
Leukemic bone marrow.
Cell suspension.


title: SS126

source_name: shoulder


title: SS125

source_name: right dij


title: SS123

source_name: shouder


title: SS027


title: SS026


title: dPRP-null decidual-placental-embryonic tissues, biological rep2

city: Kansas City

first: Michael

middle: J

last: Soares

state: KS

address: 3901 Rainbow Blvd

department: Department of Pathology and Laboratory Medicine

country: USA

institute: University of Kansas Medical Center

hyb_protocol: RNA samples were hybridized to Affymetrix Mouse Genome 430 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix, Santa Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.

data_processing: Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages.  The RMA method from the BioConductor software was used for background correction, normalization, and summarization of the DNA microarray data.

source_name: dPRP-null_gestation day 7.5_decidual-placental-embryonic tissues

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry and quality was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies,  Santa Clara, CA).

treatment_protocol: Tissue gene expression were compared between mice possessing wild type and null mutation at the the dPRP (Prl8a2) locus.

tag: strain background

value: dPRP-null

tag: gestational stage

value: day 7.5 of pregnancy

tag: tissue

value: decidual-placental-embryonic tissues


title: dPRP-null decidual-placental-embryonic tissues, biological rep3


title: SS124

source_name: femur right


title: SS122

source_name: paravertebral lumbosarcal


title: wild-type decidual-placental-embryonic tissues, biological rep2

source_name: WT_gestation day 7.5_decidual-placental-embryonic tissues

value: wild-type


title: SS025


title: SS028


title: SS023


title: SS121

source_name: ankle


title: wild-type decidual-placental-embryonic tissues, biological rep3


title: SS024


title: SS129


title: dPRP-null decidual-placental-embryonic tissues, biological rep1


title: wild-type decidual-placental-embryonic tissues, biological rep1


title: SS119

source_name: thoracic wall


title: A26

type: genomic

city: Changhua City

first: Wei-Chung

last: Shia

address: 8F., No.235, Xuguang Rd.

department: Cancer Research Center

country: Taiwan

institute: Changhua Christian Hospital

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files and CHP files (generated by Affymetrix GTC 4.0 using the birdseed V2 algorithm). CNV analysis was generated by PARTEK Genomic Suite 6.5 using genomic segmentation algorithm (CN5) by default parameters (CNCHP files).

molecule: genomic DNA

source_name: gDNA from whole blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from whole blood using the Gentra Puregene Blood Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer ND-1000.

tag: sample id

tag: gender

value: F

tag: total cholesterol (tc)

tag: triglycerides (tg)

tag: ldl

tag: percent stenosis

tag: admin note

value: CAD-III


title: Global STAT5b KO BALBc male rep3

city: Madison

first: Christopher

last: Oberley

state: Wisconsin

address: 3809 Hillcrest Dr.

department: Oncology

institute: University of Wisconsin-Madison

description: pooled reference RNA

hyb_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature extraction versions 9.1 and 9..5 for background subtraction - localbackground and normalization Linear LOWESS, Goodspots were designated as those features with both channels r and g where controltype=0, issaturated=0,isfeatnonunifol=0,isfeatpopnol=0,iswellabovebg=1 in 80% of arrays

source_name: STAT5b KO BALBc male liver

label_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

growth_protocol: Ad lib feeding and drinking. Initiated with DEN at 12 doa. Harvest whole liver at 10wks.

extract_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

treatment_protocol: Polytron 10 seconds  and processed with an Qiagen Rneasy Mini kit

tag: strain

value: BALB/c

tag: age

value: 10 weeks

value: whole liver

tag: Sex

value: male

source_name: pooled mixed-sex whole liver

value: male and female mix


title: SS022

source_name: member

tag: cinsarc group

tag: fusion transcrit


title: Global STAT5b KO BALBc male rep2

description: pooled reference RNA


title: A32

value: 50-70% stenosis


title: SS118

source_name: foot right

tag: metastasis

value: yes

tag: time


title: SS021

tag: age group


title: SS120

source_name: right knee

value: no


title: A33

value: M

value: Chest 3 days , Aging (70.5),Hyperlipidemia


title: SS117

source_name: lung

value: adult


title: Global STAT5b KO BALBc male rep1

description: pooled reference RNA


title: SS116

source_name: knee


title: SS115

source_name: femur


title: Control WT BALBc male rep3

description: pooled reference RNA

source_name: WT BALBc male liver


title: SS018

source_name: trunk


title: A28

value: CAD-II


title: SS019


title: SS114

source_name: kidney, left


title: SS020

value: pediatric


title: SS017


title: A22

value: CAD-I


title: A14


title: Control WT BALBc male rep1

description: pooled reference RNA


title: Control WT BALBc male rep2

description: pooled reference RNA


title: Global STAT5b KO B6 male rep3

description: pooled reference RNA

source_name: STAT5b KO B6 male liver


title: SS113

source_name: foot left


title: SS015


title: FCUB05

value: Non Detected

value: n/a (control)

tag: note

value: Control Sample


title: A21

value: F

value: First-episode


title: SS016


title: FCUB09


title: A20


title: Global STAT5b KO B6 male rep2

description: pooled reference RNA

value: 10 weeks

tag: tissue

value: whole liver


title: A05

tag: sample id


title: Global STAT5b KO B6 male rep1

description: pooled reference RNA

value: male

value: male and female mix


title: SS112

source_name: femur right

value: yes


title: FCUB08

tag: gender


title: FCUB11

tag: total cholesterol (tc)


title: SS110

source_name: pharynx


title: SS014


title: Control WTb B6 male rep3

description: pooled reference RNA

source_name: WT B6 male liver


title: SS013


title: A15

source_name: gDNA from whole blood

tag: triglycerides (tg)


title: A04

tag: ldl


title: Control WTb B6 male rep2

description: pooled reference RNA


title: A29

tag: percent stenosis


title: SS108

source_name: rigth groin (ileum)


title: SS109

value: no


title: SS107

source_name: upper leg left


title: SS010

source_name: member


title: Control WTb B6 male rep1

description: pooled reference RNA

source_name: pooled mixed-sex whole liver


title: SS011


title: A02

value: M

tag: admin note


title: SS106

source_name: stomach


title: SS111

source_name: left inguinal region


title: A01


title: SS105


title: SS012


title: AR-null Tfm B6 male rep2

description: pooled reference RNA

source_name: Tfm B6 male liver

tag: strain


title: FCUA07

value: Patient-Reported meet the critria

value: CAD-III


title: SS007

value: adult


title: SS009


title: AR-null Tfm B6 male rep1

description: pooled reference RNA

tag: age


title: SS104

source_name: left ankle


title: A46

value: CAD-II


title: FCUA06

value: CAD-I


title: GHRHR-mutant little B6 male rep3

description: pooled reference RNA

source_name: Little B6 male liver

tag: Sex


title: AR-null Tfm B6 male rep3

description: pooled reference RNA


title: SS103

tag: cinsarc group


title: A48


title: SS008

tag: fusion transcrit


title: SS006

tag: metastasis

value: pediatric


title: GHRHR-mutant little B6 male rep2

description: pooled reference RNA


title: SS102

source_name: wrist, radiocarpal joint

tag: time


title: SS005

tag: age group


title: GHRHR-mutant little B6 male rep1

description: pooled reference RNA


title: A47


title: SS004


title: SS101

source_name: femur left


title: A44

value: Non Detected


title: Control WTa B6 male rep3

description: pooled reference RNA


title: SS100


title: SS003

source_name: trunk


title: Control WTa B6 male rep1

description: pooled reference RNA


title: SEQC_RTPCR_C

status: Public on Aug 08 2014

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

data_processing: non-normalized raw Cq data. With single molecule Cq = 35

label: SYBR Green

source_name: Mix of A and B (3:1)

label_protocol: PCR assay; total volume: 5 μl; instrument: CFX384 (with automation); mastermix: SsoAdvanced SYBR; primer concentration: 250 nM each; Samples: cDNA: 25 ng (total RNA equivalents); gDNA: 2.5 ng (Roche); NTC: water + carrier (5 ng/μl yeast transfer RNA); synthetic template (pooled 60-mers in concentration range: 2E7 – 2E1 copies); PCR program: default cycling protocol for SsoAdvanced SYBR (Ta=60°C)

tag: seqc sample

value: C


title: SEQC_RTPCR_A

source_name: Universal Human Reference RNA (UHRR) from Stratagene

value: A


title: SS001


title: Microvesicles replicate 2

city: Atlanta

first: Dong

last: Liu

state: GA

address: 720 Westview Drive, SW

department: Cardiovascular Research Institute

institute: Morehouse School of Medicine

description: Test

data_processing:
The normalization and all the data analysis were performed by Life Technologies using Applied Biosystems RQ Manager 1.2 software
Matrix Normalized worksheet reports normalized signal against Mammalian U6.

source_name: Adipose Derived Stem Cells

growth_protocol: Human ASCs (Life Technologies; Carlsbad, CA) were maintained in ASC growth medium (Life Technologies).

extract_protocol: The conditioned medium was harvested for MV isolation. The small RNA extracted from the MVs was used for microRNA array.

treatment_protocol: Human ASCs were preconditioned in EDM (PromoCell; Heidelberg, Germany) for four days and then incubated in EBM supplemented with 1% MV-free FBS for two days.

tag: passage

tag: preconditioning

value: EDM


title: Control WTa B6 male rep2

description: pooled reference RNA

source_name: WT B6 male liver

value: 10 weeks

tag: tissue


title: SEQC_RTPCR_B

source_name: Human Brain Reference RNA (HBRR) from Ambion

value: B


title: SEQC_RTPCR_D

source_name: Mix of A and B (1:3)

value: D


title: SS002


title: Microvesicles replicate 1

description: Test


title: InVivoBMDM_1hr_Dead_4

city: Gifu

first: Takashi

last: MaruYama

address: 1-1 Yanagido

country: Japan

institute: Gifu University

description: Gene expression in cultured BMDM in the presence of necrotic cells

hyb_protocol: 600 ng 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 25 μl   containing 25x Agilent fragmentation buffer and 10x Agilent blocking   agent following the manufacturers instructions. On completion of the   fragmentation reaction,25 μl of 2x Agilent hybridization buffer was   added to the fragmentation mixture and hybridized to SurePrint G3 Mouse   GE 8x60K Microarray (G4852A) for 17 hours at 65°C in a rotating Agilent   hybridization oven.  After hybridization, microarrays were washed 1   minute at room temperature with GE Wash Buffer 1 (Agilent Technologies)   and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on theAgilent Technologies   DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K   array slides (Scan Area 61x21.6 mm, Scan resolution3 um, Dye channel is   set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software   10.7.3.1 (Agilent Technologies) using default parameters (protocol   GE1_107_Sep09 and Grid: 028005_D_F_20130207) to obtain background   subtracted and spatially detrended Processed Signal intensities.

source_name: BMDM, 1hr, necrotic cells stimulation, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the   One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies)   according to the manufacturer's instructions, followed by RNeasy column   purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield   were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bone marrow cells were cultured by using L929 culture medium (DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: total RNA was prepared using the RNeasy kit (QIAGEN) following the manufacturer's recommendations. total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BMDM from C57/BL6 mice cultred in the presence (Sample name: Dead-4) or absence (Sample name: Non-4) of heat shock necrotic A20 cells (1x10E8/ml) for 1hr.

value: Bone marrow derived macrohpage

tag: treatment

value: cultured in the presence of heat shock necrotic A20 cells (1x10E8/ml) for 1hr


title: A38

source_name: gDNA from whole blood

tag: sample id

tag: gender

tag: total cholesterol (tc)

tag: triglycerides (tg)


title: A35

tag: ldl

tag: percent stenosis

tag: admin note


title: A36


title: A37

value: coronany atherosclerosis of native coronary artery chromic ischemic heart disease


title: A42

value: M


title: A25


title: A23

value: F


title: A24

value: CAD-III


title: InVivoBMDM_1hr_Non_4

description: Gene expression in cultured BMDM in the absence of necrotic cells

source_name: BMDM, 1hr, Non necrotic cells, replicate 4

tag: strain

value: cultured in the absense of necrotic cells


title: GS0001679

city: Oslo

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
Illumina chip: 5808922022
Illumina position: R06C01

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

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

data_processing: Touleimat and Tost, Epigenomics 2012

label: Cy5 and Cy3

source_name: breast cancer tissue

label_protocol: Standard Illumina Protocol

extract_protocol: not provided

value: Female

tag: sample tissue

value: invasive

tag: disease state

value: breast cancer

tag: age


title: RP13

description:
Illumina chip: 5808922033
Illumina position: R04C02

source_name: normal tissue

value: mammoplastic reduction

value: normal


title: RP20

description:
Illumina chip: 5808922033
Illumina position: R06C02


title: GS0005726

description:
Illumina chip: 5808922053
Illumina position: R03C02

value: needle biopsy


title: RP16

description:
Illumina chip: 5808922033
Illumina position: R05C02


title: A18


title: GS0001687

description:
Illumina chip: 5808922053
Illumina position: R06C02


title: GS0005647

description:
Illumina chip: 5808922053
Illumina position: R04C02


title: A30

value: CAD-II


title: GS0001447

description:
Illumina chip: 5808922053
Illumina position: R05C02


title: A13


title: GS0020476

description:
Illumina chip: 5808922033
Illumina position: R01C02


title: A31


title: GS0023333

description:
Illumina chip: 5808922033
Illumina position: R03C02


title: A34


title: MEF3T3_SR_rep1

city: Frederick

first: Masahiko

last: Ajiro

state: MD

address: 1050 Boyles St Bldg 539 Rm 153

institute: National Cancer Institute

hyb_protocol: Standard methods following recommendations of the manufacturer were used to hybridize the samples to the SpliceArrays.  The arrays were washed and stained using the FS450-0001 Fluidics protocol.

scan_protocol: the Affymetrix GeneChip® Scanner 3000 7G

data_processing: The .CEL files were imported into Partek® Genomics Suite and the data was processed using the Robust Multichip Average (RMA) method which only utilizes the PM values to correct background.  Quantile normalization was performed across all arrays, and then data was Log2 transformed and median polish applied for probeset summarization. ANOVA analysis was performed to identify probes that are differentially expressed between the sample groups specified.  For ease of analysis and interpretation, the “evidenced” and “discovery” probes (for known or unknown splice events) were input separately for the analysis.

source_name: MEF3T3 tet-off cells transfected with pRevTRE/T7-SRSF3 expression vector

label_protocol: the FL-Ovation cDNA Biotin Module v2 (NuGen, Inc., part # ‘s 4200-60)

growth_protocol: Dulbecco’s modified Eagle medium (DMEM, Invitrogen, Carlsbad, CA) supplemented with 10% calf serum (FBS) (HyClone, Logan, UT), 2 mM L-glutamine, 100U/ml penicillin, and 100µg/ml streptomycin (Invitrogen).

extract_protocol: Total cell RNA was prepared from the cells using TRIzol (Invitrogen) following the manufacturer's instructions.

treatment_protocol: Plasmid transfection was conducted by two separate transfections with intervals of 48 h by transfection reagent Lipofectamine 2000.

tag: cell type

value: fibroblasts”, tet-off


title: GS0005724

description:
Illumina chip: 5808922053
Illumina position: R01C02


title: GS0023277

description:
Illumina chip: 5808922033
Illumina position: R06C01


title: MEF3T3_Vec_rep3

source_name: MEF3T3 tet-off cells transfected with pFLAG-CMV5.1 empty vector


title: A16


title: MEF3T3_Vec_rep2


title: A17


title: MEF3T3_Vec_rep1


title: GS0005640

description:
Illumina chip: 5808922053
Illumina position: R06C01


title: GS0020470

description:
Illumina chip: 5808922033
Illumina position: R02C02


title: GS0023275

description:
Illumina chip: 5808922033
Illumina position: R05C01


title: GS0023273

description:
Illumina chip: 5808922033
Illumina position: R03C01


title: MEF3T3_SR_rep3


title: GS0005715

description:
Illumina chip: 5808922032
Illumina position: R06C02


title: GS0005637

description:
Illumina chip: 5808922053
Illumina position: R05C01


title: GS0005623

description:
Illumina chip: 5808922032
Illumina position: R05C02


title: GS0005721

description:
Illumina chip: 5808922033
Illumina position: R02C01


title: GS0020475

description:
Illumina chip: 5808922033
Illumina position: R04C01


title: MEF3T3_SR_rep2


title: GS0005644

description:
Illumina chip: 5808922053
Illumina position: R02C02


title: GS0020474

description:
Illumina chip: 5808922032
Illumina position: R04C02


title: GS0005718

description:
Illumina chip: 5808922033
Illumina position: R01C01


title: GS0005615

description:
Illumina chip: 5808922053
Illumina position: R04C01


title: A19


title: GS0005613

description:
Illumina chip: 5808922053
Illumina position: R03C01


title: GS0005671

description:
Illumina chip: 5808922022
Illumina position: R03C02


title: GS0005704

description:
Illumina chip: 5808922032
Illumina position: R02C02


title: GS0005676

description:
Illumina chip: 5808922022
Illumina position: R04C02


title: GS0005756

description:
Illumina chip: 5808922032
Illumina position: R06C01

value: DCIS


title: GS0005609

description:
Illumina chip: 5808922053
Illumina position: R01C01


title: GS0005831

description:
Illumina chip: 5808922055
Illumina position: R05C02

value: mixed DCIS-invasive


title: GS0005755

description:
Illumina chip: 5808922022
Illumina position: R05C01


title: GS0005662

description:
Illumina chip: 5808922022
Illumina position: R02C02


title: GS0005780

description:
Illumina chip: 5808922071
Illumina position: R02C01


title: GS0005678

description:
Illumina chip: 5808922022
Illumina position: R05C02


title: GS0005752

description:
Illumina chip: 5808922004
Illumina position: R03C01


title: GS0005832

description:
Illumina chip: 5808922032
Illumina position: R04C01


title: GS0005841

description:
Illumina chip: 5808922071
Illumina position: R04C01


title: GS0005743

description:
Illumina chip: 5808922004
Illumina position: R01C01


title: GS0005702

description:
Illumina chip: 5808922053
Illumina position: R02C01


title: GS0005746

description:
Illumina chip: 5808922022
Illumina position: R01C01


title: GS0005838

description:
Illumina chip: 5808922071
Illumina position: R03C01


title: GS0005682

description:
Illumina chip: 5808922032
Illumina position: R01C02


title: GS0005705

description:
Illumina chip: 5808922032
Illumina position: R03C02


title: GS0005688

description:
Illumina chip: 5808922022
Illumina position: R06C02


title: GS0005834

description:
Illumina chip: 5808922022
Illumina position: R02C01


title: GS0005657

description:
Illumina chip: 5808922022
Illumina position: R01C02


title: GS0005779

description:
Illumina chip: 5808922022
Illumina position: R03C01


title: GS0005744

description:
Illumina chip: 5808922055
Illumina position: R04C02


title: GS0005836

description:
Illumina chip: 5808922032
Illumina position: R05C01


title: GS0005748

description:
Illumina chip: 5808922004
Illumina position: R02C01


title: GS0005829

description:
Illumina chip: 5808922055
Illumina position: R03C02


title: GS0005745

description:
Illumina chip: 5808922055
Illumina position: R06C02


title: GS0005830

description:
Illumina chip: 5808922071
Illumina position: R01C01


title: GS0005824

description:
Illumina chip: 5808922055
Illumina position: R06C01


title: GS0005825

description:
Illumina chip: 5808922032
Illumina position: R03C01


title: GS0005819

description:
Illumina chip: 5808922065
Illumina position: R05C02


title: GS0005821

description:
Illumina chip: 5808922065
Illumina position: R06C02


title: GS0005828

description:
Illumina chip: 5808922055
Illumina position: R02C02


title: GS0005818

description:
Illumina chip: 5808922055
Illumina position: R04C01


title: GS0005806

description:
Illumina chip: 5808922065
Illumina position: R01C01


title: GS0005820

description:
Illumina chip: 5808922055
Illumina position: R05C01


title: GS0005772

description:
Illumina chip: 5808922065
Illumina position: R03C02


title: GS0005770

description:
Illumina chip: 5808922065
Illumina position: R06C01


title: GS0005822

description:
Illumina chip: 5808922032
Illumina position: R01C01


title: GS0005771

description:
Illumina chip: 5808922065
Illumina position: R01C02


title: GS0005826

description:
Illumina chip: 5808922055
Illumina position: R01C02


title: GS0005768

description:
Illumina chip: 5808922071
Illumina position: R06C02


title: GS0005807

description:
Illumina chip: 5808922065
Illumina position: R02C01


title: GS0005823

description:
Illumina chip: 5808922032
Illumina position: R02C01


title: GS0005817

description:
Illumina chip: 5808922065
Illumina position: R04C02


title: GS0005814

description:
Illumina chip: 5808922065
Illumina position: R02C02


title: GS0005816

description:
Illumina chip: 5808922055
Illumina position: R03C01


title: GS0005810

description:
Illumina chip: 5808922065
Illumina position: R04C01


title: GS0005811

description:
Illumina chip: 5808922055
Illumina position: R02C01


title: GS0005809

description:
Illumina chip: 5808922071
Illumina position: R03C02


title: GS0005808

description:
Illumina chip: 5808922065
Illumina position: R03C01


title: GS0005766

description:
Illumina chip: 5808922071
Illumina position: R04C02


title: GS0005813

description:
Illumina chip: 5808922065
Illumina position: R05C01


title: GS0005765

description:
Illumina chip: 5808922004
Illumina position: R05C02


title: GS0005804

description:
Illumina chip: 5808922004
Illumina position: R06C02


title: GS0005767

description:
Illumina chip: 5808922071
Illumina position: R05C02


title: GS0005803

description:
Illumina chip: 5808922071
Illumina position: R02C02


title: GS0005799

description:
Illumina chip: 5808922071
Illumina position: R06C01


title: GS0005762

description:
Illumina chip: 5808922004
Illumina position: R04C02


title: GS0005764

description:
Illumina chip: 5808922071
Illumina position: R01C02


title: GS0005733

description:
Illumina chip: 5808922004
Illumina position: R01C02


title: GS0005761

description:
Illumina chip: 5808922004
Illumina position: R03C02


title: GS0005769

description:
Illumina chip: 5808922055
Illumina position: R01C01


title: RP14

description:
Illumina chip: 5815073004
Illumina position: R03C02


title: GS0005728

description:
Illumina chip: 5808922004
Illumina position: R04C01


title: RP18

description:
Illumina chip: 5815073004
Illumina position: R05C02


title: RP09

description:
Illumina chip: 5815073004
Illumina position: R05C01


title: GS0005763

description:
Illumina chip: 5808922071
Illumina position: R05C01


title: GS0005760

description:
Illumina chip: 5808922004
Illumina position: R02C02


title: RP10

description:
Illumina chip: 5815073004
Illumina position: R06C01


title: RP08

description:
Illumina chip: 5815073004
Illumina position: R04C01


title: RP01

description:
Illumina chip: 5815073005
Illumina position: R04C02


title: RP11

description:
Illumina chip: 5815073004
Illumina position: R01C02


title: RP05

description:
Illumina chip: 5815073004
Illumina position: R01C01


title: RP04

description:
Illumina chip: 5815073005
Illumina position: R06C02


title: GS0005729

description:
Illumina chip: 5808922004
Illumina position: R05C01


title: RP06

description:
Illumina chip: 5815073004
Illumina position: R02C01


title: GS0001723

description:
Illumina chip: 5815073005
Illumina position: R01C01


title: RP02

description:
Illumina chip: 5815073005
Illumina position: R05C02


title: GS0005732

description:
Illumina chip: 5808922004
Illumina position: R06C01


title: GS0001719

description:
Illumina chip: 5815073017
Illumina position: R06C02


title: GS0001717

description:
Illumina chip: 5808922073
Illumina position: R01C02


title: GS0001709

description:
Illumina chip: 5815073017
Illumina position: R05C02


title: RP07

description:
Illumina chip: 5815073004
Illumina position: R03C01


title: RP17

description:
Illumina chip: 5815073004
Illumina position: R04C02


title: GS0001703

description:
Illumina chip: 5815073017
Illumina position: R03C02


title: RP12

description:
Illumina chip: 5815073004
Illumina position: R02C02


title: GS0001697

description:
Illumina chip: 5815073017
Illumina position: R02C02


title: GS0001705

description:
Illumina chip: 5815073017
Illumina position: R04C02


title: GS0001695

description:
Illumina chip: 5815073017
Illumina position: R01C02


title: GS0001691

description:
Illumina chip: 5815073017
Illumina position: R06C01


title: GS0001675

description:
Illumina chip: 5815073017
Illumina position: R05C01


title: GS0001711

description:
Illumina chip: 5815073004
Illumina position: R06C02


title: GS0001715

description:
Illumina chip: 5808922073
Illumina position: R06C01


title: GS0001582

description:
Illumina chip: 5808922031
Illumina position: R04C02


title: GS0001532

description:
Illumina chip: 5808922031
Illumina position: R01C02


title: GS0001604

description:
Illumina chip: 5808922031
Illumina position: R06C02


title: GS0001600

description:
Illumina chip: 5808922031
Illumina position: R05C02


title: GS0001559

description:
Illumina chip: 5808922073
Illumina position: R03C01


title: GS0001606

description:
Illumina chip: 5815073017
Illumina position: R01C01


title: GS0001564

description:
Illumina chip: 5808922031
Illumina position: R03C02


title: GS0001527

description:
Illumina chip: 5808922031
Illumina position: R06C01


title: GS0001663

description:
Illumina chip: 5808922073
Illumina position: R04C01


title: GS0001634

description:
Illumina chip: 5815073017
Illumina position: R03C01


title: GS0001456

description:
Illumina chip: 5808922031
Illumina position: R05C01


title: GS0001435

description:
Illumina chip: 5808922031
Illumina position: R04C01


title: GS0001556

description:
Illumina chip: 5808922031
Illumina position: R02C02


title: GS0001379

description:
Illumina chip: 5808922031
Illumina position: R01C01


title: GS0001665

description:
Illumina chip: 5808922073
Illumina position: R05C01


title: GS0001350

description:
Illumina chip: 5815073006
Illumina position: R01C02


title: GS0001417

description:
Illumina chip: 5808922031
Illumina position: R02C01


title: GS0001364

description:
Illumina chip: 5815073006
Illumina position: R04C02


title: GS0020467

description:
Illumina chip: 5815073006
Illumina position: R05C01


title: GS0001362

description:
Illumina chip: 5815073006
Illumina position: R03C02


title: GS0001375

description:
Illumina chip: 5815073006
Illumina position: R06C02


title: GS0001620

description:
Illumina chip: 5815073017
Illumina position: R02C01


title: GS0005654

description:
Illumina chip: 5815073006
Illumina position: R04C01


title: GS0001366

description:
Illumina chip: 5815073006
Illumina position: R05C02


title: GS0001667

description:
Illumina chip: 5815073017
Illumina position: R04C01


title: GS0001355

description:
Illumina chip: 5815073006
Illumina position: R02C02


title: GS0001372

description:
Illumina chip: 5808922073
Illumina position: R02C01


title: GS0001428

description:
Illumina chip: 5808922031
Illumina position: R03C01


title: GS0005727

description:
Illumina chip: 5815073006
Illumina position: R03C01


title: GS0005645

description:
Illumina chip: 5808922087
Illumina position: R06C02


title: GS0001347

description:
Illumina chip: 5808922073
Illumina position: R01C01


title: GS0005725

description:
Illumina chip: 5808922087
Illumina position: R05C02


title: GS0005648

description:
Illumina chip: 5815073006
Illumina position: R01C01


title: GS0005642

description:
Illumina chip: 5808922087
Illumina position: R04C02


title: GS0005649

description:
Illumina chip: 5815073006
Illumina position: R02C01


title: GS0020469

description:
Illumina chip: 5815073006
Illumina position: R06C01


title: GS0005634

description:
Illumina chip: 5808922087
Illumina position: R02C02


title: GS0005632

description:
Illumina chip: 5808922087
Illumina position: R01C02


title: GS0005641

description:
Illumina chip: 5808922087
Illumina position: R03C02


title: GS0005627

description:
Illumina chip: 5808922087
Illumina position: R04C01


title: GS0005628

description:
Illumina chip: 5808922087
Illumina position: R05C01


title: GS0005629

description:
Illumina chip: 5808922087
Illumina position: R06C01


title: GS0005618

description:
Illumina chip: 5808922074
Illumina position: R04C02


title: GS0005626

description:
Illumina chip: 5808922087
Illumina position: R03C01


title: GS0005624

description:
Illumina chip: 5808922087
Illumina position: R01C01


title: GS0005619

description:
Illumina chip: 5808922074
Illumina position: R05C02


title: GS0005625

description:
Illumina chip: 5808922087
Illumina position: R02C01


title: GS0005708

description:
Illumina chip: 5808922074
Illumina position: R05C01


title: GS0005608

description:
Illumina chip: 5808922074
Illumina position: R01C01


title: GS0005607

description:
Illumina chip: 5808922073
Illumina position: R06C02


title: GS0005600

description:
Illumina chip: 5808922073
Illumina position: R04C02


title: GS0005612

description:
Illumina chip: 5808922074
Illumina position: R03C01


title: GS0005617

description:
Illumina chip: 5808922074
Illumina position: R06C01


title: GS0005710

description:
Illumina chip: 5808922074
Illumina position: R02C02


title: GS0005603

description:
Illumina chip: 5808922073
Illumina position: R05C02


title: GS0005621

description:
Illumina chip: 5808922074
Illumina position: R06C02


title: GS0005739

description:
Illumina chip: 5815073005
Illumina position: R02C02


title: GS0005614

description:
Illumina chip: 5808922074
Illumina position: R04C01


title: GS0005656

description:
Illumina chip: 5808922073
Illumina position: R03C02


title: GS0005598

description:
Illumina chip: 5808922073
Illumina position: R02C02


title: GS0005738

description:
Illumina chip: 5815073005
Illumina position: R01C02


title: GS0005711

description:
Illumina chip: 5808922074
Illumina position: R03C02


title: GS0005736

description:
Illumina chip: 5815073005
Illumina position: R05C01


title: GS0005737

description:
Illumina chip: 5815073005
Illumina position: R06C01


title: GS0005611

description:
Illumina chip: 5808922074
Illumina position: R02C01


title: GS0005730

description:
Illumina chip: 5815073005
Illumina position: R02C01


title: GS0001699

description:
Illumina chip: 5808922009
Illumina position: R05C02


title: GS0001713

description:
Illumina chip: 5808922018
Illumina position: R04C01


title: GS0005734

description:
Illumina chip: 5815073005
Illumina position: R04C01


title: GS0005731

description:
Illumina chip: 5815073005
Illumina position: R03C01


title: GS0001693

description:
Illumina chip: 5808922009
Illumina position: R04C02


title: GS0001669

description:
Illumina chip: 5808922009
Illumina position: R02C01


title: GS0001681

description:
Illumina chip: 5808922009
Illumina position: R06C01


title: GS0001701

description:
Illumina chip: 5808922009
Illumina position: R06C02


title: GS0001685

description:
Illumina chip: 5808922009
Illumina position: R02C02


title: GS0001677

description:
Illumina chip: 5808922009
Illumina position: R05C01


title: GS0001683

description:
Illumina chip: 5808922009
Illumina position: R01C02


title: GS0005753

description:
Illumina chip: 5815073005
Illumina position: R03C02


title: GS0001655

description:
Illumina chip: 5808922034
Illumina position: R05C02


title: GS0001649

description:
Illumina chip: 5808922018
Illumina position: R03C01


title: GS0001689

description:
Illumina chip: 5808922009
Illumina position: R03C02


title: GS0001643

description:
Illumina chip: 5808922034
Illumina position: R01C02


title: GS0001645

description:
Illumina chip: 5808922034
Illumina position: R02C02


title: GS0001651

description:
Illumina chip: 5808922034
Illumina position: R03C02


title: GS0001673

description:
Illumina chip: 5808922009
Illumina position: R04C01


title: GS0001641

description:
Illumina chip: 5808922034
Illumina position: R06C01


title: GS0001657

description:
Illumina chip: 5808922034
Illumina position: R06C02


title: GS0001661

description:
Illumina chip: 5808922009
Illumina position: R01C01


title: GS0001636

description:
Illumina chip: 5808922018
Illumina position: R02C01


title: GS0001671

description:
Illumina chip: 5808922009
Illumina position: R03C01


title: GS0001639

description:
Illumina chip: 5808922034
Illumina position: R05C01


title: GS0014643

description:
Illumina chip: 5808922034
Illumina position: R04C01


title: GS0001628

description:
Illumina chip: 5808922018
Illumina position: R01C01


title: GS0001630

description:
Illumina chip: 5808922034
Illumina position: R02C01


title: GS0001610

description:
Illumina chip: 5808922013
Illumina position: R02C02


title: GS0001721

description:
Illumina chip: 5808922018
Illumina position: R05C01


title: GS0001614

description:
Illumina chip: 5808922013
Illumina position: R04C02


title: GS0001622

description:
Illumina chip: 5808922034
Illumina position: R01C01


title: GS0001626

description:
Illumina chip: 5808922035
Illumina position: R06C02


title: GS0001612

description:
Illumina chip: 5808922013
Illumina position: R03C02


title: GS0001618

description:
Illumina chip: 5808922013
Illumina position: R06C02


title: GS0001632

description:
Illumina chip: 5808922034
Illumina position: R03C01


title: GS0001608

description:
Illumina chip: 5808922013
Illumina position: R01C02


title: GS0001624

description:
Illumina chip: 5808922035
Illumina position: R05C02


title: GS0001616

description:
Illumina chip: 5808922013
Illumina position: R05C02


title: GS0001579

description:
Illumina chip: 5808922035
Illumina position: R03C02


title: GS0001602

description:
Illumina chip: 5808922013
Illumina position: R06C01


title: GS0001553

description:
Illumina chip: 5808922013
Illumina position: R03C01


title: GS0001653

description:
Illumina chip: 5808922034
Illumina position: R04C02


title: GS0001598

description:
Illumina chip: 5808922013
Illumina position: R05C01


title: GS0001586

description:
Illumina chip: 5808922013
Illumina position: R04C01


title: GS0001522

description:
Illumina chip: 5806636040
Illumina position: R05C02


title: GS0001525

description:
Illumina chip: 5806636040
Illumina position: R06C02


title: GS0001505

description:
Illumina chip: 5806636040
Illumina position: R03C02


title: GS0001535

description:
Illumina chip: 5808922013
Illumina position: R01C01


title: GS0001538

description:
Illumina chip: 5808922013
Illumina position: R02C01


title: GS0001494

description:
Illumina chip: 5806636040
Illumina position: R01C02


title: GS0001594

description:
Illumina chip: 5808922035
Illumina position: R04C02


title: GS0014641

description:
Illumina chip: 5806636040
Illumina position: R06C01


title: GS0001461

description:
Illumina chip: 5808922046
Illumina position: R03C02


title: GS0001488

description:
Illumina chip: 5806636040
Illumina position: R05C01


title: GS0001482

description:
Illumina chip: 5806636040
Illumina position: R04C01


title: GS0001477

description:
Illumina chip: 5806636040
Illumina position: R02C01


title: GS0001480

description:
Illumina chip: 5806636040
Illumina position: R03C01


title: GS0001459

description:
Illumina chip: 5808922046
Illumina position: R02C02


title: GS0001469

description:
Illumina chip: 5806636040
Illumina position: R01C01


title: GS0001450

description:
Illumina chip: 5808922035
Illumina position: R02C02


title: GS0001464

description:
Illumina chip: 5808922046
Illumina position: R05C02


title: GS0001452

description:
Illumina chip: 5808922046
Illumina position: R01C02


title: GS0001431

description:
Illumina chip: 5808922046
Illumina position: R05C01


title: GS0001430

description:
Illumina chip: 5808922046
Illumina position: R04C01


title: GS0014640

description:
Illumina chip: 5808922046
Illumina position: R04C02


title: GS0001466

description:
Illumina chip: 5808922046
Illumina position: R06C02


title: GS0001516

description:
Illumina chip: 5806636040
Illumina position: R04C02


title: GS0001420

description:
Illumina chip: 5808922046
Illumina position: R03C01


title: GS0001501

description:
Illumina chip: 5806636040
Illumina position: R02C02


title: GS0001412

description:
Illumina chip: 5808922046
Illumina position: R01C01


title: GS0001403

description:
Illumina chip: 5808922048
Illumina position: R06C02


title: GS0001437

description:
Illumina chip: 5808922046
Illumina position: R06C01


title: GS0001414

description:
Illumina chip: 5808922046
Illumina position: R02C01


title: GS0001440

description:
Illumina chip: 5808922035
Illumina position: R01C02


title: GS0001387

description:
Illumina chip: 5808922035
Illumina position: R03C01


title: GS0001433

description:
Illumina chip: 5808922035
Illumina position: R06C01


title: GS0001368

description:
Illumina chip: 5808922048
Illumina position: R03C02


title: SEQC_AFX_USF_C_2_PRV

hyb_protocol: Affymetrix standard array hyb protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner M10.

data_processing:
Probe signal are processed by gcrma and rma algorithms to probe set level for GPL17930 and GPL16043 respectively and further summarized to gene level using median when multiple probe sets exist for a gene
Series supplementary files GSE56457_SEQC_USF_GEOSub_HuGene2.txt and GSE56457_SEQC_USF_GEOSub_PrimeView.txt include log2 transformed intensity

label: Biotin

label_protocol: Affymetrix standard array label protocol

tag: seqc sample

value: C


title: SEQC_AFX_USF_C_1_PRV


title: SEQC_AFX_USF_C_4_PRV


title: SEQC_AFX_USF_D_3_PRV

value: D


title: SEQC_AFX_USF_D_4_PRV


title: SEQC_AFX_USF_B_4_PRV

value: B


title: SEQC_AFX_USF_D_1_PRV


title: SEQC_AFX_USF_B_1_PRV


title: SEQC_AFX_USF_B_2_PRV


title: SEQC_AFX_USF_A_3_PRV

value: A


title: SEQC_AFX_USF_A_1_PRV


title: GS0001345

description:
Illumina chip: 5808922048
Illumina position: R01C02


title: SEQC_AFX_USF_A_4_PRV


title: SEQC_AFX_USF_A_2_PRV


title: GS0001370

description:
Illumina chip: 5808922048
Illumina position: R04C02


title: GS0020484

description:
Illumina chip: 5808922048
Illumina position: R06C01


title: SEQC_AFX_USF_D_2_PRV


title: SEQC_AFX_USF_D_4_HUG


title: GS0001377

description:
Illumina chip: 5808922048
Illumina position: R05C02


title: GS0005653

description:
Illumina chip: 5808922048
Illumina position: R04C01


title: GS0023365

description:
Illumina chip: 5808922048
Illumina position: R05C01


title: GS0001400

description:
Illumina chip: 5808922035
Illumina position: R05C01


title: GS0001360

description:
Illumina chip: 5808922048
Illumina position: R02C02


title: SEQC_AFX_USF_D_1_HUG


title: SEQC_AFX_USF_C_1_HUG


title: SEQC_AFX_USF_C_4_HUG


title: SEQC_AFX_USF_C_3_HUG


title: SEQC_AFX_USF_D_3_HUG


title: GS0005638

description:
Illumina chip: 5808922018
Illumina position: R04C02


title: SEQC_AFX_USF_B_4_HUG


title: SEQC_AFX_USF_B_3_HUG


title: SEQC_AFX_USF_B_1_HUG


title: SEQC_AFX_USF_A_3_HUG


title: SEQC_AFX_USF_D_2_HUG


title: GS0005643

description:
Illumina chip: 5808922018
Illumina position: R05C02


title: SEQC_AFX_USF_A_4_HUG


title: SEQC_AFX_USF_A_2_HUG


title: SEQC_AFX_USF_A_1_HUG


title: GS0005651

description:
Illumina chip: 5808922048
Illumina position: R02C01


title: GS0005646

description:
Illumina chip: 5808922018
Illumina position: R06C02


title: GS0005652

description:
Illumina chip: 5808922048
Illumina position: R03C01


title: SEQC_AFX_USF_B_2_HUG


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 1

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

description:
P3Nod2 DSS 72-1
DSS exposure for 72 hrs

data_processing: For each gene, ΔCt was calculated using the same threshold (0.2) for all genes and Ct>35 considered as no expression, followed by normalization to 5 housekeeping genes (Hsp90ab1, Gusb, Hprt1, Gapdh, and Actb) included in each array, followed by calculation of ΔΔCt for each gene from two arrays: ΔΔCt = ΔCt1 – ΔCt2, where ΔCt1 is the DSS-treated mice group and ΔCT2 is the untreated mice group, using the program provided by Qiagen/SA Biosciences.

source_name: Colon

label_protocol: Quantitative reverse transcription real-time PCR (qRT-PCR) was used to quantify the amounts of mRNA in the colon using inflammatory gene RT2 Profiler PCR Arrays manufactured by Qiagen/SA Biosciences. The arrays included 84 assay genes, 5 housekeeping genes, and reverse transcription efficiency and DNA contamination controls. cDNA was synthesized from 2 µg of RNA using RT2 PCR Array First Strand Kit (Qiagen/SA Biosciences) and the arrays were performed according to the manufacturer instructions using Qiagen/SA Biosciences Master Mix. Each experiment was performed on RNA pooled from 3 mice/group and repeated 3 times with new groups of mice (total of 9 mice for each time point and each strain).

extract_protocol: RNA was isolated from entire colon of untreated or DSS-treated mice using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen). In each experiment, for qRT-PCR gene expression array RNA was pooled from 3 mice per group.

value: Entire colon

value: BALB/c


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 2

description:
P3Nod2 DSS 72-2
DSS exposure for 72 hrs


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 3

description:
P3Nod2 DSS 48-3
DSS exposure for 48 hrs


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 2

description:
P3Nod2 DSS 48-2
DSS exposure for 48 hrs


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 3

description:
P3Nod2 DSS 72-3
DSS exposure for 72 hrs


title: GS0005610

description:
Illumina chip: 5808922018
Illumina position: R02C02


title: GS0005630

description:
Illumina chip: 5808922018
Illumina position: R03C02


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 3

description:
P3Nod2 DSS 96-3
DSS exposure for 96 hrs


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 3

description:
P3 DSS 72-3
DSS exposure for 72 hrs


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 1

description:
P3 DSS 96-1
DSS exposure for 96 hrs


title: Pglyrp3-/-Nod2-/- mice, untreated, expt 1

description:
P3Nod2 Untr-1
Control


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 3

description:
P3 DSS 96-3
DSS exposure for 96 hrs


title: GS0001391

description:
Illumina chip: 5808922035
Illumina position: R04C01


title: Pglyrp3-/-Nod2-/- mice, untreated, expt 2

description:
P3Nod2 Untr-2
Control


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 2

description:
P3 DSS 72-2
DSS exposure for 72 hrs


title: SEQC_AFX_USF_B_3_PRV


title: Pglyrp3-/-Nod2-/- mice, untreated, expt 3

description:
P3Nod2 Untr-3
Control


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 2

description:
P3 DSS 96-2
DSS exposure for 96 hrs


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 1

description:
P3 DSS 48-1
DSS exposure for 48 hrs


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 2

description:
P3 DSS 48-2
DSS exposure for 48 hrs


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 2

description:
P3Nod2 DSS 96-2
DSS exposure for 96 hrs


title: Pglyrp3-/- mice, untreated, expt 3

description:
P3 Untr-3
Control


title: Pglyrp3-/- mice, untreated, expt 2

description:
P3 Untr-2
Control


title: GS0005599

description:
Illumina chip: 5808922018
Illumina position: R06C01


title: Nod2-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 3

description:
Nod2 DSS 72-3
DSS exposure for 72 hrs


title: Nod2-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 1

description:
Nod2 DSS 96-1
DSS exposure for 96 hrs


title: Pglyrp3-/- mice, untreated, expt 1

description:
P3 Untr-1
Control


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 1

description:
P3 DSS 72-1
DSS exposure for 72 hrs


title: SEQC_AFX_USF_C_3_PRV


title: GS0005604

description:
Illumina chip: 5808922018
Illumina position: R01C02


title: GS0005740

description:
Illumina chip: 5808922035
Illumina position: R02C01


title: Pglyrp3-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 3

description:
P3 DSS 48-3
DSS exposure for 48 hrs


title: Nod2-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 3

description:
Nod2 DSS 96-3
DSS exposure for 96 hrs


title: Nod2-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 2

description:
Nod2 DSS 96-2
DSS exposure for 96 hrs


title: Nod2-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 1

description:
Nod2 DSS 72-1
DSS exposure for 72 hrs


title: Nod2-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 3

description:
Nod2 DSS 48-3
DSS exposure for 48 hrs


title: Nod2-/- mice, treated with 5% DSS in drinking water for 72 hrs, expt 2

description:
Nod2 DSS 72-2
DSS exposure for 72 hrs


title: Nod2-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 2

description:
Nod2 DSS 48-2
DSS exposure for 48 hrs


title: Nod2-/- mice, untreated, expt 2

description:
Nod2 Untr-2
Control


title: Nod2-/- mice, untreated, expt 3

description:
Nod2 Untr-3
Control


title: WT mice, treated with 5% DSS in drinking water for 48 hrs, expt 1

description:
WT DSS 48-1
DSS exposure for 48 hrs


title: WT mice, treated with 5% DSS in drinking water for 72 hrs, expt 3

description:
WT DSS 72-3
DSS exposure for 72 hrs


title: WT mice, treated with 5% DSS in drinking water for 96 hrs, expt 3

description:
WT DSS 96-3
DSS exposure for 96 hrs


title: WT mice, treated with 5% DSS in drinking water for 96 hrs, expt 2

description:
WT DSS 96-2
DSS exposure for 96 hrs


title: Nod2-/- mice, untreated, expt 1

description:
Nod2 Untr-1
Control


title: WT mice, treated with 5% DSS in drinking water for 48 hrs, expt 2

description:
WT DSS 48-2
DSS exposure for 48 hrs


title: WT mice, treated with 5% DSS in drinking water for 48 hrs, expt 3

description:
WT DSS 48-3
DSS exposure for 48 hrs


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 96 hrs, expt 1

description:
P3Nod2 DSS 96-1
DSS exposure for 96 hrs


title: WT mice, treated with 5% DSS in drinking water for 72 hrs, expt 1

description:
WT DSS 72-1
DSS exposure for 72 hrs


title: WT mice, untreated, expt 1

description:
WT Untr-1
Control


title: WT mice, untreated, expt 2

description:
WT Untr-2
Control


title: WT mice, treated with 5% DSS in drinking water for 72 hrs, expt 2

description:
WT DSS 72-2
DSS exposure for 72 hrs


title: WT mice, treated with 5% DSS in drinking water for 96 hrs, expt 1

description:
WT DSS 96-1
DSS exposure for 96 hrs


title: SEQC_AFX_USF_C_2_HUG


title: WT mice, untreated, expt 3

description:
WT Untr-3
Control


title: Ror2 mutant primordial germ cells from embryo 4, biological rep4

city: San Francisco

first: Diana

middle: J.

last: Laird

state: CA

address: 35 Medical Center Way

department: ObGyn

institute: UCSF

description: gene expression data from migratory PGCs

hyb_protocol: Conducted by the Gladstone Genomics Core at UCSF: GeneChip Expression Analysis Technical Manual 702232 Rev. 3

scan_protocol: Conducted by the Gladstone Genomics Core at UCSF: GCS3000

data_processing: Conducted by the Gladstone Genomics Core at UCSF: AGCC 3.2.2

source_name: Ror2 mutant primordial germ cells at embryonic day 9.5

label_protocol: Conducted by the Gladstone Genomics Core at UCSF: NuGEN Ovation FFPE WTA System and NuGEN Encore Module

growth_protocol: Ror2Y324C/+ females were mated to Ror2Y324C/+;Oct4-ΔPETg/Tg males and copulatory plugs were recorded to collect litters at embryonic day 9.5.

extract_protocol: RNeasy Micro Kit (Qiagen).

treatment_protocol: Posteriors from single embryos at E9.5 were digested in Trypsin+EDTA and GFP+ primordial germ cells were sorted directly in RLT Buffer (Qiagen).

value: Migratory primordial germ cells

tag: embryo age

value: 21-22 somites

tag: genotype

tag: genetic strain

value: Mixed


title: GS0005650

description:
Illumina chip: 5808922048
Illumina position: R01C01

value: Female

value: invasive

value: breast cancer


title: DLPFC_Control_101

city: Baltimore

first: Andrew

last: Jaffe

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

description:
5591989011_I
R4279

hyb_protocol: Refer to the Illumina DASL Assay System Manual

data_processing: The raw intensities were exported from GenomeStudio and read into R using the lumi package. Background correction (bgAdjust.affy option), variance stabilizing transform, and quantile normalization were then performed to normalize the data.

source_name: DLPFC

extract_protocol: Total RNA was extracted from ~ 100 mg of tissue using the RNeasy Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Total RNA was extracted from dissected frozen postmortem human brain tissue.

tag: rin

tag: ocd

value: Control

tag: rinmatched

tag: dx

tag: ph

tag: pmi

tag: Sex

value: M

tag: race

value: CAUC


title: DLPFC_Control_102

description:
5591989011_J
R4386

scan_protocol: Refer to the Illumina DASL Assay System Manual


title: DLPFC_Control_99

description:
5591989071_F
R4397

label_protocol: Refer to the Illumina DASL Assay System Manual


title: Ror2 mutant primordial germ cells from embryo 1, biological rep1

tag: tissue

value: 24 somites


title: WT primordial germ cells from embryo 4, biological rep4

source_name: WT primordial germ cells at embryonic day 9.5

value: 21 somites


title: DLPFC_Control_91

description:
5591997017_D
R3502


title: DLPFC_Control_100

description:
5591989011_G
R3489


title: DLPFC_Control_97

description:
5591989053_C
R4363


title: DLPFC_Control_94

description:
5591989044_B
R3560


title: DLPFC_Control_95

description:
5591989045_D
R4326


title: DLPFC_Control_92

description:
5591997017_F
R3503


title: WT primordial germ cells from embryo 3, biological rep3

value: 22 somites


title: Ror2 mutant primordial germ cells from embryo 3, biological rep3

value: 23 somites


title: DLPFC_ED_15

description:
5591989005_H
R4031

value: ED

value: MDD

value: F


title: DLPFC_ED_14

description:
5591989045_C
R3682


title: DLPFC_Control_93

description:
5591989044_I
R4303


title: Ror2 mutant primordial germ cells from embryo 2, biological rep2

value: 22-23 somites


title: DLPFC_Control_96

description:
5591989055_D
R4348


title: DLPFC_Control_90

description:
5591997017_A
R3063


title: DLPFC_Control_98

description:
5591989071_E
R4354


title: Rat_Liver_ETHINYLESTRADIOL_10mg/kg_5d_NU_OG_Rep3

description: Test set

hyb_protocol: The array hybridization cocktail was as follows: 15 μg cRNA, 5 μL control oligo B2 (3 nM), 15 μL 20X eukaryotic hybridization controls (bioB, bioC, bioD and cre), 150 μL 2X hybridization mix, 10 μL DMSO, and water to a final volume of 300 μL.  Arrays were hybridized for 16 hours in the GeneChip® hybridization oven 640.

scan_protocol: The arrays were washed, stained and scanned in accordance with protocols outlined in Affymetrix GeneChip® Expression Analysis Technical Manual (subsection: Eukaryotic Arrays: Washing, Staining, and Scanning)  using a GeneChip® Fluidics Station 450.

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

organism: Rattus norvegicus

source_name: Liver

label_protocol: cRNA target preparation and fragmentation was carried out using the GeneChip® One-Cycle Target Labeling and Control Reagents Kit (P/N 900493) from Affymetrix (Affymetrix Inc., Santa Clara, CA) according to the Affymetrix GeneChip® Expression Analysis Technical Manual (subsections: Total RNA and mRNA isolation for one-cycle target labeling,  one-cycle cDNA synthesis, cleanup of double-stranded cDNA for both the one-cycle and two-cycle target labeling assays,  synthesis of biotin-labeled cRNA for both the one-cycle and two-cycle target labeling assays, cleanup and quantification of biotin-labeled cRNA, and fragmenting the cRNA for target preparation) using 20 mg of isolated RNA. cRNA fragmentation mix was as follows: 20 μg RNA, 8 μL 5X Fragmentation Buffer, RNase-free water to a final volume of 40μL.

growth_protocol: Upon delivery to testing laboratory male Sprague-Dawley (Crl:CD® (SD)|GS BR) were housed individually in hanging, stainless steel, wire-bottom cages in a ventilated room (temperature, 22±3 ◦C; humidity, 30–70%; 12-h light:12-h dark cycle per day, 6:00 a.m.–6:00 p.m.) and received Certified Rodent Diet #5002 (PMI Feeds Inc.. Richmond, IN); chlorinated tap water was available ad libidum.

extract_protocol: Automated RNA isolation was performed according to the manufacture’s protocol using the RNeasy Kit from Qiagen (Germantown, MD).

treatment_protocol: Animals were acclimated for one week to the testing laboratory prior to dosing.  After dosing, all liver samples were harvested as 100 mg punches using six millimeter disposable biopsy punches. An appropriately staggered schedule was employed so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.

tag: strain

value: Sprague Dawley

value: ER

tag: chemical

value: ETHINYLESTRADIOL

tag: dose

value: 10 mg/kg

tag: vehicle

value: CORN OIL 100 %

tag: route

value: ORAL GAVAGE

tag: duration

value: 5 d

value: LIVER


title: WT primordial germ cells from embryo 2, biological rep2

value: Migratory primordial germ cells

tag: embryo age

value: 25 somites

tag: genotype

value: Mixed


title: Pglyrp3-/-Nod2-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 1

description:
P3Nod2 DSS 48-1
DSS exposure for 48 hrs

value: Entire colon

value: BALB/c


title: Rat_Liver_ETHINYLESTRADIOL_10mg/kg_5d_NU_OG_Rep2

description: Test set

value: M


title: Rat_Liver_SIMVASTATIN_1200mg/kg_3d_NU_OG_Rep3

description: Test set

value: HMGCOA

value: SIMVASTATIN

value: 3 d


title: WT primordial germ cells from embryo 1, biological rep1

tag: genetic strain


title: DLPFC_Control_88

description:
5630132024_B
R4076

tag: rin

tag: ocd

value: Control

tag: age

value: CAUC


title: DLPFC_Control_89

description:
5630132024_D
R4232

tag: rinmatched

tag: dx

tag: ph


title: Rat_Liver_SIMVASTATIN_1200mg/kg_3d_NU_OG_Rep2

description: Test set

value: Sprague Dawley

tag: Sex


title: Rat_Liver_SIMVASTATIN_1200mg/kg_3d_NU_OG_Rep1

description: Test set

tag: tissue


title: Rat_Liver_ROSIGLITAZONE_1800mg/kg_5d_NU_OG_Rep3

description: Test set

tag: strain

value: PPARA

value: ROSIGLITAZONE


title: DLPFC_OCD_16

description:
5630132024_E
R4069

value: OCD

tag: pmi

tag: race


title: Rat_Liver_ETHINYLESTRADIOL_10mg/kg_5d_NU_OG_Rep1

description: Test set

value: ER

tag: chemical

value: ETHINYLESTRADIOL

tag: dose

value: 10 mg/kg

tag: vehicle

value: CORN OIL 100 %

value: ORAL GAVAGE

value: 5 d


title: DLPFC_Control_85

description:
5630132024_C
R4048


title: DLPFC_Control_87

description:
5630132024_K
R4075


title: DLPFC_Control_83

description:
5630132023_B
R3509


title: Rat_Liver_ROSIGLITAZONE_1800mg/kg_5d_NU_OG_Rep1

description: Test set

tag: route

tag: duration

value: LIVER


title: Rat_Liver_ROSIGLITAZONE_1800mg/kg_5d_NU_OG_Rep2

description: Test set

value: M


title: Rat_Liver_MICONAZOLE_920mg/kg_5d_NU_OG_Rep2

description: Test set

value: CAR/PXR

value: MICONAZOLE

value: 920 mg/kg


title: DLPFC_Control_82

description:
5630132023_A
R3522

value: Control

value: F


title: DLPFC_Control_80

description:
5630132023_H
R3548

value: CAUC


title: Rat_Liver_MICONAZOLE_920mg/kg_5d_NU_OG_Rep3

description: Test set

value: Sprague Dawley


title: Rat_Liver_GEMFIBROZIL_700mg/kg_7d_NU_OG_Rep2

description: Test set

value: PPARA

value: GEMFIBROZIL

value: 700 mg/kg

value: 7 d


title: Rat_Liver_Vehicle__5d_NU_OG_Test_Rep5

description: Test set

value: Vehicle


title: DLPFC_Control_84

description:
5630132024_A
R4047


title: DLPFC_Control_79

description:
5630132009_H
R4038


title: Nod2-/- mice, treated with 5% DSS in drinking water for 48 hrs, expt 1

description:
Nod2 DSS 48-1
DSS exposure for 48 hrs

value: Entire colon

value: BALB/c


title: Rat_Liver_Vehicle__7d_NU_OG_Test_Rep6

description: Test set

value: CORN OIL 100 %

value: ORAL GAVAGE


title: DLPFC_Control_81

description:
5591997083_G
R3447

value: M


title: Rat_Liver_GEMFIBROZIL_700mg/kg_7d_NU_OG_Rep3

description: Test set

value: LIVER


title: Rat_Liver_GEMFIBROZIL_700mg/kg_7d_NU_OG_Rep1

description: Test set


title: DLPFC_ED_13

description:
5591997084_H
R3006

value: ED

value: Bipolar


title: DLPFC_Control_86

description:
5630132024_G
R4070

value: Control


title: Rat_Liver_CERIVASTATIN_7mg/kg_5d_NU_OG_Rep3

description: Test set

value: HMGCOA

value: CERIVASTATIN

value: 7 mg/kg

value: 5 d


title: Rat_Liver_CERIVASTATIN_7mg/kg_5d_NU_OG_Rep2

description: Test set

value: Sprague Dawley


title: Rat_Liver_Vehicle__5d_NU_OG_Test_Rep2

description: Test set


title: Rat_Liver_Vehicle__5d_NU_OG_Test_Rep3

description: Test set


title: Rat_Liver_Vehicle__5d_NU_OG_Test_Rep4

description: Test set


title: DLPFC_Control_76

description:
5591997084_G
R3518

value: CAUC


title: DLPFC_Control_78

description:
5591989008_K
R4424


title: DLPFC_OCD_15

description:
5630132009_K
R4032

value: OCD


title: Rat_Liver_BETA-ESTRADIOL_150mg/kg_5d_NU_OG_Rep3

description: Test set

value: ER

value: BETA-ESTRADIOL

value: 150 mg/kg


title: Rat_Liver_CERIVASTATIN_7mg/kg_5d_NU_OG_Rep1

description: Test set

value: CORN OIL 100 %


title: DLPFC_OCD_12

description:
5591989065_E
R5707


title: Rat_Liver_CLOFIBRIC-ACID_448mg/kg_5d_NU_OG_Rep2

description: Test set

value: PPARA

value: CLOFIBRIC ACID

value: 448 mg/kg

value: ORAL GAVAGE


title: DLPFC_OCD_14

description:
5591989084_C
R5835

value: F


title: DLPFC_Control_75

description:
5591997084_E
R3472

value: Control

value: M


title: DLPFC_ED_10

description:
5591989062_A
R5609

value: ED

value: Bipolar


title: Rat_Liver_CLOTRIMAZOLE_89mg/kg_5d_NU_OG_Rep3

description: Test set

value: CAR/PXR

value: CLOTRIMAZOLE

value: 89 mg/kg

value: 5 d

value: LIVER


title: DLPFC_Control_74

description:
5591989016_L
R3014

value: CAUC


title: Rat_Liver_LOVASTATIN_450mg/kg_5d_NU_OG_Rep3

description: Test set

value: Sprague Dawley

value: HMGCOA

value: LOVASTATIN

value: 450 mg/kg


title: DLPFC_Control_73

description:
5591989084_H
R5748


title: Rat_Liver_CLOFIBRIC-ACID_448mg/kg_5d_NU_OG_Rep1

description: Test set

value: PPARA

value: CLOFIBRIC ACID

value: 448 mg/kg

value: CORN OIL 100 %


title: DLPFC_OCD_13

description:
5591989084_A
R5777

value: OCD

value: F


title: DLPFC_ED_12

description:
5591989065_D
R5834

value: ED


title: Rat_Liver_NORETHINDRONE_375mg/kg_5d_NU_OG_Rep3

description: Test set

value: ER

value: NORETHINDRONE

value: 375 mg/kg

value: ORAL GAVAGE

value: M


title: Rat_Liver_CLOFIBRIC-ACID_448mg/kg_5d_NU_OG_Rep3

description: Test set

value: 5 d

value: LIVER


title: DLPFC_ED_11

description:
5591989062_L
R5831

value: Bipolar

value: CAUC


title: Rat_Liver_FLUCONAZOLE_394mg/kg_5d_NU_OG_Rep3

description: Test set

value: Sprague Dawley

value: CAR/PXR

value: FLUCONAZOLE

value: 394 mg/kg


title: DLPFC_Control_72

description:
5591989062_C
R5749

value: Control


title: Rat_Liver_BETA-ESTRADIOL_150mg/kg_5d_NU_OG_Rep2

description: Test set

value: BETA-ESTRADIOL

value: 150 mg/kg

value: CORN OIL 100 %


title: DLPFC_Control_77

description:
5591989008_A
R4281


title: DLPFC_Control_71

description:
5591989016_G
R2999


title: DLPFC_ED_9

description:
5591989073_K
R5719

value: ED

value: F


title: Rat_Liver_CLOTRIMAZOLE_89mg/kg_5d_NU_OG_Rep2

description: Test set

value: CLOTRIMAZOLE

value: 89 mg/kg


title: Rat_Liver_NORETHINDRONE_375mg/kg_5d_NU_OG_Rep2

description: Test set

value: ER

value: NORETHINDRONE

value: 375 mg/kg

value: ORAL GAVAGE

value: M


title: Rat_Liver_LOVASTATIN_450mg/kg_5d_NU_OG_Rep2

description: Test set

value: Sprague Dawley

value: HMGCOA

value: LOVASTATIN

value: 450 mg/kg

value: 5 d

value: LIVER


title: DLPFC_OCD_11

description:
5591989061_E
R5695

value: OCD

value: MDD

value: CAUC


title: Rat_Liver_BETA-ESTRADIOL_150mg/kg_5d_NU_OG_Rep1

description: Test set

value: BETA-ESTRADIOL

value: 150 mg/kg

value: CORN OIL 100 %


title: Rat_Liver_FLUCONAZOLE_394mg/kg_5d_NU_OG_Rep2

description: Test set

value: CAR/PXR

value: FLUCONAZOLE

value: 394 mg/kg


title: Rat_Liver_FLUCONAZOLE_394mg/kg_5d_NU_OG_Rep1

description: Test set

value: ORAL GAVAGE


title: DLPFC_OCD_9

description:
5591989061_A
R5693

value: M


title: Rat_Liver_LOVASTATIN_450mg/kg_5d_NU_OG_Rep1

description: Test set

value: Sprague Dawley


title: Rat_Liver_MICONAZOLE_920mg/kg_5d_NU_OG_Rep1

description: Test set

value: MICONAZOLE

value: 920 mg/kg


title: DLPFC_OCD_10

description:
5591989061_C
R5694


title: Rat_Liver_Vehicle__5d_NU_OG_Test_Rep1

description: Test set

value: Control

value: Vehicle


title: DLPFC_ED_8

description:
5591989058_I
R5632

value: ED

value: Bipolar

value: F


title: DLPFC_ED_7

description:
5591989058_H
R5690

value: MDD

value: CAUC


title: Rat_Liver_METHIMAZOLE_100mg/kg_3d_NN_OG_Rep3

description: Training Set

value: METHIMAZOLE

value: 100 mg/kg

value: WATER 100 %

value: 3 d

value: LIVER


title: DLPFC_Control_67

description:
5591989058_E
R5628


title: DLPFC_Control_68

description:
5591989058_K
R5633


title: Rat_Liver_METHIMAZOLE_100mg/kg_3d_NN_OG_Rep1

description: Training Set

value: CAR/PXR

value: ORAL GAVAGE


title: DLPFC_Control_70

description:
5591989016_B
R4324

value: M


title: DLPFC_Control_66

description:
5591989050_I
R5599


title: Rat_Liver_NORETHINDRONE_375mg/kg_5d_NU_OG_Rep1

description: Test set

value: Sprague Dawley

value: ER

value: NORETHINDRONE

value: 375 mg/kg

value: CORN OIL 100 %

value: 5 d


title: DLPFC_Control_64

description:
5591989043_I
R5625

value: Control


title: Rat_Liver_N-NITROSODIMETHYLAMINE_10mg/kg_5d_NN_IP_Rep3

description: Training Set

value: DNA Damage

value: N-NITROSODIMETHYLAMINE

value: 10 mg/kg

value: SALINE 100 %

value: INTRAPERITONEAL


title: Rat_Liver_METHIMAZOLE_100mg/kg_3d_NN_OG_Rep2

description: Training Set

value: METHIMAZOLE

value: 100 mg/kg

value: WATER 100 %

value: 3 d


title: Rat_Liver_CLOTRIMAZOLE_89mg/kg_5d_NU_OG_Rep1

description: Test set

value: CAR/PXR

value: CLOTRIMAZOLE

value: 89 mg/kg

value: ORAL GAVAGE

value: LIVER

value: M


title: DLPFC_OCD_5

description:
5591989037_F
R4262

value: OCD

value: CAUC


title: DLPFC_Control_65

description:
5591989050_E
R5596

value: Control


title: Rat_Liver_IFOSFAMIDE_143mg/kg_3d_NN_OG_Rep3

description: Training Set

value: Sprague Dawley

value: DNA Damage

value: IFOSFAMIDE

value: 143 mg/kg


title: DLPFC_OCD_8

description:
5591989058_L
R5692

value: MDD


title: DLPFC_OCD_7

description:
5591989037_J
R4265

value: Tics


title: DLPFC_Control_69

description:
5591989073_F
R5741


title: Rat_Liver_CHLOROFORM_600mg/kg_5d_NU_OG_Rep3

description: Training Set

value: Cytotoxic

value: CHLOROFORM

value: 600 mg/kg

value: CORN OIL 100 %

value: 5 d


title: DLPFC_OCD_6

description:
5591989037_H
R4263


title: Rat_Liver_CHLOROFORM_600mg/kg_5d_NU_OG_Rep1

description: Training Set

value: ORAL GAVAGE


title: Rat_Liver_Vehicle__3d_NU_OG_Rep5

description: Training Set

value: Vehicle

value: 3 d

value: LIVER


title: DLPFC_Control_63

description:
5591989031_E
R5601

value: M

value: CAUC


title: Rat_Liver_BEZAFIBRATE_617mg/kg_7d_NU_OG_Rep3

description: Training Set

value: Sprague Dawley

value: PPARA

value: BEZAFIBRATE

value: 617 mg/kg

value: 7 d


title: DLPFC_OCD_4

description:
5591989037_D
R4261

value: OCD

value: Tics


title: Rat_Liver_CHLOROFORM_600mg/kg_5d_NU_OG_Rep2

description: Training Set

value: Cytotoxic

value: CHLOROFORM


title: Rat_Liver_BETA-NAPHTHOFLAVONE_1500mg/kg_5d_NN_OG_Rep3

description: Training Set

value: AhR

value: BETA-NAPHTHOFLAVONE

value: CMC .5 %


title: Rat_Liver_Vehicle__1d_NN_IP_Rep4

description: Training Set

value: Control

value: Vehicle

value: SALINE 100 %

value: INTRAPERITONEAL

value: 1 d


title: Rat_Liver_Vehicle__3d_NU_OG_Rep4

description: Training Set

value: Sprague Dawley

value: CORN OIL 100 %

value: ORAL GAVAGE

value: 3 d

value: LIVER

value: M


title: Rat_Liver_CARBON-TETRACHLORIDE_1175mg/kg_7d_NU_OG_Rep3

description: Training Set

value: CARBON TETRACHLORIDE

value: 7 d


title: DLPFC_Control_60

description:
4447846111_K
R4356

value: CAUC


title: Rat_Liver_N-NITROSODIMETHYLAMINE_10mg/kg_5d_NN_IP_Rep2

description: Training Set

value: DNA Damage

value: N-NITROSODIMETHYLAMINE

value: 10 mg/kg

value: 5 d


title: DLPFC_Control_56

description:
4447846025_G
R3052

value: Control

value: F


title: DLPFC_Control_54

description:
4447846010_J
R3582


title: DLPFC_OCD_3

description:
4447846034_K
R4061

value: OCD

value: Bipolar


title: DLPFC_Control_62

description:
4447846033_E
R4360


title: DLPFC_Control_53

description:
4447846010_H
R3557


title: Rat_Liver_IFOSFAMIDE_143mg/kg_3d_NN_OG_Rep2

description: Training Set

value: Sprague Dawley

value: IFOSFAMIDE

value: 143 mg/kg

value: SALINE 100 %


title: Rat_Liver_LEFLUNOMIDE_60mg/kg_5d_NU_OG_Rep3

description: Training Set

value: AhR

value: LEFLUNOMIDE

value: 60 mg/kg

value: CORN OIL 100 %

value: ORAL GAVAGE

value: LIVER


title: Rat_Liver_LEFLUNOMIDE_60mg/kg_5d_NU_OG_Rep2

description: Training Set

value: M


title: DLPFC_Control_52

description:
4447846010_F
R3499

value: CAUC


title: Rat_Liver_Vehicle__1d_NN_IP_Rep3

description: Training Set

value: Vehicle

value: RSA/SALINE .1 %

value: INTRAPERITONEAL

value: 1 d


title: DLPFC_Control_58

description:
4447846003_I
R4044

value: Control


title: DLPFC_Control_57

description:
4447846253_L
R2966

value: F


title: Rat_Liver_Vehicle__1d_NN_IP_Rep2

description: Training Set

value: Sprague Dawley


title: DLPFC_Control_59

description:
4447846073_F
R4371


title: DLPFC_Control_55

description:
4447846010_K
R3581


title: Rat_Liver_IFOSFAMIDE_143mg/kg_3d_NN_OG_Rep1

description: Training Set

value: DNA Damage

value: IFOSFAMIDE

value: 143 mg/kg

value: 3 d


title: Rat_Liver_LEFLUNOMIDE_60mg/kg_5d_NU_OG_Rep1

description: Training Set

value: AhR

value: LEFLUNOMIDE

value: 60 mg/kg

value: 5 d


title: Rat_Liver_AFLATOXIN-B1_.3mg/kg_5d_NN_OG_Rep3

description: Training Set

value: AFLATOXIN B1

value: .3 mg/kg

value: CMC .5 %

value: ORAL GAVAGE

value: LIVER

value: M


title: Rat_Liver_NAFENOPIN_338mg/kg_5d_NU_OG_Rep3

description: Training Set

value: PPARA

value: NAFENOPIN

value: 338 mg/kg

value: CORN OIL 100 %


title: DLPFC_Control_47

description:
4447846002_I
R3059

value: Control

value: F

value: CAUC


title: DLPFC_Control_49

description:
4447846010_B
R3523


title: DLPFC_Control_48

description:
4447846002_K
R2915


title: DLPFC_Control_50

description:
4447846010_D
R3498


title: DLPFC_Control_51

description:
4447846010_E
R3497


title: DLPFC_Control_45

description:
4447846002_D
R2855


title: DLPFC_Control_46

description:
4447846002_G
R2902


title: Rat_Liver_BEZAFIBRATE_617mg/kg_7d_NU_OG_Rep2

description: Training Set

value: Sprague Dawley

value: BEZAFIBRATE

value: 617 mg/kg

value: 7 d


title: Rat_Liver_AFLATOXIN-B1_.3mg/kg_5d_NN_OG_Rep2

description: Training Set

value: DNA Damage

value: AFLATOXIN B1

value: 5 d


title: Rat_Liver_Vehicle__5d_NN_OG_Rep6

description: Training Set

value: Vehicle

value: CMC .5 %

value: ORAL GAVAGE


title: Rat_Liver_3-METHYLCHOLANTHRENE_300mg/kg_5d_NN_OG_Rep2

description: Training Set

value: AhR

value: 300 mg/kg

value: LIVER

value: M


title: Rat_Liver_N-NITROSODIMETHYLAMINE_10mg/kg_5d_NN_IP_Rep1

description: Training Set

value: N-NITROSODIMETHYLAMINE

value: 10 mg/kg

value: SALINE 100 %

value: INTRAPERITONEAL


title: DLPFC_Control_40

description:
4447846263_I
R3455

value: Control

value: CAUC


title: Rat_Liver_3-METHYLCHOLANTHRENE_300mg/kg_5d_NN_OG_Rep3

description: Training Set

value: Sprague Dawley


title: DLPFC_Control_41

description:
4447846285_A
R3639


title: Rat_Liver_3-METHYLCHOLANTHRENE_300mg/kg_5d_NN_OG_Rep1

description: Training Set


title: Rat_Liver_CARBON-TETRACHLORIDE_1175mg/kg_7d_NU_OG_Rep2

description: Training Set

value: Cytotoxic

value: CARBON TETRACHLORIDE

value: CORN OIL 100 %

value: 7 d


title: DLPFC_Control_38

description:
4447846263_A
R3602


title: DLPFC_Control_42

description:
4447846285_C
R3480


title: DLPFC_Control_43

description:
4447846285_G
R3460

value: F


title: DLPFC_Control_61

description:
4447846112_L
R4394


title: DLPFC_Control_37

description:
4447846099_E
R2954


title: Rat_Liver_NAFENOPIN_338mg/kg_5d_NU_OG_Rep2

description: Training Set

value: PPARA

value: NAFENOPIN

value: 338 mg/kg

value: ORAL GAVAGE

value: 5 d


title: DLPFC_ED_6

description:
4447846099_H
R3043

value: ED

value: MDD

value: M


title: Rat_Liver_CARBON-TETRACHLORIDE_1175mg/kg_7d_NU_OG_Rep1

description: Training Set

value: LIVER


title: DLPFC_Control_44

description:
4447846002_B
R2879

value: Control


title: Rat_Liver_NAFENOPIN_338mg/kg_5d_NU_OG_Rep1

description: Training Set


title: DLPFC_Control_36

description:
4493594399_G
R3421

value: CAUC


title: DLPFC_Control_35

description:
4493594399_A
R3375


title: DLPFC_Control_39

description:
4447846263_G
R3539


title: DLPFC_Control_33

description:
4447846022_B
R3675


title: Rat_Liver_THIOACETAMIDE_200mg/kg_5d_NN_IP_Rep3

description: Training Set

value: Sprague Dawley

value: THIOACETAMIDE

value: 200 mg/kg

value: SALINE 100 %

value: INTRAPERITONEAL


title: Rat_Liver_Vehicle__7d_NU_OG_Rep6

description: Training Set

value: Vehicle

value: CORN OIL 100 %

value: 7 d


title: Rat_Liver_Vehicle__1d_NN_IP_Rep1

description: Training Set

value: 1 d


title: DLPFC_Control_31

description:
4447846005_D
R3583

value: F


title: DLPFC_Control_32

description:
4447846005_H
R3584


title: DLPFC_Control_29

description:
4493594342_G
R2996


title: DLPFC_Control_34

description:
4447846022_C
R3500


title: DLPFC_Control_30

description:
4447846005_C
R3546


title: DLPFC_Control_28

description:
4493594342_E
R2829


title: Rat_Liver_Vehicle__5d_NN_IP_Rep6

description: Training Set

value: 5 d


title: Rat_Liver_Vehicle__5d_NN_OG_Rep4

description: Training Set

value: CMC .5 %

value: ORAL GAVAGE


title: DLPFC_Control_26

description:
4447846023_C
R2892


title: Rat_Liver_THIOACETAMIDE_200mg/kg_5d_NN_IP_Rep2

description: Training Set

value: Cytotoxic

value: M


title: DLPFC_Control_27

description:
4447846001_E
R2798

value: Control


title: Rat_Liver_THIOACETAMIDE_200mg/kg_5d_NN_IP_Rep1

description: Training Set

value: LIVER


title: Rat_Liver_Vehicle__5d_NN_OG_Rep5

description: Training Set

value: Sprague Dawley


title: Rat_Liver_BETA-NAPHTHOFLAVONE_1500mg/kg_5d_NN_OG_Rep2

description: Training Set

value: AhR

value: BETA-NAPHTHOFLAVONE


title: DLPFC_Control_24

description:
4493594421_K
R2826

value: CAUC


title: Rat_Liver_Vehicle__5d_NN_OG_Rep3

description: Training Set


title: Rat_Liver_BETA-NAPHTHOFLAVONE_1500mg/kg_5d_NN_OG_Rep1

description: Training Set


title: DLPFC_Control_25

description:
4447846023_A
R3465


title: Rat_Liver_Vehicle__3d_NU_OG_Rep3

description: Training Set

value: 3 d


title: Rat_Liver_BEZAFIBRATE_617mg/kg_7d_NU_OG_Rep1

description: Training Set

value: PPARA

value: BEZAFIBRATE

value: 617 mg/kg


title: DLPFC_Control_22

description:
4493594421_C
R2853


title: DLPFC_Control_20

description:
4493594421_A
R3017


title: DLPFC_Control_18

description:
4493594381_C
R2985


title: DLPFC_Control_16

description:
4493594380_G
R2899


title: Rat_Liver_PIRINIXIC-ACID_364mg/kg_5d_NN_OG_Rep3

description: Training Set

value: PIRINIXIC ACID

value: 364 mg/kg


title: Rat_Liver_PHENOBARBITAL_54mg/kg_5d_NN_OG_Rep3

description: Training Set

value: CAR/PXR

value: PHENOBARBITAL

value: 54 mg/kg

value: WATER 100 %

value: 5 d


title: Rat_Liver_Vehicle__5d_NN_OG_Rep1

description: Training Set

value: Control

value: Vehicle

value: SALINE 100 %

value: ORAL GAVAGE

value: M


title: Rat_Liver_PIRINIXIC-ACID_364mg/kg_5d_NN_OG_Rep2

description: Training Set

value: Sprague Dawley

value: CMC .5 %

value: LIVER


title: Rat_Liver_PHENOBARBITAL_54mg/kg_5d_NN_OG_Rep2

description: Training Set


title: DLPFC_Control_21

description:
4493594421_B
R3034

value: CAUC


title: DLPFC_Control_19

description:
4493594381_I
R2839


title: DLPFC_Control_17

description:
4493594380_I
R2874


title: DLPFC_Control_15

description:
4493594380_A
R2984

value: F


title: DLPFC_Control_23

description:
4493594421_G
R3619


title: Rat_Liver_PIRINIXIC-ACID_364mg/kg_5d_NN_OG_Rep1

description: Training Set

value: PPARA

value: PIRINIXIC ACID


title: Rat_Liver_Vehicle__5d_NN_OG_Rep2

description: Training Set


title: Rat_Liver_ECONAZOLE_334mg/kg_5d_NU_OG_Rep3

description: Training Set

value: CAR/PXR

value: ECONAZOLE

value: 334 mg/kg

value: CORN OIL 100 %


title: DLPFC_Control_14

description:
4493594390_C
R2958


title: SEQC_ILM_UTS_D_3_MA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Non-normalized signal data were generated with Illumina software (data available as series supplementary file SEQC_ILM_GEOSub.txt)

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

tag: seqc sample

value: D


title: Rat_Liver_Vehicle__1d_NU_OG_Rep1

description: Training Set

value: Control

value: 1 d


title: DLPFC_Control_13

description:
4493594350_I
R3424

tag: rin


title: Rat_Liver_PHENOBARBITAL_54mg/kg_5d_NN_OG_Rep1

description: Training Set

value: PHENOBARBITAL

value: 54 mg/kg

value: WATER 100 %

value: 5 d


title: Rat_Liver_Vehicle__3d_NN_IP_Rep5

description: Training Set

value: Sprague Dawley

value: Vehicle

value: SALINE 100 %

value: INTRAPERITONEAL

value: 3 d

value: M


title: Rat_Liver_Vehicle__3d_NU_OG_Rep2

description: Training Set

value: ORAL GAVAGE

value: LIVER


title: SEQC_ILM_UTS_D_2_MA


title: DLPFC_Control_11

description:
4493594411_C
R3374

tag: ocd

value: CAUC


title: Rat_Liver_ECONAZOLE_334mg/kg_5d_NU_OG_Rep1

description: Training Set

value: CAR/PXR

value: ECONAZOLE

value: 334 mg/kg

value: CORN OIL 100 %


title: SEQC_ILM_UTS_D_1_MA

value: D


title: Rat_Liver_AFLATOXIN-B1_.3mg/kg_5d_NN_OG_Rep1

description: Training Set

value: DNA Damage

value: AFLATOXIN B1

value: .3 mg/kg

value: CMC .5 %


title: Rat_Liver_ECONAZOLE_334mg/kg_5d_NU_OG_Rep2

description: Training Set

value: Sprague Dawley

value: 5 d


title: DLPFC_ED_5

description:
4493594350_J
R3641

value: ED

value: Bipolar

tag: age

value: F


title: Lenti-vector

city: Seoul

first: Byung-Hak

last: Kim

state: Seoul

address: 103 Daehangno, Jongno-gu

department: Pharmacology

country: South Korea

institute: Seoul National University College of Medicine

description: replicate 1

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner.

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0).

source_name: lentiviral vector-infected Huh7 cell

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: Huh7 cells were cultured in DMEM containing 10% FBS and 1% antibiotics at 37oC humidified incubator.

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturere's protocols.

treatment_protocol: Huh7 cells were transduced by lentiviral infection with either lentiviral vector or shCD133.

tag: cell line

tag: disease state

value: HCC

tag: transfection

value: vector-infected


title: DLPFC_Control_12

description:
4493594350_E
R3507

value: Control

tag: rinmatched

tag: dx

tag: ph

tag: Sex

value: M

value: CAUC


title: DLPFC_ED_3

description:
4447846110_J
R2953

value: MDD

tag: pmi

tag: race


title: DLPFC_OCD_2

description:
4447846069_B
R3090

value: OCD


title: SEQC_ILM_UTS_C_3_MA

source_name: Mix of A and B (3:1)

value: C


title: Lenti-shCD133

description: replicate 1

source_name: lentiviral shCD133-infected Huh7 cell


title: SEQC_ILM_UTS_C_1_MA


title: DLPFC_ED_4

description:
4493594331_H
R3013


title: SEQC_ILM_UTS_C_2_MA


title: SEQC_ILM_UTS_B_3_MA

source_name: Human Brain Reference RNA (HBRR) from Ambion

value: B


title: SEQC_ILM_UTS_B_2_MA


title: SEQC_ILM_UTS_B_1_MA


title: SEQC_ILM_UTS_A_2_MA

source_name: Universal Human Reference RNA (UHRR) from Stratagene

value: A


title: SEQC_ILM_UTS_A_3_MA


title: SEQC_ILM_UTS_A_1_MA


title: SEQC_ILM_COH_D_3_MA

source_name: Mix of A and B (1:3)

value: D


title: SEQC_ILM_COH_D_2_MA


title: SEQC_ILM_COH_D_1_MA


title: SEQC_ILM_COH_C_3_MA


title: SEQC_ILM_COH_C_2_MA


title: SEQC_ILM_COH_C_1_MA


title: DLPFC_Control_10

description:
4493594331_E
R2881


title: SEQC_ILM_COH_B_3_MA


title: SEQC_ILM_COH_B_2_MA


title: SEQC_ILM_COH_B_1_MA


title: DLPFC_Control_9

description:
4447846049_K
R3549


title: SEQC_ILM_COH_A_3_MA


title: SEQC_ILM_COH_A_2_MA


title: DLPFC_Control_2

description:
4493594325_I
R3445


title: DLPFC_Control_5

description:
4493594394_A
R3385


title: SEQC_ILM_COH_A_1_MA


title: testis_tbrd-1-mutant_biological replicate_3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

hyb_protocol: According to manufacturers instructions without modifications.

data_processing: RMA using Affymetrix expression console.

organism: Drosophila melanogaster

label_protocol: Biotinylated cRNA was prepared according to the appropriate Affymetrix protocol without further amplification.

growth_protocol: Drosophila melanogaster strains were maintained on standard medium at 25°C

extract_protocol: Total RNA was extracted from wild-type testes and homozygous tbrd-1 mutant testis by using TRIzol® (Invitrogen). RNA quality was validated using the Agilent Bioanalyser 2100 with the RNA 6000 Nano kit. Gene expression analysis was carried out using Affymetrix Drosophila Genome 2.0 arrays. For each array, independent RNA from whole testes pooled from 25 animals was used.

treatment_protocol: Testes from 0-2 day old wild-type and homozygous tbrd-1 mutant flies were dissected in PBS

tag: tissue

value: adult testis

tag: genotype


title: testis_wt_biological replicate_4

scan_protocol: According to manufacturers instructions without modifications.

source_name: testis_wt_biological replicate_4


title: testis_wt_biological replicate_1

source_name: testis_wt_biological replicate_1


title: DLPFC_ED_2

description:
4493594396_F
R3028


title: DLPFC_Control_8

description:
4447846049_A
R2820


title: testis_wt_biological replicate_5

source_name: testis_wt_biological replicate_5


title: 38 1500 ppm of hexanal was exposed in rats(T3 group)

first: Yoon

last: Cho

address: hwarang-ro 14

institute: KIST

description: miRNA expression after exposure to 1500ppm hexanal

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Lung, hexanal, 1500 ppm

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: Fischer-344 rats of both sexes were obtained from at the age of 7-8 weeks from OrientBio, Inc(Korea). The animals were quarantined and acclimated for 5days before the start of experiment. The animals were housed in stainless-steel wire hanging cages(255W×465L×200H ㎜).The environment in the exposure chamber was maintained constant at a temperature of 22±3 ℃ and a relative humadity of 30-70%. All rats were given sterilized commercial pellet diet ( PMI Nutrition International, USA) and sterilized water.

extract_protocol: Total RNA, including miRNA, from lung tissue in rats extracted using Trizol following manufacturer's instructions.

treatment_protocol: Hexanal was inhaled for 5 weeks in Fischer-344 rats(approximately 7-8 weeks old). Atmospheres of hexanal aerosol were generated at target concentrations of 0(control), 600, 1000, 1500 mg/m3 in air. Rats were exposed to the target concentrations for 4h/day, 5days/week.

value: lung

tag: gender

value: female

tag: treatment

value: 1500 ppm hexanal


title: testis_wt_biological replicate_2

source_name: testis_wt_biological replicate_2


title: DLPFC_Control_3

description:
4493594396_E
R3491


title: testis_tbrd-1-mutant_biological replicate_4


title: DLPFC_Control_1

description:
4493594325_G
R3477


title: DLPFC_Control_7

description:
4493594394_I
R3651


title: 37 1500 ppm of hexanal was exposed in rats(T3 group)


title: DLPFC_ED_1

description:
4493594332_D
R3067

value: ED

value: Bipolar


title: 36 1500 ppm of hexanal was exposed in rats(T3 group)


title: DLPFC_Control_4

description:
4493594376_E
R3479


title: testis_wt_biological replicate_3

source_name: testis_wt_biological replicate_3


title: DLPFC_Control_6

description:
4493594394_C
R2897


title: testis_tbrd-1-mutant_biological replicate_1


title: 16 1500 ppm of hexanal was exposed in rats(T3 group)

value: male


title: DLPFC_OCD_1

description:
4493594325_H
R3040


title: testis_tbrd-1-mutant_biological replicate_5


title: 17 1500 ppm of hexanal was exposed in rats(T3 group)


title: testis_tbrd-1-mutant_biological replicate_2


title: GBM Patient, #22

city: San Diego

first: Clark

middle: C

last: Chen

address: 3855 Health Sciences Drive, Room 5345, Bay 5M

department: Neurosurgery

institute: UC San Diego

hyb_protocol: Following manufaturers protocols for HG-U133_PLUS_2 platform

scan_protocol: unknown

data_processing: Microarray data were GC Robust Multiarray Average normalized using R and the bioconductor.org package gcrma using a gene-level probeset, in order to allow pathway signature analysis.

source_name: Glioblastoma tissue sample

label_protocol: unknown

extract_protocol: Tumors were collected as fresh-frozen specimen

treatment_protocol: Patients were newly diagnosed and yet to undergo treatment for GBM.

tag: tissue type

value: Glioblastoma tumor

tag: grade

value: IV


title: 32 1000 ppm of hexanal was exposed in rats(T2 group)

description: miRNA expression after exposure to 1000ppm hexanal

source_name: Lung, hexanal, 1000 ppm

value: 1000 ppm hexanal


title: 33 1000 ppm of hexanal was exposed in rats(T2 group)


title: GBM Patient, #20


title: 12 1000 ppm of hexanal was exposed in rats(T2 group)


title: 13 1000 ppm of hexanal was exposed in rats(T2 group)


title: 11 1000 ppm of hexanal was exposed in rats(T2 group)


title: GBM Patient, #23


title: 31 1000 ppm of hexanal was exposed in rats(T2 group)


title: GBM Patient, #21


title: GBM Patient, #19


title: 28 600 ppm of hexanal was exposed in rats(T1 group)

description: miRNA expression after exposure to 600ppm hexanal

source_name: Lung, hexanal, 600 ppm

value: 600 ppm hexanal


title: GBM Patient, #18


title: 8 600 ppm of hexanal was exposed in rats(T1 group)


title: 7 600 ppm of hexanal was exposed in rats(T1 group)


title: 26 600 ppm of hexanal was exposed in rats(T1 group)


title: GBM Patient, #14


title: 27 600 ppm of hexanal was exposed in rats(T1 group)


title: 6 600 ppm of hexanal was exposed in rats(T1 group)


title: GBM Patient, #17


title: GBM Patient, #15


title: GBM Patient, #12


title: GBM Patient, #11


title: GBM Patient, #9


title: GBM Patient, #13


title: GBM Patient, #16


title: GBM Patient, #10


title: 22 filtered clean air was exposed in rats(control group)

description: miRNA expression after exposure to filtered clean air

source_name: Lung, filtered clean air(control)

value: filtered clean air


title: 21 filtered clean air was exposed in rats(control group)


title: 3 filtered clean air was exposed in rats(control group)


title: GBM Patient, #5


title: GBM Patient, #7


title: GBM Patient, #8


title: GBM Patient, #4


title: GBM Patient, #2


title: GBM Patient, #3


title: 23 filtered clean air was exposed in rats(control group)


title: 1 filtered clean air was exposed in rats(control group)


title: 2 filtered clean air was exposed in rats(control group)


title: MCPyV(-) Patient 5 replicate 2

status: Public on Aug 07 2014

city: Rennes

first: Nicolas

last: Mouchet

state: Bretagne

address: 2 Av du Professeur Leon Bernard

department: Institut genetique et developpement de Rennes

institute: CNRS UMR6290

description:
MCPyV(-)5-2
raw data_ch1:000417(130)_2b.txt
raw data_ch2:000417(111)_1b.txt
Normal Merkel Cells obtained from 3 liftings

hyb_protocol: the samples were subjected to a predefined PIQOR® Oncology Microarray (Miltenyi Biotec) and hybridization with a a-HybTM Hybridization Station was performed according to manufacturer's guidelines (Memorec Biotech)

scan_protocol: Scanned on an Agilent scanner

data_processing: LOWESS and Scale normalized, background subtracte. log2 of processed Red signal/processed Green signal. R version 2.15.1 was used.

source_name: MCPyV(-) Patient 5

label_protocol: 250ng of each cDNA were used for Cy3 (cDNA from Merkel cells) and Cy5 (cDNA from Merkel carcinoma cells)

extract_protocol: RNA extraction was performed using the PicoPure® RNA isolation kit following manufacturer's instructions

tag: cell type

value: MCPyV(-) from flash frozen tumor

source_name: Total RNA from pooled of normal Merkel cell

value: pooled normal Merkel cells


title: MCPyV(-) Patient 5 replicate 1

description:
MCPyV(-)5-1
raw data_ch1:000417(129)_2b.txt
raw data_ch2:000417(110)_1b.txt
Normal Merkel Cells obtained from 3 liftings


title: diethylnitrosamine-1/2-48h

city: Kyoto

first: Wataru

last: Fujibuchi

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

institute: Kyoto University

description: 14P0100390-H09_7 48h

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

source_name: KhES-3 cells

growth_protocol: Cultured on mTeSR1 with Matrigel™ for human ES cells

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells are exposed to 1/2 lethal dose for 48 hours

tag: chemical category

value: genotoxin


title: MCPyV(-) Patient 5 replicate 3

description:
MCPyV(-)5-3
raw data_ch1:000417(131)_2b.txt
raw data_ch2:000417(112)_1b.txt
Normal Merkel Cells obtained from 3 liftings


title: phenytoin-1/2-48h

description: 14P0100390-H07_5 48h

value: neurotoxin


title: GBM Patient, #6


title: benzo a pyrene-1/2-48h

description: 14P0100390-H08_6 48h

value: benzo a pyrene-1/2-48h


title: 3-Methylcholanthrene-1/2-48h

description: 14P0100390-H11_9 48h


title: fetal heart_cortisol_140d_ replicate 7

city: Gainesville

first: Maureen

last: Keller-Wood

state: FL

department: Pharmacodynamics

institute: University of Florida

description: Gene expression at 140 days gestation in fetal heart septum following maternal cortisol infusion for 25 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.2 pmol Cy3/µg cRNA) was  fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized to the chip median and log transformed.

organism: Ovis aries

source_name: fetal heart_cortisol_140d_ replicate 7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Continuous infusions of cortisol to the ewe were begun at approximately day 115 of gestation

extract_protocol: RNA was extracted with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen Rneasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer

treatment_protocol: Ewes were infused with 1mg/kg/day cortisol or vehicle from approximately day 120 to 130 of pregnancy (n=6/group) or from day 115 to term (n=7, cortisol; n=8 control). Fetal heart septum samples were then collected.

value: fetal heart septum

tag: agent

value: cortisol

tag: time point

value: 140d gestation