title: PMWS-affected pig 12

source_name: PMWS-affected pig 12

value: PMWS


title: PMWS-affected pig 9

status: Public on Apr 30 2012

type: RNA

city: Bellaterra, Barcelona

first: Lana

middle: Teixeira

last: Fernandes

state: Catalunya

address: Campus de la UAB, Edifici cresa

department: Virology

country: Spain

institute: CReSA

description: Comparison of PMWS-affected pigs versus a healthy control group to investigate global expression changes in the mediastinal lymph node.

hyb_protocol: Labelled cRNA was fractioned and hybridized with the GeneChip Porcine Genome Array following the manufacturer's instructions. Subsequently, the arrays were washed and stained with a GeneChip Fluidics Station 450 using the standard fluidics protocol.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 by using the GeneChip Operating Software (GCOS) to produce a _.CEL file for further data processing.

data_processing: Data analysis was performed with Bioconductor implemented in R 2.6.0 (http://cran.r-project.org/). Data quality control assessments were performed with affyQCReport implemented in the simpleaffy package. The raw data were background corrected, normalized and converted to expression-level data using the Robust Multichip Average (RMA) algorithm. The Empirical Bayes method implemented in the limma package was used to assess differential expression. The p value cutoff for DE genes was set at 0.05.

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: PMWS-affected pig 9

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

extract_protocol: Sections of mediastinal lymph nodes were collected during necropsy and snap-frozen in dry ice for transporting to the laboratory and stored at -80ºC until RNA extraction. Total RNA was isolated from MLN using RiboPure™ kit (Ambion, Austin, USA) according to the manufacturer's instructions and quantified by spectrophotometry (ND-1000 NanoDrop Technologies, Wilmington, DE, USA). RNA quality was assessed by capillary electrophoresis analysis on an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

tag: tissue

value: mediastinal lymph node

tag: age

value: 13 to 15 week old

tag: disease state


title: Monocyte RNA 6h  X4300799018_B_t1

city: Luebeck

first: Heribert

last: Schunkert

address: Ratzeburger Allee 160

department: Medizinische Klinik II

country: Germany

description:
Monocyte RNA 6h
replicate 1 time point t1 (6h)

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Quality control, background correction, variance stabilization (Lin et al. 2008) and normalization were performed in R statistical environment using the Lumi package (Du et al. 2008). Briefly, output from Illumina’s Bead Studio software (BeadStudio User Guide. San Diego, USA 2004; 2005. http://www.illumina.com) was downloaded into R and a series of quality control and diagnostics were performed to assess the quality of raw and normalized data. Background correction was performed using the Illumina’s default algorithm which uses the signals from negative control bead types to estimates the expected background signal levels. After background correction and filtering out array outliers, variance stabilization transformation (VST) was performed on the intensity data. Data were normalized using quantile normalization method (Bolstad et al. 2003) to make the same overall distribution of expression intensities for all the arrays within the experiment. Control probes as well as transcripts absent (not expressed) in all samples were filtered out (a detection P-value < 0.01 was used as a threshold).

organism: Homo sapiens

source_name: Monocyte

label_protocol: In vitro transcription reaction of cDNA to cRNA was performed overnight at 37°C including biotin-16-UTP for labelling

extract_protocol: Isolation of monocytes was performed by an immuno-magnetic method using the Miltenyi AutoMacs cell separator using whole-blood CD14+ beads (Miltenyi) according to the manufacturers’ instructions

tag: cell type

value: monocyte

tag: stage of mi infection

tag: gender

value: male


title: PMWS-affected pig 11

source_name: PMWS-affected pig 11


title: Monocyte RNA 6h  X4300799015_E_t1

scan_protocol: Standard Illumina hybridization protocol

value: Female


title: PMWS-affected pig 10

source_name: PMWS-affected pig 10


title: PMWS-affected pig 7

source_name: PMWS-affected pig 7


title: NA11829

city: Hsinchu

first: Li-Lan

last: Li

address: 195,Sec. 4, Chung Hsing Rd. Chutung

country: Taiwan

institute: Industrial Technology Research Institute

description: no additional information

hyb_protocol: Ten micrograms of Cy5- labeled aRNA was fragmented (Ambion cat# 8740) and hybridized 16 hrs to Phalanx HOA arrays according to manufacturer’s instructions

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner G2565B (Agilent Technologies, Inc. CA, USA) at settings of 60 PMT (for Cy5) and of 10 micron, and the resulting images were quantified using the software ProbeArrayer (an in-house tool developed by ITRI)

data_processing: log2 transformed intensities were normalized across technical replicates for each individual using a ComBat (Johnson et al. 2007) normalization. The normalized replicate values were merged by median as one chip per sample, and then sample-based chips were normalized by median across individuals (n=60 for parent or n=30 for children).

source_name: lymphoblastoid cell line

label_protocol: 1.5 ug of total RNA from each sample was used in cDNA synthesis and IVT reaction using the Amino Allyl MessageAmpTMII aRNA Amplification kit (Ambion, Austin, TX 78744-1832, cat. no.1753). Single stranded aRNA labeled with Cy5 was generated using the Cy5 Mono-Reactive dye pack (Amersham. PA25001)

growth_protocol: RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 ~ 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80°C.

extract_protocol: RNAs were extracted using RNeasy mini kits with on-column DNAse I digestion (Qiagen)

tag: cell line

value: lymphoblastoid cell line

tag: parent/child

value: HapMap CEU_parent

tag: coriell sample


title: Monocyte RNA 6h  X4300799018_F_t1


title: Follicular lymphoma Grade 2 GN_U133A_491

city: New York

first: Elisa

last: Oricchio

address: 1275 York Avenue

country: USA

institute: MSKCC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with the R library affy  provided with the Bioconductor software

label: Biotin

source_name: Lymphoma

label_protocol: Biotinylated totRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

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

tag: severity

value: Grade 2

value: follicular lymphoma tumor


title: MCF7cellRNA-F05-2

city: Miami

first: Andrea

last: Johnstone

state: FL

address: 1095 NW 14th Terrace

department: The Miami Project to Cure Paralysis

institute: University of Miami Miller School of Medicine

hyb_protocol: Standard Affymetirx Procedures for Ambion MessageAmp Premier Target Labeling Service.

scan_protocol: Standard Affymetirx Procedures.

data_processing: Average probe set signal intensities (background subtracted, perfect match - mismatch) and detection calls for each array were calculated using MAS 5.0 software (Affymetrix).

source_name: MCF7_F05_5 μM_6hr

label_protocol: Total RNA was submitted to the Duke University Microarray Facility through the NINDS/NIMH Microarray Consortium.  The samples were processed using Ambion MessageAmp Premier Target Labeling Service.

growth_protocol: Human MCF7 breast adenocarcinoma cells (American Type Culture Collection) were grown to ~70% confluency over a period of 24 hours in DMEM media containing 10% fetal bovine serum and 1% penicillin-streptomycin-glutamine (Gibco).

extract_protocol: Following treatment, total RNA was isolated using a standard TRIzol isolation procedure (Invitrogen), and purified using the RNeasy Kit (Qiagen, Valencia, CA).  RNA quantity and quality (absorbance ratios 260/280>2; 260/230>1.8) were assessed using a NanoDrop Spectrophotometer (ND-1000, Thermo Scientific).

treatment_protocol: Once the cells were at ~70% confluency, they were treated for 6 hr with F05 (5 μM) or vehicle (DMSO, 0.05%).

value: breast adenocarcinoma cells

tag: treatment

value: 5 μM F05


title: Follicular lymphoma Grade 3 GN_U133A_490

value: Grade 3


title: Follicular lymphoma Grade 3 GN_U133A_201


title: PMWS-affected pig 6

source_name: PMWS-affected pig 6


title: PMWS-affected pig 8

source_name: PMWS-affected pig 8


title: Follicular lymphoma Grade 3 GN_U133A_153


title: Monocyte RNA 6h  X4300799014_E_t1


title: Monocyte RNA 6h  X4300799014_G_t1


title: MCF7cellRNA-F05-1


title: Monocyte RNA 6h  X4300799014_C_t1


title: Follicular lymphoma Grade 3 GN_U133A_228


title: MCF7cellRNA-Vehicle-2

value: 0.05% DMSO (vehicle)


title: PMWS-affected pig 5

source_name: PMWS-affected pig 5


title: 1702_Placebo_Week 0

first: Mayte

last: Suarez-Farinas

state: NY

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

institute: Mount SinaiSchool of Medicine

hyb_protocol: Quiagen single amplification protocol

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

data_processing:
GCRMA (using gcrma package from R/Bioconductor)
Normalized Expression values in log-2 scale

source_name: Patient: 1702, Dosage: Placebo, Time: Week 0

label_protocol: Quiagen single amplification protocol

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) and on-column DNAse digestion (RNAse-free DNAse Set, Qiagen)

tag: dosage

tag: patient

tag: time

value: Time:Week 0


title: 1704_Placebo_Week 2

source_name: Patient: 1704, Dosage: Placebo, Time: Week 2

value: Time:Week 2


title: 1613_Placebo_Week 2

source_name: Patient: 1613, Dosage: Placebo, Time: Week 2


title: NA12004

description: no additional information


title: MCF7cellRNA-Vehicle-3


title: PMWS-affected pig 4

source_name: PMWS-affected pig 4


title: PMWS-affected pig 2

source_name: PMWS-affected pig 2


title: 1702_Placebo_Week 2

source_name: Patient: 1702, Dosage: Placebo, Time: Week 2


title: 1614_Placebo_Week 2

source_name: Patient: 1614, Dosage: Placebo, Time: Week 2


title: MCF7cellRNA-F05-3


title: Helicobacter pylori infected vs uninfected replicate 3

city: guangzhou

first: yang

middle: ze

last: min

address: Panyu university cener

department: Pi-Wei Institute

country: China

institute: Guangzhou University of Chinese Medicine

description: Analysis of Helicobacter pylori pathogenic mechanism

hyb_protocol: Labelled cDNA hybridised using chip hybridization Kit (Biostargene, Shanghai) as manufacturers instructions.

scan_protocol: the cDNA microarray was scanned and exported as image by ScanArray4000 scanner. The Spreadsheets of the dual channel chip data were obtained by Image Reader GenePix Pro 3.0 software

data_processing: All signal intensity values below 200 was increased to 200. These gene spots, which Cy5 and Cy3 signal intensity values exceeded 200 or one of them exceeded 800, and the ratio of Cy5 and Cy3 between 0.1-10.0, were used to calculate the natural logarithm for their ratios of Cy5 and Cy3 (r=lnCy5/Cy3). Subsequently, the mean value (R) of all r value was obtained. All Cy3 signal intensity value was corrected by product of Cy3 and 1/R to decrease systemic error of Cy5 and Cy3 fluorescently labeled system.

source_name: patients of Helicobacter pylori infected replicate3

label_protocol: samples of Helicobacter pylori infected and uninfected were Labelled with Cy3 and Cy5,respectively, during cDNA synthesis from total RNA using chip hybridization Kit (Biostargene, Shanghai) as manufacturers instructions.

extract_protocol: total RNA isolation was done by using BIOSTAR UNIzol kit(Biostargene, Shanghai).

treatment_protocol: patients of helicobacter pylori uninfected and infected were directly selected to cDNA microarray experiment.

value: gastric mucosa

value: Helicobacter pylori infected

source_name: patients of Helicobacter pylori uninfected replicate3

value: Helicobacter pylori uninfected


title: Helicobacter pylori infected vs uninfected replicate 1

source_name: patients of Helicobacter pylori infected replicate1

source_name: patients of Helicobacter pylori uninfected replicate1


title: PMWS-affected pig 3

source_name: PMWS-affected pig 3

value: mediastinal lymph node

value: 13 to 15 week old

value: PMWS


title: MCF7cellRNA-Vehicle-1


title: Helicobacter pylori infected vs uninfected replicate 2

source_name: patients of Helicobacter pylori infected replicate2

source_name: patients of Helicobacter pylori uninfected replicate2


title: AEBP1 siRNA 4, biological rep4

city: Bangalore

first: Jayashree

middle: S

last: Ladha

address: Jakkur

country: India

institute: JNCASR

description: silenced RNA 46 hrs post transfection

scan_protocol: GeneChip  Scanner 3000

data_processing: RMA

source_name: AEBP1 siRNA 4, biological rep4

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

growth_protocol: Glial cells were grown in DMEM medium containing 10% FBS supplemented with antibiotics

treatment_protocol: 100nM scrambled or siRNA against AEBP1


title: AEBP1 siRNA 3, biological rep3

description: silenced RNA 46 hrs post transfection

source_name: AEBP1 siRNA 3, biological rep3


title: 1614_Placebo_Week 0

source_name: Patient: 1614, Dosage: Placebo, Time: Week 0


title: AEBP1 siRNA 5, biological rep5

description: silenced RNA 46 hrs post transfection

source_name: AEBP1 siRNA 5, biological rep5


title: AEBP1 siRNA 2, biological rep2

description: silenced RNA 46 hrs post transfection

source_name: AEBP1 siRNA 2, biological rep2


title: PMWS-affected pig 1

source_name: PMWS-affected pig 1


title: mammary tumor _WT-RU486 2.5mg

city: Washington

first: Robert

middle: I

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

description: Gene expression data from MP-DMBA induced mammary tumor in WT mice treated with 2.5mg RU-486

hyb_protocol: Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.

scan_protocol: The GeneChip® was scanned using an Agilent Gene Array scanner.

data_processing: Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal <300 in all experimental groups were excluded from analysis.

organism: Mus musculus

source_name: Wild-type group, treated with MP-DMBA and then were implanted with 60 day release 2.5mg RU-486 pellet

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

growth_protocol: All animal studies were conducted under GUACUC protocol 09-061. Female nulliparious MMTV-PAX8PPARg mice and age-matched FVB/wild-type littermates were used in this study.

extract_protocol: Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).

treatment_protocol: Mice were maintained on standard rodent chow and injected s.c. with  15 mg MP suspension (Depo-Provera™), followed by four weekly doses of 1 mg DMBA/0.1 ml cottonseed oil  administered by gavage. 60 day relaese pellets were implanded by trocar s.c. into scapular region one day after the last dose of DMBA, and again after 60 days

value: mammary tumor

tag: strain

value: FVB

tag: genotype

value: WT


title: 1507_Placebo_Week 2

source_name: Patient: 1507, Dosage: Placebo, Time: Week 2


title: 1507_Placebo_Week 0

source_name: Patient: 1507, Dosage: Placebo, Time: Week 0


title: 1613_Placebo_Week 0

source_name: Patient: 1613, Dosage: Placebo, Time: Week 0


title: mammary tumor _PAX8-RU486 2.5mg

description: Gene expression data from MP-DMBA induced mammary tumor in MMTV-PAX8PPARg mice treated with 2.5 mg RU-486

source_name: MMTV-PAX8PPARg group, treated with MP-DMBA and then were implanted with 60 day release 2.5mg RU-486 pellet


title: C306 (Drought tolerant) drought condition rep 2

city: new delhi

first: suhas

middle: baliram

last: kadam

state: delhi

address: lbs pusa campas

department: biotechnology

institute: NRCPb

description: Gene expression profile of drought tolerant wheat cultivar in drought condition

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2

organism: Triticum aestivum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Sigma) RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

tag: cultivar

value: Flag leaf at reproductive stage

tag: drought susceptibility

value: Drought tolerant


title: C306 (Drought tolerant)drought condition rep 3

tag: tissue


title: Bulk (Drought tolerant) drought condition rep 3

description: Gene expression profile of drought tolerant bulk (10 RILs) wheat cultivar in drought condition

value: progeny bulks


title: 1503_Placebo_Week 0

source_name: Patient: 1503, Dosage: Placebo, Time: Week 0


title: Bulk (Drought tolerant) drought condition  rep 2


title: Bulk (Drought tolerant) drought condition rep 1


title: mammary tumor _PAX8-Placebo

description: Gene expression data from MP-DMBA induced mammary tumor in MMTV-PAX8PPARg mice treated with Placebo

source_name: MMTV-PAX8PPARg group, treated with MP-DMBA and then were implanted with Placebo pellet


title: WT_MEF_VN_24H_a

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: Sample name: 251486819410_1_1

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. RNA sample was hybridized to one Agilent 4X44K mouse whole genome array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 10.7.3.1) and the GE1_107_Sep09 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: WT, IFNgR-/-, IFNabR-/-, or IFNabgR-/- MEFs were mock-infected or infected with the A/WSN/33 (WSN), reconstructed 1918 (r1918), or A/Vietnam/1203/2004 (VN1203) strains of influenza virus at an MOI of 2 PFU/cell.  At 24 h p.i., cells were harvested for microarray analysis.

extract_protocol: RNA was isolated using Qiagen RNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). The quantity of total RNA was determined by spectrophotometry using a NanoDrop ND-1000 fluorospectrometer. Contaminating DNA was removed by treating samples with RNase-free DNase and removal reagents (Ambion).

treatment_protocol: Cells were lysed in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M  -mercaptoethanol) and stored at -80 degrees C prior to RNA extraction.

tag: background strain

tag: genotype/variation

value: Wild type

tag: experiment

value: a

value: embryonic fibroblasts

tag: sample collection time post infection

tag: virus strain

tag: infection

value: influenza infected


title: 1503_Placebo_Week 2

source_name: Patient: 1503, Dosage: Placebo, Time: Week 2

value: Time:Week 2


title: C306 (Drought tolerant) drought condition rep 1


title: AEBP1 siRNA 1, biological rep1

description: silenced RNA 46 hrs post transfection

source_name: AEBP1 siRNA 1, biological rep1

tag: cell line


title: Scrambled siRNA 4, biological rep4

description: control RNA 46 hrs post transfection

source_name: Scrambled siRNA 4, biological rep4


title: 1405_Placebo_Week 2

source_name: Patient: 1405, Dosage: Placebo, Time: Week 2


title: WT_MEF_WSN_24H_b

description: Sample name: 251486819414_1_2

value: b

tag: cell type

value: WSN


title: Bulk (Drought susceptible) drought condition rep 3

description: Gene expression profile of drought susceptible bulk (10 RILs) wheat cultivar in drought condition

value: Drought susceptible


title: mammary tumor _WT-Placebo

description: Gene expression data from MP-DMBA induced mammary tumor in WT mice treated with Placebo

source_name: Wild-type group, treated with MP-DMBA and then were implanted with Placebo pellet

tag: treatment


title: Scrambled siRNA 2, biological rep2

description: control RNA 46 hrs post transfection

source_name: Scrambled siRNA 2, biological rep2


title: WT_MEF_Mock_24H_b

description: Sample name: 251486814093_1_2

value: mock infected


title: Scrambled siRNA 3, biological rep3

description: control RNA 46 hrs post transfection

source_name: Scrambled siRNA 3, biological rep3


title: Bulk (Drought susceptible) drought condition rep 1


title: Scrambled siRNA 1, biological rep1

description: control RNA 46 hrs post transfection

source_name: Scrambled siRNA 1, biological rep1


title: Bulk (Drought susceptible) drought condition rep 2


title: 1405_Placebo_Week 0

source_name: Patient: 1405, Dosage: Placebo, Time: Week 0

tag: dosage

value: Time:Week 0


title: 1108_Placebo_Week 0

source_name: Patient: 1108, Dosage: Placebo, Time: Week 0

tag: patient


title: WT_MEF_18_24H_a

description: Sample name: 251486819474_1_1


title: DN-anti-DLL4-3

city: Tarrytown

first: Wen

last: Zhang

address: 777 Old Saw Mill River Road

institute: Regeneron Pharma.

description: DN (CD4-CD8-) cells sorted from total thymocytes treated with anti-DLL4

hyb_protocol: Cy3 labeled cRNA from each sample was then hybridized to a custom Agilent array comprising of 43538 60mer oligos covering mouse transcriptome.  The hybridization and wash of the arrays were performed according to the Agilent protocol.

scan_protocol: Arrays were scanned on an Agilent Microarray scanner.

data_processing: The data was extracted from scanned array images using Agilent Feature Extraction Software 9.5. Global normalization was done by normalizing each chip to the 75 percentile of the measurements taken from that chip.

label_protocol: RNA from each sample was amplified by TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit (Epicentre).  Cy3-CTP was incorporated into amplified cRNA from 500 ng of total RNA using QuickAmp RNA Amplification Kit (Agilent).

extract_protocol: Samples were transfered to TRIzol (Invitrogen). Total RNA was isolated according to manufacturer´s instructions.

treatment_protocol: C57BL/6 mice were injected with anti-DLL4 or isotype control mAb. Two weeks later, mice were sacrified and thymi were harvested. Total thymocytes were isolated from treatment and control animals. The rest of the thymocytes were stained and two cell subsets were sorted based on the expression of CD4 and CD8 cell surface markers: DN cells (CD4-CD8-) and DN1(CD4-CD8-CD44+CD25-).

value: thymus


title: 1803_150 mg_Week 0

source_name: Patient: 1803, Dosage: 150 mg, Time: Week 0

value: Dosage:150 mg

tag: time


title: 1108_Placebo_Week 2

source_name: Patient: 1108, Dosage: Placebo, Time: Week 2


title: DN-isotype control-3

description: DN (CD4-CD8-) cells sorted from total thymocytes treated with isotype control

source_name: DN-isotype control

tag: strain


title: DN-isotype control-1


title: WL711 (Drought susceptible) drought condition rep 2

description: Gene expression profile of drought susceptible wheat cultivar in drought condition


title: WT_MEF_Mock_24H_a

description: Sample name: 251486819472_1_3


title: 1304_Placebo_Week 0

source_name: Patient: 1304, Dosage: Placebo, Time: Week 0


title: WL711 (Drought susceptible) drought condition rep 1


title: WL711 (Drought susceptible) drought condition rep 3


title: IFN-G-KO_MEF_WSN_24H_b

description: Sample name: 251486814093_1_3

value: Gamma IFNR KO


title: IFN-G-KO_MEF_Mock_24H_a

description: Sample name: 251486819413_1_1


title: DN-anti-DLL4-1


title: DN-anti-DLL4-2


title: 1710_150 mg_Week 0

source_name: Patient: 1710, Dosage: 150 mg, Time: Week 0


title: IFN-G-KO_MEF_Mock_24H_b

description: Sample name: 251486814095_1_1


title: 1615_150 mg_Week 2

source_name: Patient: 1615, Dosage: 150 mg, Time: Week 2


title: Bulk (Drought tolerant) irrigated condition rep 3

description: Gene expression profile of drought tolerant bulk (10 RILs) wheat cultivar in irrigated condition


title: Bulk (Drought tolerant) irrigated  condition rep 2


title: DN-isotype control-2


title: 1710_150 mg_Week 2

source_name: Patient: 1710, Dosage: 150 mg, Time: Week 2


title: DN1-isotype controls-1

description: DN1 (CD4-CD8- CD44+CD25-) cells sorted from total thymocytes treated with isotype control

source_name: DN1-isotype controls


title: Bulk (Drought tolerant) irrigated condition rep 1


title: IFN-AB-KO_MEF_WSN_24H_b

description: Sample name: 251486819414_1_1

value: Alpha/beta IFNR KO


title: IFN-G-KO_MEF_VN_24H_a

description: Sample name: 251486819411_1_3


title: 1610_150 mg_Week 2

source_name: Patient: 1610, Dosage: 150 mg, Time: Week 2


title: 1615_150 mg_Week 0

source_name: Patient: 1615, Dosage: 150 mg, Time: Week 0


title: C306 (Drought tolerant) irrigated condition rep 2

description: Gene expression profile of drought tolerant wheat cultivar in irrigated condition

value: Flag leaf at reproductive stage


title: 1611_150 mg_Week 0

source_name: Patient: 1611, Dosage: 150 mg, Time: Week 0


title: DN1-isotype controls-2


title: 1610_150 mg_Week 0

source_name: Patient: 1610, Dosage: 150 mg, Time: Week 0


title: IFN-G-KO_MEF_18_24H_a

description: Sample name: 251486819475_1_3


title: IFN-AB-KO_MEF_VN_24H_a

description: Sample name: 251486819410_1_4


title: DN1-anti-DLL4-3

description: DN1 (CD4-CD8- CD44+CD25-) cells sorted from total thymocytes treated with anti-DLL4


title: C306 (Drought tolerant) irrigated condition rep 1

value: Drought tolerant


title: DN1-anti-DLL4-2


title: C306 (Drought tolerant) irrigated  condition rep 3


title: IFN-AB-KO_MEF_Mock_24H_b

description: Sample name: 251486814093_1_4


title: IFN-AB-KO_MEF_18_24H_a

description: Sample name: 251486819474_1_4


title: Bulk (Drought susceptible) irrigated condition rep 3

description: Gene expression profile of drought susceptible bulk (10 RILs) wheat cultivar in irrigated condition

value: progeny bulks


title: IFN-AB-KO_MEF_Mock_24H_a

description: Sample name: 251486819473_1_2


title: DN1-anti-DLL4-1


title: Thymocytes-isotype control-4

description: Total thymocytes from thymus treated with isotype control for two weeks

source_name: Thymocytes-isotype control


title: 1208_150 mg_Week 0

source_name: Patient: 1208, Dosage: 150 mg, Time: Week 0


title: Thymocytes-anti-DLL4-2

description: Total thymocytes from thymus treated with anti-DLL4 for two weeks


title: Normal Adjacent sample 268

status: Public on Apr 29 2012

type: genomic

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

institute: University of Pittsburgh Medical Center

hyb_protocol: Samples were hybridized on Genome-Wide SNP 6.0 arrays for 18 hours at 500C with rotation (60 rpm) in an Affymetrix Gene Chip Hybridization Oven (Model 640).

scan_protocol: Arrays were washed, stained and scanned according to the Affymetrix Genome-Wide SNP 6.0 protocol using the Affymetrix GeneChip Fluidics Station (Model 450), GeneChip Scanner 3000 7G, and GeneChip Command Console (v3.0.2) software.

data_processing:
The Affymetrix Genotyping Console (v3.0.2) was used to generate a SNP call for each probe set on each array. SNP calls were determined for an average of 96.78% (S.D.= 4.27%) of the array probe sets per specimen throughout the study. Affymetrix CEL and CHP files were transferred to Partek Genomics Suite v6.5 (Partek Inc, St Louis, MI) for copy number and loss of heterozygosity (LOH) analysis respectively. CEL files were imported using the default setting, which adjusts hybridized intensities based on fragment length and probe sequence. Copy number was generated by comparing the hybridized intensities of each array to the laboratory normal tissue reference set (n=31) eliminating inter-laboratory variability introduced by comparison to other databases such as the HapMap. Copy number measurements were smoothed based on local GC content using a 1 Mb window. Partek segmentation algorithm was used to identify regions of significant copy number variation (CNV) from normal consisting of a minimum of 30 genomic markers and p-value of less than .001, with signal to noise and expected range set to 0.3. The median length of inter-marker spacing on the SNP 6.0 array is 680 bp with a median length of a 30 marker region approximately 20Kb. Regions of LOH were identified for tumors with a matched normal pair (2 chromophobe, 1 clear cell, 1 papillary type 1, and 1 papillary type 2 sample) using the Hidden Markov Model in Partek Genomics Suite.
There is copy number data for each tumor sample supplied in the matrix. This copy number data was created using the laboratory unpaired normal reference set (available in CEL file format) and has been GC corrected.

molecule: genomic DNA

source_name: Lung, Normal Adjacent

label_protocol: Sty I and Nsp I restriction enzymes (New England Biolabs, Ipswich, MA) were used to separately digest 250ng of DNA resulting in a total digest of 500 ng of whole genomic DNA per sample. Each sample was ligated with the appropriate adaptor (Sty or Nsp) provided in the Affymetrix 6.0 protocol and a total of seven PCR reactions were performed per sample (three Sty I restriction digest/ligation DNA reactions and four Nsp I restriction digest/ligation DNA reactions) and pooled into one tube with a total volume of 700µl. Purification of resulting PCR products was performed using the protocol associated with the Affymetrix Cytogenetics Copy Number Assay which required the use of Agencourt AMPure beads (Beckman Coulter, Danvers, MA). Each pooled sample was fragmented with DNAse1, biotinylated and end-labeled.

extract_protocol: Genomic DNA was purified from frozen samples following the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Briefly, 0.25 mg of frozen tissue was placed in Qiagen buffer and Proteinase K (>600 mAU/ml) and incubated for 3 hours at 150 rpm. Following tissue lysis and protein removal, genomic DNA was eluted in 100µl of Buffer AE (Qiagen). Only samples with a spectrophotometric absorption ratio of 260/280 > 1.8 (Nanodrop ND-1000 spectrophotometer, NanoDrop , Wilmington, DE) were included in subsequent assays. Purified genomic DNA was evaluated using agarose gels (2%) or microfluidic chips (12000 DNA Chip, Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA) to confirm that the DNA from each specimen was of high molecular weight (> 10Kb) with minimal detectable degradation.

tag: gender

value: M


title: 1209_150 mg_Week 2

source_name: Patient: 1209, Dosage: 150 mg, Time: Week 2


title: Normal Adjacent sample 267


title: Thymocytes-isotype control-3


title: 1209_150 mg_Week 0

source_name: Patient: 1209, Dosage: 150 mg, Time: Week 0


title: Bulk (Drought susceptible) irrigated  condition rep 1

tag: cultivar


title: Thymocytes-isotype control-2


title: WL711 (Drought susceptible) irrigated condition rep 3

description: Gene expression profile of drought susceptible wheat cultivar in irrigated condition

tag: drought susceptibility


title: Thymocytes-isotype control-1

tag: tissue


title: IFN-ABG-KO_MEF_VN_24H_a

description: Sample name: 251486819412_1_2

tag: background strain

value: Alpha/beta/gamma IFNR KO

value: a


title: IFN-ABG-KO_MEF_18_24H_a

description: Sample name: 251486819476_1_2

tag: genotype/variation

value: embryonic fibroblasts

value: influenza infected


title: WL711 (Drought susceptible) irrigated condition rep 1


title: IFN-ABG-KO_MEF_Mock_24H_b

description: Sample name: 251486815520_1_2

tag: experiment

value: b


title: Normal Adjacent sample 265


title: Normal Adjacent sample 264

source_name: Kidney, Normal Adjacent

value: F


title: Normal Adjacent sample 266


title: 1208_150 mg_Week 2

source_name: Patient: 1208, Dosage: 150 mg, Time: Week 2

value: Time:Week 2


title: Bulk (Drought susceptible) irrigated condition rep 2

value: Drought susceptible


title: Thymocytes-anti-DLL4-3


title: Thymocytes-anti-DLL4-1


title: WL711 (Drought susceptible) irrigated condition rep 2


title: IFN-ABG-KO_MEF_Mock_24H_a

description: Sample name: 251486819413_1_4

tag: sample collection time post infection

value: mock infected


title: 1207_150 mg_Week 0

source_name: Patient: 1207, Dosage: 150 mg, Time: Week 0

value: Time:Week 0


title: Normal Adjacent sample 238


title: Normal Adjacent sample 237


title: Normal Adjacent sample 523


title: Normal Adjacent sample 239


title: Normal Adjacent sample 242


title: Normal Adjacent sample 206

source_name: Thyroid, Normal Adjacent


title: Normal Adjacent sample 205


title: IFN-ABG-KO_MEF_WSN_24H_b

description: Sample name: 251486815539_1_1

tag: virus strain

value: WSN


title: Normal Adjacent sample 207


title: Normal Adjacent sample 330


title: Normal Adjacent sample 338


title: Normal Adjacent sample 342


title: Normal Adjacent sample 354


title: Normal Adjacent sample 340


title: Normal Adjacent sample 521


title: Normal Adjacent sample 335


title: Normal Adjacent sample 347


title: Normal Adjacent sample 360


title: Normal Adjacent sample 520


title: Normal Adjacent sample 522


title: Normal Adjacent sample 269


title: Normal Adjacent sample 518


title: Normal Adjacent sample 271


title: Normal Adjacent sample 358


title: Normal Adjacent sample 274


title: Normal Adjacent sample 203


title: Normal Adjacent sample 204


title: 1207_150 mg_Week 2

source_name: Patient: 1207, Dosage: 150 mg, Time: Week 2

value: Dosage:150 mg


title: Treg Trim28 conditional KO rep2

city: Kyoto

first: Tasuku

last: Honjo

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Kyoto University

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slide were washed and then scanned with an Agilent G2505B scanner

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software(v9.5).  The resulting data were imported into Expressionist and quantile normalized intensities were exported.

source_name: Trim28 conditional KO mice Treg cell, replicate 2

label_protocol: Cy3 labeled cRNA was produced using Agilent Low Input QuickAmp Labeling Kit according to manufacturer's protocol.

growth_protocol: Mice were maintained under specific pathogen-free conditions according to institutional guidelines under approved protocols in Kyoto University.

extract_protocol: Total RNAs were extracted with Qiagen RNeasy mini kit with on-column DNaseI treatment.  RNA quality was assessed using Agilent 2100 Bioanalyzer according to manufacturer's instructions.

treatment_protocol: Stimulations were done with plate-coated anti-CD3(1mg/ml) and anti-CD28 (1mg/ml)for 13 hours.

value: Female

tag: age

value: 6 weeks old

value: Treg

value: TCR-stimulated

tag: genotype


title: Treg Trim28 conditional KO rep4

source_name: Trim28 conditional KO mice Treg cell, replicate 4

value: 7 weeks old

tag: cell type


title: Treg Trim28 conditional KO rep3

source_name: Trim28 conditional KO mice Treg cell, replicate 3

tag: treatment


title: Treg WT rep4

source_name: wild type Treg, replicate 4

value: unstimulated

value: WT


title: Treg Trim28 conditional KO rep1

source_name: Trim28 conditional KO mice Treg cell, replicate 1


title: Treg WT rep2

source_name: wild type Treg, replicate 2


title: Treg WT rep1

source_name: wild type Treg, replicate 1


title: Treg WT rep3

source_name: wild type Treg, replicate 3


title: Trim28CKO TCR-stimulated CD4 positve T cell rep4

source_name: Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 4

value: CD4 positive T cell


title: Trim28CKO TCR-stimulated CD4 positve T cell rep3

source_name: Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 3


title: Trim28CKO TCR-stimulated CD4 positve T cell rep2

source_name: Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 2


title: Clear Cell sample 230

source_name: Renal neoplasm, Clear Cell

value: M


title: Trim28CKO TCR-stimulated CD4 positve T cell rep1

source_name: Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 1


title: Clear Cell sample 514


title: Trim28CKO unstimulated CD4 positve T cell rep3

source_name: Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 3


title: Chromophobe sample 509

source_name: Renal neoplasm, Chromophobe


title: Papillary Type 2 sample 227

source_name: Renal neoplasm, Papillary Type 2


title: Papillary Type 1 sample 223

source_name: Renal neoplasm, Papillary Type 1


title: Clear Cell sample 513


title: Papillary Type 1 sample 224


title: Trim28CKO unstimulated CD4 positve T cell rep1

source_name: Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 1


title: Oncocytoma sample 526

source_name: Renal neoplasm, Oncocytoma


title: Chromophobe sample 512


title: Trim28CKO unstimulated CD4 positve T cell rep2

source_name: Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 2


title: Trim28CKO unstimulated CD4 positve T cell rep4

source_name: Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 4


title: Chromophobe sample 511


title: CD positive WT T cell TCR-stimulated rep4

source_name: wild type naïve CD4 positive cell, TCR-stimulated, replicate 4


title: Chromophobe sample 510


title: Papillary Type 1 sample 531


title: Papillary Type 2 sample 532


title: CD positive WT T cell TCR-stimulated rep3

source_name: wild type naïve CD4 positive cell, TCR-stimulated, replicate 3


title: Chromophobe sample 508


title: Oncocytoma sample 221


title: CAOV-3_No

city: Richmond

first: Jessica

last: Bell

state: VA

address: 1101 E. Marshall St.

institute: VCU

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Ovarian Cancer CAOV-3 cells untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Human ovarian cancer cells were cultured in 50% MCDB 105/50% M199 medium, pH 7.2, 5% low endotoxin FBS, 2 mM L-glutamine, and 50 ug/mL gentamicin.

treatment_protocol: polyriboinosinic:polyribocytidylic acid (pI:pC) was purchased from Sigma-Aldrich and was added to the culture medium at various concentrations.

tag: cell line


title: Papillary Type 2 sample 226


title: Papillary Type 2 sample 229


title: Papillary Type 2 sample 530


title: Papillary Type 2 sample 228


title: Papillary Type 1 sample 529


title: CD positive WT T cell TCR-stimulated rep1

source_name: wild type naïve CD4 positive cell, TCR-stimulated, replicate 1


title: Papillary Type 1 sample 528


title: CD positive WT T cell TCR-stimulated rep2

source_name: wild type naïve CD4 positive cell, TCR-stimulated, replicate 2


title: Oncocytoma sample 524


title: DOV-13_Yes

source_name: Ovarian Cancer DOV-13 cells treated with pI:pC


title: CD positive WT T cell unstimulated rep3

source_name: wild type naïve CD4 positive cell, unstimulated, replicate 3


title: CD positive WT T cell unstimulated rep4

source_name: wild type naïve CD4 positive cell, unstimulated, replicate 4


title: CD positive WT T cell unstimulated rep1

source_name: wild type naïve CD4 positive cell, unstimulated, replicate 1


title: Oncocytoma sample 525


title: Oncocytoma sample 527


title: Clear Cell sample 516

source_name: Renal neoplasm, Clear Cell


title: OVCAR-3_Yes

source_name: Ovarian Cancer OVCAR-3 cells treated with pI:pC


title: bipolar sperm29

status: Public on Apr 28 2012

city: Toronto

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

country: Canada

institute: Centre for Addiction and Mental Health

description: Sperm29 vs. common reference pool

hyb_protocol: The enriched PCR products were hybridized overnight at 48°C onto the 8.1k human CpG island microarray (Microarray Facility, University Health Network, Toronto) as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .

scan_protocol: The arrays were scanned using the Genepix 4000B scanner and Genepix Pro 6.0 (Axon Instruments). The automated photomultiplier (PMT) function of the scanner was used to optimize signal intensity and channel balances.

data_processing: Linear Models for Microarray Data (LIMMA) package (Bioconductor) for R was used for background correction, normalization, and to extract the signal intensities. Briefly, normexp was used for background correction, print-tip loess was used for within-array normalization, and Gquantile was used for between-array normalization.

source_name: sperm, bipolar

label_protocol: 1 μg of purified enriched PCR products were fluorescently labelled with Cy3 (Roche) for the reference and with Cy5 (Roche) for the sample, as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .

extract_protocol: The samples were first digested using proteinase K (20mg/ml) and lysis buffer mixture at 55°C overnight.  A mixture of phenol, chloroform, and iso-amyl alcohol (in ratios of 25:24:1) was used to remove the proteins, followed by two times chloroform wash, precipitation of DNA using cold isopropanol, and a final wash using 70% ethanol.  After the extraction, the DNA samples were suspended in 0.1M Tris-EDTA buffer and were kept in -80°C for storage prior to use.  The purity and the concentrations of DNA were checked using a UV spectrophotometer (Nanodrop ND1000).

value: sperm

tag: disease status

value: bipolar

source_name: sperm, common reference pool

tag: sample type

value: common reference pool


title: bipolar sperm28

description: Sperm28 vs. common reference pool


title: bipolar sperm30

description: Sperm30 vs. common reference pool


title: OVCAR-3_No

source_name: Ovarian Cancer OVCAR-3 cells untreated


title: bipolar sperm32

description: Sperm32 vs. common reference pool


title: bipolar sperm31

description: Sperm31 vs. common reference pool


title: CTRL(F)

city: Shanghai

first: Yahong

last: Jiang

address: 2140 Xietu Road

institute: Shanghai Institute of Planned Parenthood Research

description: Cells transfected with control siRNA

scan_protocol: Standard Illumina scanning protocol

data_processing: Total RNA extracted from HTR-8/SVneo cells was genotyped using Human WG-6 v3 BeadChips (Illumina).

source_name: Trophoblast cells from human first-trimester placenta

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

growth_protocol: HTR-8/SVneo cells were routinely maintained in RPMI1640 medium containing 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 2 mM L-glutamine, 100 μg/ml streptomycin, and 100 U/ml penicillin.

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: HTR-8/SVneo cells were transfected with SPARC siRNA or a 25-nucleotide universal negative control siRNA using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s protocol. Seventy-two hours after transfection, cells were harvested.

tag: tranfected

value: control siRNA


title: bipolar sperm26

description: Sperm26 vs. common reference pool


title: SPARC(E)

description: Cells transfected with SPARC siRNA

value: SPARC siRNA


title: bipolar sperm25

description: Sperm25 vs. common reference pool


title: bipolar sperm33

description: Sperm33 vs. common reference pool


title: SKOV-3_No

source_name: Ovarian Cancer SKOV-3 cells untreated


title: CAOV-3_Yes

source_name: Ovarian Cancer CAOV-3 cells treated with pI:pC


title: control sperm20

description: Sperm20 vs. common reference pool

source_name: sperm, control

value: control


title: control sperm19

description: Sperm19 vs. common reference pool


title: control sperm22

description: Sperm22 vs. common reference pool


title: control sperm16

description: Sperm16 vs. common reference pool


title: control sperm21

description: Sperm21 vs. common reference pool


title: control sperm15

description: Sperm15 vs. common reference pool


title: bipolar sperm24

description: Sperm24 vs. common reference pool


title: bipolar sperm23

description: Sperm23 vs. common reference pool


title: bipolar sperm11

description: Sperm11 vs. common reference pool


title: control sperm10

description: Sperm10 vs. common reference pool


title: DOV-13_No

source_name: Ovarian Cancer DOV-13 cells untreated


title: Clear Cell sample 515

tag: gender


title: control sperm9

description: Sperm9 vs. common reference pool


title: bipolar sperm6

description: Sperm6 vs. common reference pool


title: bipolar sperm7

description: Sperm7 vs. common reference pool


title: control sperm18

description: Sperm18 vs. common reference pool


title: control sperm8

description: Sperm8 vs. common reference pool


title: control sperm5

description: Sperm5 vs. common reference pool


title: bipolar sperm4

description: Sperm4 vs. common reference pool


title: control sperm12

description: Sperm12 vs. common reference pool


title: SKOV-3_Yes

source_name: Ovarian Cancer SKOV-3 cells treated with pI:pC


title: control sperm1

description: Sperm1 vs. common reference pool


title: Papillary Type 1 sample 222

source_name: Renal neoplasm, Papillary Type 1


title: control sperm2

description: Sperm2 vs. common reference pool


title: control prefrontal cortex SU35

description: Quebec Suicide Brain Bank prefrontal cortex35 vs. common reference pool

source_name: prefrontal cortex, control

value: pre-frontal cortex

source_name: prefrontal cortex, common reference pool


title: control prefrontal cortex SU33

description: Quebec Suicide Brain Bank prefrontal cortex33 vs. common reference pool


title: depression prefrontal cortex SU34

description: Quebec Suicide Brain Bank prefrontal cortex34 vs. common reference pool

source_name: prefrontal cortex, depression

value: depression


title: depression prefrontal cortex SU32

description: Quebec Suicide Brain Bank prefrontal cortex32 vs. common reference pool


title: control prefrontal cortex SU31

description: Quebec Suicide Brain Bank prefrontal cortex31 vs. common reference pool


title: bipolar sperm13

description: Sperm13 vs. common reference pool


title: control prefrontal cortex SU36

description: Quebec Suicide Brain Bank prefrontal cortex36 vs. common reference pool


title: control sperm3

description: Sperm3 vs. common reference pool


title: control prefrontal cortex SU30

description: Quebec Suicide Brain Bank prefrontal cortex30 vs. common reference pool


title: control prefrontal cortex SU28

description: Quebec Suicide Brain Bank prefrontal cortex28 vs. common reference pool


title: depression prefrontal cortex SU27

description: Quebec Suicide Brain Bank prefrontal cortex27 vs. common reference pool


title: control prefrontal cortex SU29

description: Quebec Suicide Brain Bank prefrontal cortex29 vs. common reference pool


title: depression prefrontal cortex SU24

description: Quebec Suicide Brain Bank prefrontal cortex24 vs. common reference pool


title: depression prefrontal cortex SU23

description: Quebec Suicide Brain Bank prefrontal cortex23 vs. common reference pool


title: control prefrontal cortex SU25

description: Quebec Suicide Brain Bank prefrontal cortex25 vs. common reference pool


title: depression prefrontal cortex SU26

description: Quebec Suicide Brain Bank prefrontal cortex26 vs. common reference pool


title: depression prefrontal cortex SU22

description: Quebec Suicide Brain Bank prefrontal cortex22 vs. common reference pool


title: depression prefrontal cortex SU20

description: Quebec Suicide Brain Bank prefrontal cortex20 vs. common reference pool


title: depression prefrontal cortex SU21

description: Quebec Suicide Brain Bank prefrontal cortex21 vs. common reference pool


title: control prefrontal cortex SU15

description: Quebec Suicide Brain Bank prefrontal cortex15 vs. common reference pool


title: control prefrontal cortex SU11

description: Quebec Suicide Brain Bank prefrontal cortex11 vs. common reference pool


title: bipolar sperm27

description: Sperm27 vs. common reference pool


title: control prefrontal cortex SU17

description: Quebec Suicide Brain Bank prefrontal cortex17 vs. common reference pool


title: depression prefrontal cortex SU16

description: Quebec Suicide Brain Bank prefrontal cortex16 vs. common reference pool


title: depression prefrontal cortex SU18

description: Quebec Suicide Brain Bank prefrontal cortex18 vs. common reference pool


title: depression prefrontal cortex SU14

description: Quebec Suicide Brain Bank prefrontal cortex14 vs. common reference pool


title: depression prefrontal cortex SU19

description: Quebec Suicide Brain Bank prefrontal cortex19 vs. common reference pool


title: depression prefrontal cortex SU10

description: Quebec Suicide Brain Bank prefrontal cortex10 vs. common reference pool


title: depression prefrontal cortex SU13

description: Quebec Suicide Brain Bank prefrontal cortex13 vs. common reference pool


title: control prefrontal cortex SU12

description: Quebec Suicide Brain Bank prefrontal cortex12 vs. common reference pool


title: CD positive WT T cell unstimulated rep2

source_name: wild type naïve CD4 positive cell, unstimulated, replicate 2

tag: strain

value: Female


title: control prefrontal cortex SU03

description: Quebec Suicide Brain Bank prefrontal cortex3 vs. common reference pool


title: control prefrontal cortex SU06

description: Quebec Suicide Brain Bank prefrontal cortex6 vs. common reference pool


title: control prefrontal cortex SU08

description: Quebec Suicide Brain Bank prefrontal cortex8 vs. common reference pool


title: control prefrontal cortex SU07

description: Quebec Suicide Brain Bank prefrontal cortex7 vs. common reference pool


title: depression prefrontal cortex SU04

description: Quebec Suicide Brain Bank prefrontal cortex4 vs. common reference pool


title: depression prefrontal cortex SU02

description: Quebec Suicide Brain Bank prefrontal cortex2 vs. common reference pool


title: depression prefrontal cortex SU01

description: Quebec Suicide Brain Bank prefrontal cortex1 vs. common reference pool


title: control prefrontal cortex SU09

description: Quebec Suicide Brain Bank prefrontal cortex9 vs. common reference pool


title: control prefrontal cortex SU05

description: Quebec Suicide Brain Bank prefrontal cortex5 vs. common reference pool


title: control prefrontal cortex35

description: Stanley Medical Research Institute prefrontal cortex35 vs. common reference pool


title: depression prefrontal cortex32

description: Stanley Medical Research Institute prefrontal cortex32 vs. common reference pool


title: depression prefrontal cortex34

description: Stanley Medical Research Institute prefrontal cortex34 vs. common reference pool


title: depression with psychosis prefrontal cortex29

description: Stanley Medical Research Institute prefrontal cortex29 vs. common reference pool

value: depression with psychosis


title: control prefrontal cortex33

description: Stanley Medical Research Institute prefrontal cortex33 vs. common reference pool


title: depression prefrontal cortex30

description: Stanley Medical Research Institute prefrontal cortex30 vs. common reference pool


title: depression prefrontal cortex31

description: Stanley Medical Research Institute prefrontal cortex31 vs. common reference pool


title: control prefrontal cortex28

description: Stanley Medical Research Institute prefrontal cortex28 vs. common reference pool


title: depression with psychosis prefrontal cortex27

description: Stanley Medical Research Institute prefrontal cortex27 vs. common reference pool


title: depression with psychosis prefrontal cortex25

description: Stanley Medical Research Institute prefrontal cortex25 vs. common reference pool


title: control prefrontal cortex26

description: Stanley Medical Research Institute prefrontal cortex26 vs. common reference pool


title: depression prefrontal cortex24

description: Stanley Medical Research Institute prefrontal cortex24 vs. common reference pool


title: control prefrontal cortex23

description: Stanley Medical Research Institute prefrontal cortex23 vs. common reference pool


title: control prefrontal cortex19

description: Stanley Medical Research Institute prefrontal cortex19 vs. common reference pool


title: depression prefrontal cortex18

description: Stanley Medical Research Institute prefrontal cortex18 vs. common reference pool


title: depression prefrontal cortex20

description: Stanley Medical Research Institute prefrontal cortex20 vs. common reference pool


title: depression prefrontal cortex21

description: Stanley Medical Research Institute prefrontal cortex21 vs. common reference pool


title: depression prefrontal cortex22

description: Stanley Medical Research Institute prefrontal cortex22 vs. common reference pool


title: depression with psychosis prefrontal cortex14

description: Stanley Medical Research Institute prefrontal cortex14 vs. common reference pool


title: depression with psychosis prefrontal cortex13

description: Stanley Medical Research Institute prefrontal cortex13 vs. common reference pool


title: control prefrontal cortex8

description: Stanley Medical Research Institute prefrontal cortex8 vs. common reference pool


title: control prefrontal cortex6

description: Stanley Medical Research Institute prefrontal cortex6 vs. common reference pool


title: depression with psychosis prefrontal cortex9

description: Stanley Medical Research Institute prefrontal cortex9 vs. common reference pool


title: depression with psychosis prefrontal cortex10

description: Stanley Medical Research Institute prefrontal cortex10 vs. common reference pool


title: depression with psychosis prefrontal cortex1

description: Stanley Medical Research Institute prefrontal cortex1 vs. common reference pool


title: control prefrontal cortex11

description: Stanley Medical Research Institute prefrontal cortex11 vs. common reference pool


title: depression prefrontal cortex16

description: Stanley Medical Research Institute prefrontal cortex16 vs. common reference pool


title: depression prefrontal cortex12

description: Stanley Medical Research Institute prefrontal cortex12 vs. common reference pool


title: depression with psychosis prefrontal cortex7

description: Stanley Medical Research Institute prefrontal cortex7 vs. common reference pool


title: depression prefrontal cortex17

description: Stanley Medical Research Institute prefrontal cortex17 vs. common reference pool


title: control prefrontal cortex2

description: Stanley Medical Research Institute prefrontal cortex2 vs. common reference pool


title: depression prefrontal cortex5

description: Stanley Medical Research Institute prefrontal cortex5 vs. common reference pool


title: control prefrontal cortex4

description: Stanley Medical Research Institute prefrontal cortex4 vs. common reference pool


title: Netherlands Twin Registry monozygotic twin100a depression white blood cells199

description: Netherlands Twin Registry monozygotic twin100a vs. common reference pool

source_name: white blood cells, depression

value: white blood cells

tag: individual

tag: twin pair

source_name: white blood cells, common reference pool


title: Netherlands Twin Registry monozygotic twin100b depression white blood cells200

description: Netherlands Twin Registry monozygotic twin100b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin99b depression white blood cells198

description: Netherlands Twin Registry monozygotic twin99b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin98a depression white blood cells195

description: Netherlands Twin Registry monozygotic twin98a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin98b control white blood cells196

description: Netherlands Twin Registry monozygotic twin98b vs. common reference pool

source_name: white blood cells, control


title: depression with psychosis prefrontal cortex3

description: Stanley Medical Research Institute prefrontal cortex3 vs. common reference pool

tag: tissue


title: Netherlands Twin Registry monozygotic twin96b depression white blood cells192

description: Netherlands Twin Registry monozygotic twin96b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin97b control white blood cells194

description: Netherlands Twin Registry monozygotic twin97b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin99a depression white blood cells197

description: Netherlands Twin Registry monozygotic twin99a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin96a control white blood cells191

description: Netherlands Twin Registry monozygotic twin96a vs. common reference pool


title: control sperm17

description: Sperm17 vs. common reference pool


title: Netherlands Twin Registry monozygotic twin94b depression white blood cells188

description: Netherlands Twin Registry monozygotic twin94b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin97a depression white blood cells193

description: Netherlands Twin Registry monozygotic twin97a vs. common reference pool


title: control sperm14

description: Sperm14 vs. common reference pool


title: Netherlands Twin Registry monozygotic twin95b depression white blood cells190

description: Netherlands Twin Registry monozygotic twin95b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin95a control white blood cells189

description: Netherlands Twin Registry monozygotic twin95a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin90a control white blood cells179

description: Netherlands Twin Registry monozygotic twin90a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin89b depression white blood cells178

description: Netherlands Twin Registry monozygotic twin89b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin94a control white blood cells187

description: Netherlands Twin Registry monozygotic twin94a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin90b depression white blood cells180

description: Netherlands Twin Registry monozygotic twin90b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin91a control white blood cells181

description: Netherlands Twin Registry monozygotic twin91a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin89a control white blood cells177

description: Netherlands Twin Registry monozygotic twin89a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin88b control white blood cells176

description: Netherlands Twin Registry monozygotic twin88b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin91b depression white blood cells182

description: Netherlands Twin Registry monozygotic twin91b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin92a depression white blood cells183

description: Netherlands Twin Registry monozygotic twin92a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin86a control white blood cells171

description: Netherlands Twin Registry monozygotic twin86a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin88a depression white blood cells175

description: Netherlands Twin Registry monozygotic twin88a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin85b depression white blood cells170

description: Netherlands Twin Registry monozygotic twin85b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin87a depression white blood cells173

description: Netherlands Twin Registry monozygotic twin87a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin93b control white blood cells186

description: Netherlands Twin Registry monozygotic twin93b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin87b control white blood cells174

description: Netherlands Twin Registry monozygotic twin87b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin86b depression white blood cells172

description: Netherlands Twin Registry monozygotic twin86b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin93a depression white blood cells185

description: Netherlands Twin Registry monozygotic twin93a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin85a control white blood cells169

description: Netherlands Twin Registry monozygotic twin85a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin84b control white blood cells168

description: Netherlands Twin Registry monozygotic twin84b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin84a depression white blood cells167

description: Netherlands Twin Registry monozygotic twin84a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin82b control white blood cells164

description: Netherlands Twin Registry monozygotic twin82b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin83b control white blood cells166

description: Netherlands Twin Registry monozygotic twin83b vs. common reference pool


title: depression with psychosis prefrontal cortex15

description: Stanley Medical Research Institute prefrontal cortex15 vs. common reference pool


title: Netherlands Twin Registry monozygotic twin80a control white blood cells159

description: Netherlands Twin Registry monozygotic twin80a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin80b depression white blood cells160

description: Netherlands Twin Registry monozygotic twin80b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin92b control white blood cells184

description: Netherlands Twin Registry monozygotic twin92b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin79b control white blood cells158

description: Netherlands Twin Registry monozygotic twin79b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin79a depression white blood cells157

description: Netherlands Twin Registry monozygotic twin79a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin81a control white blood cells161

description: Netherlands Twin Registry monozygotic twin81a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin83a depression white blood cells165

description: Netherlands Twin Registry monozygotic twin83a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin78a control white blood cells155

description: Netherlands Twin Registry monozygotic twin78a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin77b control white blood cells154

description: Netherlands Twin Registry monozygotic twin77b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin78b depression white blood cells156

description: Netherlands Twin Registry monozygotic twin78b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin81b depression white blood cells162

description: Netherlands Twin Registry monozygotic twin81b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin74b control white blood cells148

description: Netherlands Twin Registry monozygotic twin74b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin74a depression white blood cells147

description: Netherlands Twin Registry monozygotic twin74a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin75a depression white blood cells149

description: Netherlands Twin Registry monozygotic twin75a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin72a control white blood cells143

description: Netherlands Twin Registry monozygotic twin72a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin75b control white blood cells150

description: Netherlands Twin Registry monozygotic twin75b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin71b depression white blood cells142

description: Netherlands Twin Registry monozygotic twin71b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin71a control white blood cells141

description: Netherlands Twin Registry monozygotic twin71a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin76a depression white blood cells151

description: Netherlands Twin Registry monozygotic twin76a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin73b control white blood cells146

description: Netherlands Twin Registry monozygotic twin73b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin72b depression white blood cells144

description: Netherlands Twin Registry monozygotic twin72b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin76b control white blood cells152

description: Netherlands Twin Registry monozygotic twin76b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin69a control white blood cells137

description: Netherlands Twin Registry monozygotic twin69a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin69b depression white blood cells138

description: Netherlands Twin Registry monozygotic twin69b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin68b control white blood cells136

description: Netherlands Twin Registry monozygotic twin68b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin70b depression white blood cells140

description: Netherlands Twin Registry monozygotic twin70b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin73a depression white blood cells145

description: Netherlands Twin Registry monozygotic twin73a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin66b depression white blood cells132

description: Netherlands Twin Registry monozygotic twin66b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin70a control white blood cells139

description: Netherlands Twin Registry monozygotic twin70a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin67a depression white blood cells133

description: Netherlands Twin Registry monozygotic twin67a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin67b control white blood cells134

description: Netherlands Twin Registry monozygotic twin67b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin66a control white blood cells131

description: Netherlands Twin Registry monozygotic twin66a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin64b depression white blood cells128

description: Netherlands Twin Registry monozygotic twin64b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin63b depression white blood cells126

description: Netherlands Twin Registry monozygotic twin63b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin63a control white blood cells125

description: Netherlands Twin Registry monozygotic twin63a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin64a control white blood cells127

description: Netherlands Twin Registry monozygotic twin64a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin68a depression white blood cells135

description: Netherlands Twin Registry monozygotic twin68a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin65a depression white blood cells129

description: Netherlands Twin Registry monozygotic twin65a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin60b depression white blood cells120

description: Netherlands Twin Registry monozygotic twin60b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin60a control white blood cells119

description: Netherlands Twin Registry monozygotic twin60a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin77a depression white blood cells153

description: Netherlands Twin Registry monozygotic twin77a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin65b control white blood cells130

description: Netherlands Twin Registry monozygotic twin65b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin61b depression white blood cells122

description: Netherlands Twin Registry monozygotic twin61b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin59b depression white blood cells118

description: Netherlands Twin Registry monozygotic twin59b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin62b control white blood cells124

description: Netherlands Twin Registry monozygotic twin62b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin62a depression white blood cells123

description: Netherlands Twin Registry monozygotic twin62a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin57a control white blood cells113

description: Netherlands Twin Registry monozygotic twin57a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin61a control white blood cells121

description: Netherlands Twin Registry monozygotic twin61a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin53a depression white blood cells105

description: Maudsley Hospital Twin Registry monozygotic twin53a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin59a depression white blood cells117

description: Netherlands Twin Registry monozygotic twin59a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin53b control white blood cells106

description: Maudsley Hospital Twin Registry monozygotic twin53b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin57b depression white blood cells114

description: Netherlands Twin Registry monozygotic twin57b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin56a depression white blood cells111

description: Netherlands Twin Registry monozygotic twin56a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin54a control white blood cells107

description: Maudsley Hospital Twin Registry monozygotic twin54a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin58a control white blood cells115

description: Netherlands Twin Registry monozygotic twin58a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin56b control white blood cells112

description: Netherlands Twin Registry monozygotic twin56b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin52a depression white blood cells103

description: Maudsley Hospital Twin Registry monozygotic twin52a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin51b control white blood cells102

description: Maudsley Hospital Twin Registry monozygotic twin51b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin52b control white blood cells104

description: Maudsley Hospital Twin Registry monozygotic twin52b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin50a control white blood cells99

description: Maudsley Hospital Twin Registry monozygotic twin50a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin50b depression white blood cells100

description: Maudsley Hospital Twin Registry monozygotic twin50b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin54b depression white blood cells108

description: Maudsley Hospital Twin Registry monozygotic twin54b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin51a depression white blood cells101

description: Maudsley Hospital Twin Registry monozygotic twin51a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin55a control white blood cells109

description: Netherlands Twin Registry monozygotic twin55a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin55b depression white blood cells110

description: Netherlands Twin Registry monozygotic twin55b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin49a depression white blood cells97

description: Maudsley Hospital Twin Registry monozygotic twin49a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin49b control white blood cells98

description: Maudsley Hospital Twin Registry monozygotic twin49b vs. common reference pool


title: Netherlands Twin Registry monozygotic twin58b depression white blood cells116

description: Netherlands Twin Registry monozygotic twin58b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin48b control white blood cells96

description: Maudsley Hospital Twin Registry monozygotic twin48b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin46a depression white blood cells91

description: Maudsley Hospital Twin Registry monozygotic twin46a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin47b control white blood cells94

description: Maudsley Hospital Twin Registry monozygotic twin47b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin47a depression white blood cells93

description: Maudsley Hospital Twin Registry monozygotic twin47a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin43b depression white blood cells86

description: Maudsley Hospital Twin Registry monozygotic twin43b vs. common reference pool


title: Australian Twin Registry monozygotic twin38a control white blood cells75

description: Australian Twin Registry monozygotic twin38a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin45a depression white blood cells89

description: Maudsley Hospital Twin Registry monozygotic twin45a vs. common reference pool


title: Australian Twin Registry monozygotic twin38b depression white blood cells76

description: Australian Twin Registry monozygotic twin38b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin41b control white blood cells82

description: Maudsley Hospital Twin Registry monozygotic twin41b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin43a control white blood cells85

description: Maudsley Hospital Twin Registry monozygotic twin43a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin45b control white blood cells90

description: Maudsley Hospital Twin Registry monozygotic twin45b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin44b control white blood cells88

description: Maudsley Hospital Twin Registry monozygotic twin44b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin42b control white blood cells84

description: Maudsley Hospital Twin Registry monozygotic twin42b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin42a depression white blood cells83

description: Maudsley Hospital Twin Registry monozygotic twin42a vs. common reference pool


title: Australian Twin Registry monozygotic twin39a control white blood cells77

description: Australian Twin Registry monozygotic twin39a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin48a depression white blood cells95

description: Maudsley Hospital Twin Registry monozygotic twin48a vs. common reference pool


title: Australian Twin Registry monozygotic twin40b control white blood cells80

description: Australian Twin Registry monozygotic twin40b vs. common reference pool


title: Australian Twin Registry monozygotic twin40a depression white blood cells79

description: Australian Twin Registry monozygotic twin40a vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin46b control white blood cells92

description: Maudsley Hospital Twin Registry monozygotic twin46b vs. common reference pool


title: Australian Twin Registry monozygotic twin39b depression white blood cells78

description: Australian Twin Registry monozygotic twin39b vs. common reference pool


title: Australian Twin Registry monozygotic twin37a control white blood cells73

description: Australian Twin Registry monozygotic twin37a vs. common reference pool


title: Australian Twin Registry monozygotic twin36a depression white blood cells71

description: Australian Twin Registry monozygotic twin36a vs. common reference pool


title: Australian Twin Registry monozygotic twin36b control white blood cells72

description: Australian Twin Registry monozygotic twin36b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin44a depression white blood cells87

description: Maudsley Hospital Twin Registry monozygotic twin44a vs. common reference pool


title: Australian Twin Registry monozygotic twin35a control white blood cells69

description: Australian Twin Registry monozygotic twin35a vs. common reference pool


title: Netherlands Twin Registry monozygotic twin82a depression white blood cells163

description: Netherlands Twin Registry monozygotic twin82a vs. common reference pool


title: Australian Twin Registry monozygotic twin37b depression white blood cells74

description: Australian Twin Registry monozygotic twin37b vs. common reference pool


title: Australian Twin Registry monozygotic twin35b depression white blood cells70

description: Australian Twin Registry monozygotic twin35b vs. common reference pool


title: Maudsley Hospital Twin Registry monozygotic twin41a depression white blood cells81

description: Maudsley Hospital Twin Registry monozygotic twin41a vs. common reference pool


title: Australian Twin Registry monozygotic twin34b depression white blood cells68

description: Australian Twin Registry monozygotic twin34b vs. common reference pool


title: Australian Twin Registry monozygotic twin34a control white blood cells67

description: Australian Twin Registry monozygotic twin34a vs. common reference pool


title: Australian Twin Registry monozygotic twin33a depression white blood cells65

description: Australian Twin Registry monozygotic twin33a vs. common reference pool


title: Australian Twin Registry monozygotic twin33b control white blood cells66

description: Australian Twin Registry monozygotic twin33b vs. common reference pool


title: Australian Twin Registry monozygotic twin30a control white blood cells59

description: Australian Twin Registry monozygotic twin30a vs. common reference pool


title: Australian Twin Registry monozygotic twin32a control white blood cells63

description: Australian Twin Registry monozygotic twin32a vs. common reference pool


title: Australian Twin Registry monozygotic twin32b depression white blood cells64

description: Australian Twin Registry monozygotic twin32b vs. common reference pool


title: Australian Twin Registry monozygotic twin30b depression white blood cells60

description: Australian Twin Registry monozygotic twin30b vs. common reference pool


title: Australian Twin Registry monozygotic twin27a control white blood cells53

description: Australian Twin Registry monozygotic twin27a vs. common reference pool


title: Australian Twin Registry monozygotic twin31b control white blood cells62

description: Australian Twin Registry monozygotic twin31b vs. common reference pool


title: Australian Twin Registry monozygotic twin28a depression white blood cells55

description: Australian Twin Registry monozygotic twin28a vs. common reference pool


title: Australian Twin Registry monozygotic twin29b control white blood cells58

description: Australian Twin Registry monozygotic twin29b vs. common reference pool


title: Australian Twin Registry monozygotic twin31a depression white blood cells61

description: Australian Twin Registry monozygotic twin31a vs. common reference pool


title: Australian Twin Registry monozygotic twin26a depression white blood cells51

description: Australian Twin Registry monozygotic twin26a vs. common reference pool


title: Australian Twin Registry monozygotic twin29a depression white blood cells57

description: Australian Twin Registry monozygotic twin29a vs. common reference pool


title: Australian Twin Registry monozygotic twin28b control white blood cells56

description: Australian Twin Registry monozygotic twin28b vs. common reference pool


title: Australian Twin Registry monozygotic twin26b control white blood cells52

description: Australian Twin Registry monozygotic twin26b vs. common reference pool


title: Australian Twin Registry monozygotic twin25b depression white blood cells50

description: Australian Twin Registry monozygotic twin25b vs. common reference pool


title: Australian Twin Registry monozygotic twin24a control white blood cells47

description: Australian Twin Registry monozygotic twin24a vs. common reference pool


title: Australian Twin Registry monozygotic twin23b depression white blood cells46

description: Australian Twin Registry monozygotic twin23b vs. common reference pool


title: KV473 in liquid medium (3)

city: Leuven

first: Dries

last: De Maeyer

address: Gaston Geenslaan 1

country: Belgium

institute: CMPG/Bioincubator

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: We computed the correlation between the RMA expression values for all samples. The intensities that were below the background signal (i.e., absent detection call), were omitted.

organism: Saccharomyces cerevisiae

source_name: KV473(FLO11 mutant) in liquid medium

label_protocol: Affymetrix sample processing protocol

growth_protocol: Yeast colonies were grown for 5 days on YPS at 30°C, harvested and frozen at -80°C before processing for RNA extraction.

tag: growth condition

value: liquid medium

value: Sigma1278b FLO11 deletion mutant


title: KV473 in liquid medium (2)

extract_protocol: Yeast colonies were grown for 5 days on YPS at 30°C, harvested and frozen at -80°C before processing for RNA extraction.


title: Australian Twin Registry monozygotic twin25a control white blood cells49

description: Australian Twin Registry monozygotic twin25a vs. common reference pool


title: KV2668 in liquid medium (3)

source_name: KV2668(WT) in liquid medium


title: KV2668 in liquid medium (1)


title: Australian Twin Registry monozygotic twin24b depression white blood cells48

description: Australian Twin Registry monozygotic twin24b vs. common reference pool


title: Australian Twin Registry monozygotic twin27b depression white blood cells54

description: Australian Twin Registry monozygotic twin27b vs. common reference pool


title: Australian Twin Registry monozygotic twin22a depression white blood cells43

description: Australian Twin Registry monozygotic twin22a vs. common reference pool


title: Australian Twin Registry monozygotic twin22b control white blood cells44

description: Australian Twin Registry monozygotic twin22b vs. common reference pool


title: KV2668 in liquid medium (2)


title: KV473 in liquid medium (1)

extract_protocol: Total RNA was extracted using the hot phenol extraction method (Guthrie & Fink 1991) and dissolved in 40µl RNase free water.


title: Australian Twin Registry monozygotic twin21b control white blood cells42

description: Australian Twin Registry monozygotic twin21b vs. common reference pool


title: KV2668 on solid medium (3)

source_name: KV2668(WT) on solid medium

value: solid medium


title: Australian Twin Registry monozygotic twin21a depression white blood cells41

description: Australian Twin Registry monozygotic twin21a vs. common reference pool


title: Australian Twin Registry monozygotic twin23a control white blood cells45

description: Australian Twin Registry monozygotic twin23a vs. common reference pool


title: Australian Twin Registry monozygotic twin20a control white blood cells39

description: Australian Twin Registry monozygotic twin20a vs. common reference pool


title: Australian Twin Registry monozygotic twin19b control white blood cells38

description: Australian Twin Registry monozygotic twin19b vs. common reference pool


title: KV63 on solid medium (2)

source_name: KV63(FLO11 mutant) on solid medium


title: Australian Twin Registry monozygotic twin19a depression white blood cells37

description: Australian Twin Registry monozygotic twin19a vs. common reference pool


title: KV68 on solid medium (2)

source_name: KV68(WT) on solid medium


title: KV63 on solid medium (3)


title: Australian Twin Registry monozygotic twin18a control white blood cells35

description: Australian Twin Registry monozygotic twin18a vs. common reference pool


title: KV473 on solid medium (2)

source_name: KV473(FLO11 mutant) on solid medium


title: KV68 on solid medium (3)


title: KV2668 on solid medium (1)


title: Australian Twin Registry monozygotic twin17b control white blood cells34

description: Australian Twin Registry monozygotic twin17b vs. common reference pool


title: Australian Twin Registry monozygotic twin20b depression white blood cells40

description: Australian Twin Registry monozygotic twin20b vs. common reference pool


title: KV2668 on solid medium (2)


title: KV473 on solid medium (3)


title: Australian Twin Registry monozygotic twin16b depression white blood cells32

description: Australian Twin Registry monozygotic twin16b vs. common reference pool


title: KV68 on solid medium (1)


title: KV473 on solid medium (1)


title: Australian Twin Registry monozygotic twin16a control white blood cells31

description: Australian Twin Registry monozygotic twin16a vs. common reference pool


title: KV63 on solid medium (1)


title: Australian Twin Registry monozygotic twin15b depression white blood cells30

description: Australian Twin Registry monozygotic twin15b vs. common reference pool


title: Australian Twin Registry monozygotic twin18b depression white blood cells36

description: Australian Twin Registry monozygotic twin18b vs. common reference pool


title: Australian Twin Registry monozygotic twin13b depression white blood cells26

description: Australian Twin Registry monozygotic twin13b vs. common reference pool


title: Australian Twin Registry monozygotic twin17a depression white blood cells33

description: Australian Twin Registry monozygotic twin17a vs. common reference pool


title: Australian Twin Registry monozygotic twin13a control white blood cells25

description: Australian Twin Registry monozygotic twin13a vs. common reference pool


title: Australian Twin Registry monozygotic twin14b control white blood cells28

description: Australian Twin Registry monozygotic twin14b vs. common reference pool


title: Australian Twin Registry monozygotic twin14a depression white blood cells27

description: Australian Twin Registry monozygotic twin14a vs. common reference pool


title: Australian Twin Registry monozygotic twin15a control white blood cells29

description: Australian Twin Registry monozygotic twin15a vs. common reference pool


title: Australian Twin Registry monozygotic twin11b control white blood cells22

description: Australian Twin Registry monozygotic twin11b vs. common reference pool


title: Australian Twin Registry monozygotic twin12a depression white blood cells23

description: Australian Twin Registry monozygotic twin12a vs. common reference pool


title: Australian Twin Registry monozygotic twin11a depression white blood cells21

description: Australian Twin Registry monozygotic twin11a vs. common reference pool


title: Maize_GiantCell_Root_21d_BioRep2

city: Gainesville

first: Lauren

last: McIntyre

address: 2033 Mowry Rd

department: Department of Molecular Genetics and Microbiology

institute: University of Florida

description: cDNA amplified from total RNA isolated from giant cells.

hyb_protocol: The hybridization mixture was prepared according to NuGEN and Affymetrix procedures and hybridized to GeneChip© Maize Genome Arrays.

scan_protocol: GeneChips were scanned at the University of Pennsylvania School of Medicine Microarray Facility according to standard manufacturer protocols.

data_processing: Data were quantified with the Expression Console (Affymetrix) software application using the MAS5 algorithm.

organism: Zea mays

source_name: LCM of maize giant cells, 21 days

label_protocol: NuGEN FL module.

growth_protocol: Zea mays seeds were sown in a 2:1 sand:turface mix and grown in a greenhouse for 2 weeks prior to infestation with stage 2 Meloidogyne incognita juveniles.

extract_protocol: Total RNA samples were isolated using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA was amplified according to NuGEN WT-Ovation Pico kit instructions.

treatment_protocol: Two-week-old Zea mays seedlings planted on a 2:1 sand:turface mixture were inoculated with 1,000 M. incognita stage 2 juveniles near the root. Twenty-one days after inoculation, the infested portions of the roots were harvested and frozen in cryomatrix. An area of approximately 5,000,000 um2 (~40-60 cells) was captured from infested regions of the root. Giant cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

value: Meloidogyne incognita infestation

tag: time

value: 21 days post challenge with M. incognita

value: laser-captured giant cells

value: IS A A188 C B73 Cross

tag: sample size


title: Maize_GiantCell_Root_14d_BioRep2

source_name: LCM of maize giant cells, 14 days

treatment_protocol: Two-week-old Zea mays seedlings planted on a 2:1 sand:turface mixture were inoculated with 1,000 M. incognita stage 2 juveniles near the root. Fourteen days after inoculation, the infested portions of the roots were harvested and frozen in cryomatrix. An area of approximately 5,000,000 um2 (~40-60 cells) was captured from infested regions of the root. Giant cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

value: 14 days post challenge with M. incognita


title: Maize_GiantCell_Root_14d_BioRep3


title: Australian Twin Registry monozygotic twin10b control white blood cells20

description: Australian Twin Registry monozygotic twin10b vs. common reference pool

value: common reference pool


title: Maize_GiantCell_Root_21d_BioRep1


title: Maize_GiantCell_Root_21d_BioRep3


title: Maize_Control_Root_21d_BioRep3

description: cDNA amplified from total RNA isolated from control root cells.

source_name: LCM of maize control root cells, 21 days

treatment_protocol: Two-week-old Zea mays seedlings planted on a 2:1 sand:turface mixture were inoculated with 1,000 M. incognita stage 2 juveniles near the root. Twenty-one days after inoculation, the non-infested portions of the roots were harvested and frozen in cryomatrix. An area of approximately 13,000,000 um2 (~75-150 cells) was captured from non-infested regions of the infested root. Control root cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

value: laser-captured control root cells


title: Australian Twin Registry monozygotic twin9a depression white blood cells17

description: Australian Twin Registry monozygotic twin9a vs. common reference pool


title: Australian Twin Registry monozygotic twin9b control white blood cells18

description: Australian Twin Registry monozygotic twin9b vs. common reference pool


title: Australian Twin Registry monozygotic twin10a depression white blood cells19

description: Australian Twin Registry monozygotic twin10a vs. common reference pool


title: Australian Twin Registry monozygotic twin12b control white blood cells24

description: Australian Twin Registry monozygotic twin12b vs. common reference pool


title: Australian Twin Registry monozygotic twin8b depression white blood cells16

description: Australian Twin Registry monozygotic twin8b vs. common reference pool


title: Maize_Control_Root_21d_BioRep2


title: Australian Twin Registry monozygotic twin7a control white blood cells13

description: Australian Twin Registry monozygotic twin7a vs. common reference pool


title: Maize_Control_Root_21d_BioRep1


title: Australian Twin Registry monozygotic twin7b depression white blood cells14

description: Australian Twin Registry monozygotic twin7b vs. common reference pool


title: Australian Twin Registry monozygotic twin8a control white blood cells15

description: Australian Twin Registry monozygotic twin8a vs. common reference pool


title: Control, Biological Replicate 1 [Exosc9i+GRHL3i]

city: San Diego

first: Devendra

last: Mistry

state: CA

address: 9500 Gilman Drive MC#0869

department: Medicine

institute: University of California-San Diego

description: Cell transduced with Control shRNA and then nucleofected with control siRNA

hyb_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix HG-U133 2.0 plus arrays were performed at the UCSD Genechip Microarray Core Facility.

data_processing:
For gene expression analysis, arrays were RMA normalized and differential expression was defined using the following filters: Significance Analysis of Microarrays 3.0(Tusher et al., 2001) with a false discovery rate less than 5%, an average fold change ≥ 1.5 at any time point, and an average raw expression intensity ≥ 100 at any time point. Hierarchical clustering and heat map generation were performed as previously described(Sen et al., 2010). For future analyses, Affymetrix probe IDs were converted to unique Unigene IDs. GO term enrichment was performed using DAVID analysis(Huang da et al., 2009) with the total set of genes on the appropriate microarray as the background.
The two Control samples, although represent two CEL files, are submitted as 4 Samples since they were normalized twice - once with the Exosc9i Samples, and also with the Exosc9i+GRHL3i Samples.

source_name: Control Cells

growth_protocol: Human Primary Keratinocytes were grown in self-renewing condition using KSF-M (GIBCO-BRL) supplemented with epidermal growth factor (EGF) and bovine pituitary extract (BPE).

extract_protocol: Total RNA from cells was extracted using the RNeasy mini kit according to manufacturer's protocol.

treatment_protocol: EXOSC9 gene was knocked down using retroviral delivery of shRNA in indicated samples. GRHL3 was knocked down through nucleofaction of siRNA in indicated samples.

value: Human Primary Keratinocytes


title: Exosc9i+GRHL3i Biological Replicate 2

description: Cell transduced with EXOSC9 shRNA and then nucleofected with GRHL3 siRNA

source_name: EXOSC9 and GRHL3 knocked down cells

label_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)


title: Exosc9i+GRHL3i Biological Replicate 1


title: Exosc9i Biological Replicate 2

description: Cell transduced with EXOSC9 shRNA and then nucleofected with control siRNA

source_name: EXOSC9 knocked down cells