title: whole uPA gene BD85 02

description:
15_BD85_WG++02
BD85-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from whole uPA gene homozygous mouse with BD85 transplant


title: whole uPA gene BD85 03

status: Public on Jun 17 2015

type: RNA

city: Tokai-mura

first: Shin-Ichiro

last: Nagatsuka

state: Ibaraki

address: 2117 Muramatsu

department: ADME/Tox Research Institute

country: Japan

institute: Sekisui Medical Co.

description:
16_BD85_WG++03
BD85-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, followed by Robust Multichip Averaging (RMA) normalization using Avadis (Strand Genomics, Inc.). Values for probe sets that were judged to be Absent in all 25 Chips by the MAS5.0 analysis were left blank in the Sample data tables.

label: Biotin

molecule: total RNA

organism:
Homo sapiens
Mus musculus

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: Human hepatocytes were intrasplenically transplanted to SCID host mice (2-4 weeks of age), followed by periodical monitoring of human albumin concentration in the blood to estimate the replacement index of human hepatocytes in the liver.

extract_protocol: Hepatic total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Humanized liver samples were taken at around 9:00am from non-treated chimeric mice which were estimated to be more than 70% occupancy of human hepatocytes in the liver.

tag: host mouse genotype/variation

value: whole uPA gene+/+ / SCID

tag: transplanted human hepatocytes

tag: tissue

value: humanized liver

tag: age

value: approx. 20 weeks


title: HeLa-CDK9-inhibitor-T2-1

city: emeryville

first: Zhenhai

last: Gao

state: California

address: 4560 Horton street

country: USA

institute: Novartis Institute for Biomedical Research

description: CDK9 inhibitor treatment at 2hr

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor affy package (http://bioconductor.org) with RMA method and HGU133Plus2_Hs_ENTREZG custom CDF v14.1 for target gene definition (Dai et al., 2005)

label: biotin

organism: Homo sapiens

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

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS. Cells were maintained at 37 °C under 5% CO2.

extract_protocol: Total RNA was extracted with RNAeasy Plus kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: HeLa cells were treated with DMSO or i-CDK9 for 2, 8 or 16 hours

tag: cell line

value: HeLa

tag: treatment

value: CDK9 inhibitor

tag: time (hours)


title: HeLa-CDK9-inhibitor-T8-3

description: CDK9 inhibitor treatment at 8hr


title: uPA cDNA hetero BD195 02

description:
24_BD195_cDNA+-02
BD195-transplanted uPA cDNA +/- mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from uPA cDNA heterozygous mouse with BD195 transplant

value: uPA cDNA+/- / SCID


title: uPA cDNA homo BD195 03

description:
22_BD195_cDNA++03
BD195-transplanted uPA cDNA +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from uPA cDNA homozygous mouse with BD195 transplant

value: uPA cDNA+/+ / SCID


title: whole uPA gene BD87 02

description:
18_BD87_WG++02
BD87-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from whole uPA gene homozygous mouse with BD87 transplant


title: HeLa-DMSO-T2-3

description: DMSO treatment at 2hr

value: DMSO


title: THt085

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

extract_protocol: RNA was isolated with High Pure RNA paraffin kit (Roche) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: disease state

value: hepatocellular carcinoma (HCC)

value: Yes

value: No

tag: pseudoglandular

tag: sh-hcc

tag: cc


title: THt070

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: whole uPA gene BD72 03

description:
13_BD72_WG++03
BD72-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from whole uPA gene homozygous mouse with BD72 transplant


title: THt033

label_protocol: Refer to the NanoString nCounter Assay System Manual


title: THt077


title: THt010


title: THt004.2


title: THt005


title: THt010.2


title: THt011


title: whole uPA gene BD85 01

description:
14_BD85_WG++01
BD85-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: THt008


title: whole uPA gene BD72 02

description:
12_BD72_WG++02
BD72-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: THt006


title: THt003


title: THt004.3


title: THt004


title: whole uPA gene BD195 08

description:
08_BD195_WG++08
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from whole uPA gene homozygous mouse with BD195 transplant


title: whole uPA gene BD72 01

description:
11_BD72_WG++01
BD72-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: whole uPA gene BD195 03

description:
03_BD195_WG++03
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: whole uPA gene BD195 07

description:
07_BD195_WG++07
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: whole uPA gene BD195 05

description:
05_BD195_WG++05
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: whole uPA gene BD195 10

description:
10_BD195_WG++10
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: THt002


title: whole uPA gene BD195 04

description:
04_BD195_WG++04
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: whole uPA gene BD195 09

description:
09_BD195_WG++09
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: whole uPA gene BD195 06

description:
06_BD195_WG++06
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: THt104


title: THt105


title: HMLER_MeDP_bound

type: genomic

city: LYON cedex

first: Robert

last: Dante

address: Centre Léon Bérard 28, rue Laennec

department: Tumoral escape

country: France

institute: Cancer Research Center of Lyon

description: MeDP in HMLER

hyb_protocol: Samples were prepared and hybridized to GeneChip Human Tiling 1.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 TGPLUS according to manufacturer's instruction.

data_processing: Data were processed using the R packages aroma.affymetrix with a MatSmoothing of 500bp (as described at http://aroma-project.org/vignettes/MAT-TilingArrayAnalysis) and Repitools. Annotation is in hg18. SGR files are three colmun tab delimited txt files: chromosome, position and score. They are in hg18.

molecule: genomic DNA

source_name: HMLER, sonication, MeDP

label_protocol: The samples were labelled with the GeneChip WT Double-Stranded DNA Terminal Labelling Kit

growth_protocol: HMEC-hTERT and HMLER cell lines were kindly provided by Anne-Pierre Morel (CRCL, Lyon, France). They were cultivated as previously described (Morel et al. PLoS One 2008).

extract_protocol: ChIP-chip and MeDP-chip experiments were performed as previously described (Chatagnon et al. Epigenetics 2011), by the ProfileXpert service (Lyon, France) according to AffymetrixTM protocols. Briefly, chromatin fragments were precipitated with anti-MBD2 antibody (Covalab) and a His6-tagged recombinant protein containing 4 MBD domains cloned from MBD1 (Jorgensen et al. Nucleic Acids Research 2006). The DNA fragments from the ChIP and MeDP experiments were amplified by random PCR.

treatment_protocol: No treatments.

value: HMLER

tag: protocol

value: sonication, MeDP

tag: precipitation

value: methylated DNA

tag: methylated dna capture

value: using a His6-tagged recombinant protein containing 4 MBD domains cloned from MBD1 (Jorgensen et al. Nucleic Acids Research 2006)


title: HMLER_MeDP_input

description: Control of MeDP in HMLER

source_name: HMLER, sonication

value: sonication


title: THt099


title: THt100


title: HMLER_MBD2_input

description: Control of MBD2 ChIP in HMLER

tag: chip antibody


title: THt098


title: whole uPA gene BD195 01

description:
01_BD195_WG++01
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: whole uPA gene BD195 02

description:
02_BD195_WG++02
BD195-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: SRPIN803_Rep2

city: Kyoto

first: Masatsugu

last: Denawa

address: Yoshida-Konoe-cho, Sakyo-ku

institute: Kyoto University

description: Gene expression data from SRPIN803 treated ARPE-19 cells

hyb_protocol: Following fragmentation, 12 ug of aRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained using GeneChip Hybridization Wash and Stain Kit in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000G

data_processing: The data were analyzed with RMA using Agilent GeneSpringGX 12.6.1 software.

source_name: SRPIN803 treated ARPE-19 cells

label_protocol: Biotinylated aRNA were prepared from 100 ng total RNA using GeneChip® 3' IVT Express Kit (Affymetrix) from 100 ng total RNA according to the manufacturer's instruction

growth_protocol: ARPE-19 cells were maintained at 37 ºC in a 5% CO2-air incubator with Dulbecco's modified Eagle's medium (DMEM)/Ham's F-12 supplemented with 10% fetal bovine serum and 1% Penicillin‐Streptomycin Mixed Solution

extract_protocol: Total RNA was isolated using Sepasol®-RNA I Super G (nacalai tesque) according to the manufacturer's instruction. The Isolated total RNA was treated with RQ1 DNase (QIAGEN) and was purified with Sepasol®-RNA I Super G again.

treatment_protocol: ARPE-19 cells were treated with SRPIN803 (10 µM) or the control (0.1% DMSO) for 4 hours.

tag: agent

value: SRPIN803 (10 µM)


title: THt095


title: HMEC-hTERT_MeDP_bound

description: MeDP in HMEC-hTERT

source_name: HMEC-hTERT, sonication, MeDP

value: HMEC-hTERT


title: THt093


title: THt094


title: HMEC-hTERT_MBD2_input

description: Control of MBD2 ChIP in HMEC-hTERT

source_name: HMEC-hTERT, sonication


title: SRPIN803_Rep3


title: THt092


title: SRPIN803_Rep1


title: DMSO_Rep2

description: Gene expression data from DMSO treated ARPE-19 cells

source_name: DMSO treated ARPE-19 cells


title: THt103


title: THt091


title: DMSO_Rep1


title: DMSO_Rep3


title: HMEC-hTERT_MBD2_bound

description: MBD2 ChIP in HMEC-hTERT

source_name: HMEC-hTERT, sonication, MBD2 ChIP

value: sonication, MBD2 ChIP

value: a custom-made rabbit polyclonal serum obtained after immunization with peptides corresponding to the N-terminal part of the MBD2 protein (Covalab, Villeurbanne, Lyon) (Perriaud et al. Curr. Pharm. Des 2013)


title: 95-test-RepoManRata-rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
RepoMan-RATA.wig
RepoMan-RATA.bed
RepoMan-RATA samples compared to Dam controls

hyb_protocol: A mixture of fragmented biotinylated DNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Promoter 1.0 R Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: MAT (Model-based Analysis for Tiling Arrays) analysis algorithm used to detect regions enriched by immunoprecipitation on Affymetrix tiling array.  Bed-files are text files containing the enriched genomic regions. MAT algorithm settings: Bandwidth = 300, MaxGap = 300, MinProbes = 5, p-value = 1.00E-04

source_name: HeLa cells, integrated Dam-RepoMan-RATA cassette

label_protocol: Samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Polyclonal stable HeLa cell lines with integrated Dam transgenes were generated and grown following standard cell culture procedures, using G418 as selective agent (also: see Vogel et al. 2007 as cited below)

extract_protocol: Genomic DNA was extracted from cells (Sigma GeneElute Mammalian Genomic DNA Minprep kit) and processed according to the DamID protocol published in (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. 2007. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nature protocols 2(6): 1467-1478.)

treatment_protocol: No additional treatment

value: HeLa

tag: transgene

value: integrated Dam-RepoMan-RATA  cassette


title: THt090


title: HMLER_MBD2_bound

description: MBD2 ChIP in HMLER

source_name: HMLER, sonication, MBD2 ChIP


title: HMEC-hTERT_MeDP_input

description: Control of MeDP in HMEC-hTERT


title: 88-test-RepoManRata-rep1


title: 87-test-RepoManWt-rep1

description:
RepoMan-WT.wig
RepoMan-WT.bed
RepoMan-WT samples compared to Dam controls

source_name: HeLa cells, integrated Dam-RepoMan-WT cassette

value: integrated Dam-RepoMan-WT  cassette


title: THt097


title: THt089


title: 93-test-PNUTS-Rata-rep2

description:
PNUTS-RATA.wig
PNUTS-RATA.bed
PNUTS-RATA samples compared to Dam controls

source_name: HeLa cells, integrated Dam-PNUTS-RATA cassette

value: integrated Dam-PNUTS-RATA  cassette


title: 92-test-PNUTS-Wt-rep2

description:
PNUTS-WT.wig
PNUTS-WT.bed
PNUTS-WT samples compared to Dam controls

source_name: HeLa cells, integrated Dam-PNUTS-WT cassette

value: integrated Dam-PNUTS-WT  cassette


title: THt088

value: hepatocellular carcinoma (HCC)


title: 85-test-PNUTS-Rata-rep1


title: THt084

value: Yes


title: THt087

value: No


title: THt080


title: 84-test-PNUTS-Wt-rep1


title: THt083


title: 83-test-PP1gamma-rep2

description:
PP1-GAMMA.wig
PP1-GAMMA.bed
PP1γ samples compared to Dam controls

source_name: HeLa cells, integrated Dam-PP1γ cassette

value: integrated Dam-PP1γ cassette


title: 73-test-PP1gamma-rep1


title: THt078


title: 82-test-PP1beta-rep1

description:
PP1-BETA.wig
PP1-BETA.bed
PP1β samples compared to Dam controls

source_name: HeLa cells, integrated Dam-PP1β cassette

value: integrated Dam-PP1β cassette


title: THt075


title: 91-test-PP1beta-rep2


title: THt073


title: 94-test-RepoManWt-rep2


title: 90-test-PP1alfa-rep2

description:
PP1-ALPHA.wig
PP1-ALPHA.bed
PP1α samples compared to Dam controls

source_name: HeLa cells, integrated Dam-PP1α cassette

value: integrated Dam-PP1α cassette


title: 80-test-NIPP1-RATA-rep2

description:
NIPP1-RATA.wig
NIPP1-RATA.bed
NIPP1-RATA samples compared to Dam controls

source_name: HeLa cells, integrated Dam-NIPP1-RATA cassette

value: integrated Dam-NIPP1-RATA cassette


title: THt072


title: THt071


title: 71-test-NIPP1-RATA-rep1


title: 70-test-NIPP1-WT-rep1

description:
NIPP1-WT.wig
NIPP1-WT.bed
NIPP1-WT samples compared to Dam controls

source_name: HeLa cells, integrated Dam-NIPP1-WT cassette

value: integrated Dam-NIPP1-WT cassette


title: THt068.2


title: 89-Ctrl-Dam

description: DAM controls

data_processing: MAT (Model-based Analysis for Tiling Arrays) analysis algorithm used to detect regions enriched by immunoprecipitation on Affymetrix tiling array.  Bed-files are text files containing the enriched genomic regions. MAT algorithm settings: Bandwidth = 300,

source_name: HeLa cells, integrated Dam cassette

value: integrated Dam cassette


title: THt069


title: 79-test-NIPP1-WT-rep2


title: THt082


title: THt068


title: 69-Ctrl-Dam-II(HeLa)

description: DAM controls


title: THt064


title: 86-Ctrl-Dam

description: DAM controls


title: THt062


title: 78-Ctrl-Dam

description: DAM controls


title: THt065


title: THt074


title: 81-test-PP1alfa-rep1


title: THt060


title: THt058


title: THt055


title: THt059


title: THt057


title: THt054


title: THt066


title: THt053


title: THt052


title: THt050


title: THt051


title: THt049


title: THt047


title: THt045


title: THt044


title: THt046


title: THt041


title: THt043


title: THt042


title: THt063


title: THt040


title: THt039


title: THt036


title: THt035.2


title: THt037


title: THt034


title: THt032


title: THt035


title: THt029


title: THt030


title: THt028


title: THt048


title: THt024


title: THt023


title: THt025


title: THt021.2


title: THt021


title: THt027


title: THt019


title: THt013


title: THt015


title: THt020


title: THt018


title: THt012


title: THt017


title: THt012.3


title: THt026


title: THt014


title: THt012.2


title: neocortex_Bcl11aWT_rep3

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: control tissue

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis

organism: Mus musculus

source_name: neocortex tissue E14.5

growth_protocol: Fresh frozen dissected tissue was kept at -80°C until use.

extract_protocol: Extraction of total RNA was performed with the Rneasy kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Tissue was dissected in ice-cold phosphate buffer (pH7.2).

value: neocortex

tag: developmental stage

value: Embryonic day 14.5

tag: genotype

value: wildtype Bcl11a


title: neocortex_Bcl11aKO_rep3

description: knockout tissue

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

tag: tissue

value: Bcl11a knockout mutant


title: neocortex_Bcl11aWT_rep1

description: control tissue


title: neocortex_Bcl11aWT_rep2

description: control tissue


title: neocortex_Bcl11aKO_rep2

description: knockout tissue


title: Horse-2

city: Houston

first: Mark

middle: Seungwook

last: Kim

address: 7777 Knnight rd

department: Cancer Biology

institute: MD Anderson Cancer Center

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (1500 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Parental cells

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell type

value: Breast cancer

value: MEM-10% Horse serum-90% confluence


title: SK

city: Beijing

first: Juanjuan

last: Zhu

address: 27 Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

description: control

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed using BeadStudio using the average chip normalization method

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

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

extract_protocol: Total RNA from cells were extracted using TRI regents (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s protocol.

treatment_protocol: Cells were transducted by plasmid for 48h, followed by si-RNA transfection for 48 h.

tag: strain

tag: transfection

value: Control


title: neocortex_Bcl11aKO_rep1

description: knockout tissue


title: 5E-V1-NC


title: FBS0.1-1

tag: cell line

tag: treatment

value: MEM-0.1% FBS-90% confluence


title: 5E-V1-Si2


title: Con50-1

value: MEM-10% FBS-50% confluence


title: Con50-2


title: MEM-1

value: MEM-10% FBS-90% confluence


title: 1F


title: 2712_7654_33677_PICALM6D+calm_Mouse430A+2

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® ____________ arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were analyzed with Agilent 2100 Bioanalyzer G2939A

source_name: PICALM6D Knockout cells transfected with PICALM

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Picalm null hematopoietic cell lines were generated by immortalizing fetal liver cells harvested from E14 fit1 Picalmfit1-5R mouse embryos.5 Fetal liver cells were retrovirally transduced with MLL-ENL using the MSCV-IRES-eGFP vector30 and serially replated in methylcellulose culture to select immortalized hematopoietic progenitors as previously described.31 Cells were maintained in liquid culture in RPMI medium supplemented with 10% FBS, glutamine, penicillin and streptomycin with recombinant murine interleukin-3 and stem cell factor (5 ng/ml and 50 ng/ml, respectively, Peprotech).

tag: background strain


title: 2712_7654_33676_PICALM6D+neo_Mouse430A+2

source_name: PICALM6D Knockout cells transfected with control

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® ____________ arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

growth_protocol: Cells were maintained in liquid culture in RPMI medium supplemented with 10% FBS, glutamine, penicillin and streptomycin with recombinant murine interleukin-3 and stem cell factor (5 ng/ml and 50 ng/ml, respectively, Peprotech).


title: FBS0.1-2


title: 2712_7654_33680_PICALM84+neo_Mouse430A+2

source_name: PICALM84 Knockout cells transfected with control


title: 2712_7654_33674_PICALM6B+calm_Mouse430A+2_2

source_name: PICALM6B Knockout cells transfected with PICALM


title: 2712_7654_33681_PICALM84+calm_Mouse430A+2

source_name: PICALM84 Knokcout cells transfected with PICALM


title: RPMI-1

value: RPMI1640-10% FBS-90% confluence


title: 5E-V1


title: DMEM-2

value: DMEM-10% FBS-90% confluence


title: RPMI-2


title: MEM-2


title: Horse-1


title: DMEM-1


title: 2712_7654_33673_PICALM6B+neo_Mouse430A+2

source_name: PICALM6B Knockout cells transfected with control


title: 2712_7654_33672_PICALM6A+calm_Mouse430A+2

source_name: PICALM6A Knockout cells transfected with PICALM


title: SSCs

city: yangzhou

first: zhentao

last: zhang

address: wenhui road

institute: yangzhou university

hyb_protocol: 1.0 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: SSCs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

treatment_protocol: Three kinds stem cells were isolated from different stages of chicken embryos and stained by their specific antibodies then purified by FACS.

tag: gender

value: male

tag: age

value: spermatogonial stem cells (SSCs)


title: Day 16 post-LCMV infection (-Treg D8-16), biological rep1

status: Public on Jun 16 2015

city: Seattle

first: Surojit

last: Sarkar

state: WA

address: 1100 Olive Way, Suite 100

department: Department of Pediatrics and Laboratory Medicine

institute: University of Washington School of Medicine

description: Gene expression data from FACS purified GP33-specific CD8 T cells isolated at day 16 post-LCMV infection, Tregs depleted between day 8-16

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A .Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The .CEL files were analyzed using Genespring GX 11.5 software following RMA normalization.

source_name: In vivo differentiated in the absence of regulatory T cells from Day 8-16

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Chimeric FoXP3-DTR, mice adoptively transferred with 10E5 Db-GP33-specific naive P14 CD8 T cells, were infected with LCMV Armstrong. One set of the mice were treated with 20ng of diphtheria toxin (DT) per gram of mouse bodyweight on days 8, 10 and 12 post-infection to deplete regulatory T cells (Tregs). The control group of mice were treated with an equivalent amount of vehicle (PBS) on the indicated days. At day 16 post-infection, all mice were sacrificed and splenocytes were isolated for cell sorting.

extract_protocol: Trizol extraction of total RNA  from FACS purified CD8 T cells was performed according to the manufacturer's instructions.

treatment_protocol: First, CD8 T cells were enriched from the mouse splenocytes using a negative isolation protocol using a magnetic bead based kit from Stem cell technologies. The purified CD8 T cells (~70% pure) were fluorescently labeled for CD8 and Thy 1.1 for Fluorescence Activated Cell Sorting (FACS).Finally, CD8+ Db-GP33-specific T cells were FACS purified up to >98% purity for the next step of mRNA isolation. At least 10E6 purified CD8+ Db-GP33-specific T cells were used for each replicate from three distinct experiment to serve as the individual biological replicates.

value: P14 cells from C57 Black 6 background

value: spleen

value: FACS purified GP33-specific CD8 T cells

tag: treg depletion using dt tx

value: Tx on Days 8,10 and 12

tag: days post-lcmv infection

value: Day 16

value: 8-10 weeks


title: Day 16 post-LCMV infection (+Treg), biological rep1

description: Gene expression data from FACS purified GP33-specific CD8 T cells isolated at day 16 post-LCMV infection

source_name: In vivo differentiated in the presence of regulatory T cells

value: UnTx


title: 2712_7654_33671_PICALM6A+neo_Mouse430A+2

source_name: PICALM6A Knockout cells transfected with control


title: Day 16 post-LCMV infection (-Treg D8-16), biological rep2


title: FOXO_PTEN_GCT

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor with RMA method.

source_name: Granulosa cell tumors from Foxo1f/f;Foxo3f/f;Ptenf/f;Cyp19-cre mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: Animals were housed under a 16-h light/8-h dark schedule in the Center for Comparative Medicine at Baylor College of Medicine and provided food and water ad libitum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Animals were treated in accordance with the NIH Guide for the Care and Use of Laboratory Animals, as approved by the Animal Care and Use Committee at Baylor College of Medicine.

tag: genotype/variation

value: FOXO/PTEN knockout

value: mixed

value: ovarian granulosa cell tumors


title: PGCs

source_name: PGCs

value: primordial germ cells (PGCs)


title: Day 16 post-LCMV infection (-Treg D8-16), biological rep3


title: dendritic_cell_wt_LPS-IL4_rep3

city: Marseille

first: Philippe

last: Pierre

address: Avenue de Luminy

institute: Centre d’Immunologie de Marseille-Luminy

hyb_protocol: Hybridizations were carried out following Agilent Technologies instructions for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Santa Clara, CA, USA), using whole-genome Rat GE 4x44K v3 Microarrays

scan_protocol: Images were obtained using the Agilent G2565AA microarray scanner and fluorescence quantization was performed using the Agilent Feature Extraction 10.5.1.1 software and the GE1_105_Dec08 protocol

data_processing: The signal intensity was aligned and normalized between microarrays by centering the median of the signal distribution using BRB-ArrayTools v3.8.1

label_protocol: Same amounts of RNA extract (500 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies)

growth_protocol: Male C57BL/6 mice 7-8 weeks old were purchased from Charles River Laboratories (Cambridge, Mass). Bone marrow-derived DC were cultured as described in PMID: 1460426.

extract_protocol: CD11C-positive DCs were purified by magnetic sorting prior mRNA extraction and array analysis. Total RNA from cultures was extracted.

treatment_protocol: Cultures were grown in presence or absence of IL-4 (Peprotech) at 20 ng/ml that was used from day 2 of DC culture and stimulated or not at day 6 of culture with LPS for 8h.

tag: strain background

value: 7-8 weeks

value: WT

value: bone marrow-derived DC

tag: sample group

tag: cell subtype

value: CD11C-positive DCs


title: dendritic_cell_wt_IL4_rep2

value: male


title: dendritic_cell_wt_LPS-IL4_rep2


title: dendritic_cell_wt_LPS_rep3

value: LPS


title: dendritic_cell_wt_IL4_rep3


title: dendritic_cell_wt_LPS-IL4_rep1


title: dendritic_cell_wt_control_rep3

value: control


title: dendritic_cell_wt_LPS_rep2


title: dendritic_cell_wt_LPS_rep1


title: dendritic_cell_wt_control_rep2


title: Day 16 post-LCMV infection (+Treg), biological rep3

value: P14 cells from C57 Black 6 background

value: spleen


title: ESCs

source_name: ESCs

value: embryonic stem cells (ESCs)


title: Day 16 post-LCMV infection (+Treg), biological rep2

value: FACS purified GP33-specific CD8 T cells

value: Day 16


title: dendritic_cell_wt_IL4_rep1


title: dendritic_cell_wt_control_rep1


title: dendritic_cell_ko_LPS-IL4_rep2


title: D33mir

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
microRNA expression data of control RPE
Dicer1 flox/+ Dct cre mice where mated with Dicer1folx/flox mice. Pups where sacrifced at P5 and enucleated. Eyes where the dissected isolating the RPE.

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

data_processing:
microRNA analyses was performed. RMA normalization and summarization by mean, all were done by Partek Genomics suite (version 6.6). Mouse microRNAs are shown.
Log2 expression intensities after normalization and summarization, as implicated in the data processing raw.

source_name: retinal pigmented epithelium (RPE)

extract_protocol: miRNeasy kit (Qiagen) according to the manufacturer's protocol

value: retinal pigmented epithelium (RPE)

tag: date

value: Control RPE


title: D34mir

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: D35mir

label_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: D36mir

description:
microRNA expression data of Dicer1 deficient  RPE
Dicer1 flox/+ Dct cre mice where mated with Dicer1folx/flox mice. Pups where sacrifced at P5 and enucleated. Eyes where the dissected isolating the RPE.

value: The Dct-Cre mice where crossed with Dicer1loxP to establish to establish Dicer1loxP/loxP;Dct-Cre


title: D37mir


title: D38mir


title: dendritic_cell_ko_LPS-IL4_rep1


title: dendritic_cell_ko_IL4_rep2


title: D39mir


title: dendritic_cell_ko_LPS-IL4_rep3


title: dendritic_cell_ko_LPS_rep1


title: dendritic_cell_ko_LPS_rep3


title: dendritic_cell_ko_IL4_rep1


title: dendritic_cell_ko_control_rep2


title: CD19+ cells control/healthy twin (replicate 3)

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: Control R3

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing:
Data were extracted with Genome Studio V2011.2. Each methylation data point is obtained from a combination of the Cy3 and Cy5 fluorescent intensities from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each data point. For data processing, we transformed Beta values into M-values and used limma Bioconductor package for the differential methylation analysis. Given the following observations (1) technical variability was similar to biological variability, (2) many DNA methylation changes we expected to be mild, and (3) the reduced number of samples (1 twin pair) we made a conservative selection of probes as candidate differentially methylated sites: (i) 10% or greater difference in the Betavalue DNA methylation between MZ twins, (ii) p-value smaller than 0.01 and (iii) in the three replicates the Beta-value estimated of one twin were always larger or always smaller than the other twin.
The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: CD19+ cells control/healthy twin

label_protocol: Standard Illumina Protocol

growth_protocol: Human B lymphocytes were isolated using MACS CD19 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol

extract_protocol: Proteinase K extraction

tag: subject

value: control/healthy twin

value: peripheral blood

value: CD19+ cells (B lymphocytes)


title: dendritic_cell_ko_control_rep3

value: 7-8 weeks


title: 14d mineralising +/- HDACi replicate 4

city: Dublin

first: Hnery

middle: Fergus

last: Duncan

address: Lincol Place

department: Restorative Dentistry

country: Ireland

institute: Dublin Dental University Hospital, Trinity College Dublin

description: Rat DPC alpha MEM + mineralising stimluli (B-glycerophosphate, Ascorbic acid, Dexamthasone) 24hrs SAHA, 37˚C, 5% CO2 14 days

hyb_protocol: Hybridization and washing of the arrays was carried out using the Agilent Gene Expression Hybridization Kit and Gene Expression Wash Pack according the manufacturer’s instructions.

scan_protocol: Slides were scanned using the GenePix personal 4100A scanner (Axon) and data was extracted with GenePix Pro 6.1 (Axon).

data_processing: Spots were flagged absent if the signal was less than background +1 standard deviation in both fluorescent channels. Raw data was exported to GeneSpring GX10 and signals for each replicate spot were background corrected and normalized using Loess normalization. Log2 fluorescence ratios were generated for each replicate spot and averaged. Oligonucleotides were excluded from analysis if >50% of replicates in each condition were flagged absent.

organism: Rattus norvegicus

source_name: Mineralising control, rat DPC alpha MEM + mineralising stimluli (B-glycerophosphate, Ascorbic acid, Dexamthasone) 37˚C, 5% CO2 14 days

label_protocol: mRNA was labelled with Cy5 or Cy3 using the Agilent Two-Color Low RNA input Linear Amplification Kit PLUS

growth_protocol: Cells were cultured in supplemenetd alpha MEM in the presence of differentiation stmuli for mineralisation, 37˚C 5% CO2 24h or 14 d.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen, West Sussex, UK). mRNA was isolated on the RNAeasy mini-column assembly (Qiagen)

treatment_protocol: Cultures were detached with trypsin/EDTA, homogenized for 30 s using a T10 basic S2-Ultra-Turrax tissue disrupter (IKA, Staufen, Germany)

value: Strain Wistar Hann

tag: tissue

value: dental pulp

tag: agent

value: no SAHA

source_name: HDACi, rat DPC alpha MEM + mineralising stimluli (B-glycerophosphate, Ascorbic acid, Dexamthasone) + 1uM SAHA (24 hrs) 37˚C, 5% CO2 14 days

value: 1 uM SAHA


title: dendritic_cell_ko_IL4_rep3

value: male

tag: cell type

value: bone marrow-derived DC

value: CD11C-positive DCs


title: 14d mineralising +/- HDACi replicate 3

tag: strain


title: CD19+ cells CVID twin (replicate 3)

description: CVID R3

source_name: CD19+ cells CVID twin

value: CVID twin


title: 14d mineralising +/- HDACi replicate 2


title: dendritic_cell_ko_LPS_rep2

value: LPS


title: CD19+ cells control/healthy twin (replicate 1)

description: Control R1


title: CD19+ cells CVID twin (replicate 2)

description: CVID R2


title: Left Atrial Tissue RNASeq

type: SRA

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

library_source: transcriptomic

data_processing:
Basecalls and deplexing performed using CASAVA version 1.4.
mRNAseq reads aligned using tophat version 2.0.4 to hg19 using the options: read mismatches (2).
htseq counts was used to obtain gene level counts against the ensembl transcript annotation version 71.
FeatureCounts was used to count reads that fell within the ensembl transcript annotation version 71.
Provision of raw data for this study, even to dbGaP, was not permitted per the study IRB. Therefore, raw data are not available for this study.
Genome_build: hg19
Supplementary_files_format_and_content: Count files, each column is a sample and each row is a gene; phenotype files contain covariate data.

molecule: polyA RNA

source_name: Discarded Left Atrial Tissue

growth_protocol: Left atrial discarded surgical tissues

extract_protocol:
RNA was harvested using Qiagen total RNA kits
RNA libraries for RNASeq were prepared for sequencing using standard Illumina protocols (Part # 15015050, Rev A.) at University of Chicago Genomics Facility

value: heart

tag: tissue compartment

value: Left Atrial Tissue


title: CD19+ cells CVID twin (replicate 1)

description: CVID R1


title: CD19+ cells control/healthy twin (replicate 2)

description: Control R2


title: 14d mineralising +/- HDACi replicate 1


title: 24h mineralising +/- HDACi replicate 4

description: Rat DPC alpha MEM + mineralising stimluli (B-glycerophosphate, Ascorbic acid, Dexamthasone) 37˚C, 5% CO2 24 hrs

source_name: Mineralising control, rat DPC alpha MEM + mineralising stimluli (B-glycerophosphate, Ascorbic acid, Dexamthasone) 37˚C, 5% CO2 24 hrs

source_name: HDACi, rat DPC alpha MEM + mineralising stimluli (B-glycerophosphate, Ascorbic acid, Dexamthasone) + 1uM SAHA 37˚C, 5% CO2 24 hrs


title: 24h mineralising +/- HDACi replicate 1


title: D39

description:
gene expression data of control RPE
Dicer1 flox/+ Dct cre mice where mated with Dicer1folx/flox mice. Pups where sacrifced at P5 and enucleated. Eyes where the dissected isolating the RPE.

data_processing:
Probe-set analyses was performed. RMA normalization and summarization by mean, all were done by Partek Genomics suite (version 6.6)
Log2 expression intensities after normalization and summarization, as implicated in the data processing raw.

value: retinal pigmented epithelium (RPE)

tag: treatment

value: Control RPE


title: D36

description:
gene expression data of Dicer1 deficient  RPE
Dicer1 flox/+ Dct cre mice where mated with Dicer1folx/flox mice. Pups where sacrifced at P5 and enucleated. Eyes where the dissected isolating the RPE.

value: The Dct-Cre mice where crossed with Dicer1loxP to establish to establish Dicer1loxP/loxP;Dct-Cre


title: D37


title: T59_PBK_inh_5_uM_3__Signal

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

description: replicate 3

data_processing: The non-normalized data from Illumina was imported and quantile normalized using J-Express software (Molmine).  Quantile normalisation (Bolstad et al., 2002) makes different arrays comparable by making sure that the distribution of intensities are the same across arrays. The normalisation distribution is chosen by averaging each quantile across chips.

source_name: T59_5 uM PBK-inhibitor (HI-TOPK-032)

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: glioblastoma stem-like cell line

tag: treated with

value: 5 uM PBK-inhibitor (HI-TOPK-032)


title: 24h mineralising +/- HDACi replicate 2


title: T59_PBK_inh_5_uM_2_Signal

description: replicate 2


title: T59_PBK_inh_5_uM_1_Signal

description: replicate 1


title: 24h mineralising +/- HDACi replicate 3


title: D38


title: D33


title: T59_3__Signal

description: replicate 3

source_name: T59_none (non-treated control)

value: none (non-treated control)


title: D35


title: D34


title: T08_PBK_inh_5_uM_3_Signal

description: replicate 3

source_name: T08_5 uM PBK-inhibitor (HI-TOPK-032)


title: T59_2_Signal

description: replicate 2


title: ROR_alpha_gamma_dKO_replicate3

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

description: Gene expression in mouse liver with ROR_alpha ROR_gamma double depletion at ZT22.

hyb_protocol: About 2ug cDNA was hybridized at 45°C for 16h to the Mouse Gene 2.0ST array. Arrays were washed and stained using the GeneChIP Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: Array images were captured on a GCS3000 laser scanner (Affymetrix).

data_processing: Raw images were analyzed using Partek Genomics Suite to extract individual probe intensities. Subsequent data analysis was performed using BioConductor. Raw probe signal values were background and quantile normalized and summarized by probe sets using the RMA algorithm. Final differential expression calls were determined using the SAM algorithm.

source_name: Mouse liver at ZT22

label_protocol: RNA from each liver was individually processed with the Ambion WT expression kit and GeneChIP WT terminal labeling and control kit (Affymetrix) and hybridized to the Mouse Gene 2.0 ST arrays (Affymetrix)

growth_protocol: RORalpha floxed mice (Stock Number DG15) were obtained from ICS, and RORgamma floxed mice were obtained from Jackson Laboratory. Mice were housed on a temperature-controlled specific-pathogen free facility with 12:12-hour light–dark cycle (lights on at 07:00, lights off at 19:00). Experiments were carried out on 12–16-week-old male mice. All animal studies were performed with an approved protocol from the University of Pennsylvania Perelman School of Medicine Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was extracted from each mouse liver sample using Trizol extraction followed by QIAGEN Rneasy Kit according to the manufacture's instructions.

treatment_protocol: Mice were euthanized at 5am (ZT22).

value: liver

tag: genotype

value: ROR_alpha ROR_gamma double knockout

tag: time


title: ROR_alpha_gamma_dKO_replicate4


title: ROR_alpha_gamma_dKO_replicate2


title: T59_1_Signal

description: replicate 1


title: T08_PBK_inh_5_uM_2_Signal

description: replicate 2


title: OCI-P8p [MIP]

city: Miami

first: Tan

middle: A

last: Ince

state: FL

address: 1501 NW 10th Avenue, Rm 926

department: Sylvester Cancer Center

institute: University of Miami - Miller School of Medicine

description:
A/T Array: a520683-00-805769-070211-4108258-85069.CEL
C/G Array: a520683-00-805769-070211-4108258-85000.CEL

hyb_protocol: Hybridization was performed by Affymetrix according to the platform protocol

scan_protocol: Scanning was performed by Affymetrix

data_processing:
Data processing was performed by Affymetrix
Tables contain signal A intensity and signal B intensity, copynumber, Allele Ratio and Allelic Difference as provided by Affymetrix

source_name: Ovarian cell line

label_protocol: Labeling was performed by Affymetrix according to the platform protocol

growth_protocol: Cells were grown in 10cm dishes and extracts were harvested at 80% confluency

extract_protocol: Cell monolayers were lysed directly in RLT+ buffer and homogenized with Qiashredder columns (Qiagen Allprep kit).

tag: histology

value: Papillary Serous

tag: sample origin

value: Primary

tag: sample type

value: fresh


title: OCI-P5x [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85058.CEL
C/G Array: a520683-00-805770-070211-4108258-85165.CEL

value: Xenograft


title: T08_PBK_inh_5_uM_1_Signal

description: replicate 1


title: T65_PBK_inh_5_uM_3_Signal

description: replicate 3

source_name: T65_5 uM PBK-inhibitor (HI-TOPK-032)


title: OCI-P6p [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85035.CEL
C/G Array: a520683-00-805770-070211-4108258-85125.CEL


title: T65_PBK_inh_5_uM_2_AVG_Signal

description: replicate 2


title: ROR_alpha_gamma_dKO_replicate1


title: OCI-P1a [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85074.CEL
C/G Array: a520683-00-805769-070211-4108258-85023.CEL

value: Ascites


title: WT_replicate4

description: Gene expression in mouse liver at ZT22.

value: wild type


title: OCI-C2p [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85030.CEL
C/G Array: a520683-00-805770-070211-4108258-85212.CEL

value: Clear cell

value: frozen


title: T65_PBK_inh_5_uM_1_Signal

description: replicate 1


title: OCI-D1p [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85039.CEL
C/G Array: a520683-00-805769-070211-4108258-85022.CEL

value: Dysgerminoma


title: OCI-P9a2 [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85057.CEL
C/G Array: a520683-00-805770-070211-4108258-85113.CEL


title: OCI-E3x [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85037.CEL
C/G Array: a520683-00-805769-070211-4108258-85017.CEL

value: Endometrioid


title: OCI-P7a [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85032.CEL
C/G Array: a520683-00-805769-070211-4108258-85009.CEL


title: OCI-P3a [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85028.CEL
C/G Array: a520683-00-805770-070211-4108258-85115.CEL


title: T08_3.AVG_Signal

description: replicate 3

source_name: T08_none (non-treated control)


title: OCI-CSp [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85056.CEL
C/G Array: a520683-00-805770-070211-4108258-85146.CEL

value: Carcinosarcoma


title: FCI-P1p [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85064.CEL
C/G Array: a520683-00-805769-070211-4108258-85024.CEL


title: OCI-EP1p [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85033.CEL
C/G Array: a520683-00-805770-070211-4108258-85133.CEL

value: Mixed Endometrioid and Serous


title: T08_2.AVG_Signal

description: replicate 2

value: glioblastoma stem-like cell line


title: WT_replicate1

description: Gene expression in mouse liver at ZT22.


title: T65_2.AVG_Signal

description: replicate 2

source_name: T65_none (non-treated control)


title: WT_replicate3

description: Gene expression in mouse liver at ZT22.


title: T08_NS_2.AVG_Signal

description: replicate 2

source_name: T08_non-silencing vector

value: non-silencing vector


title: T65_3.AVG_Signal

description: replicate 3

value: none (non-treated control)


title: WT_replicate2

description: Gene expression in mouse liver at ZT22.

value: liver


title: T08_NS_3.AVG_Signal

description: replicate 3


title: T65_NS_3.AVG_Signal

description: replicate 3

source_name: T65_non-silencing vector


title: T08_1.AVG_Signal

description: replicate 1


title: OCI-C1p [MIP]

description:
A/T Array: a520683-00-805769-070211-4108258-85075.CEL
C/G Array: a520683-00-805770-070211-4108258-85163.CEL


title: OCI-P4p [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85200.CEL
C/G Array: a520683-00-805770-070211-4108258-85126.CEL


title: T65_1.AVG_Signal

description: replicate 1


title: T08_NS_1.AVG_Signal

description: replicate 1


title: T65_NS_1.AVG_Signal

description: replicate 1


title: T65_NS_2.AVG_Signal

description: replicate 2


title: OCI-U1a [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85201.CEL
C/G Array: a520683-00-805770-070211-4108258-85130.CEL

value: Mullerian NOS


title: shRNA3_T08_2__AVG_Signal

description: replicate 2

source_name: T08_PBK-shRNA construct

value: PBK-shRNA construct3


title: shRNA3_T65_3__AVG_Signal

description: replicate 3

source_name: T65_PBK-shRNA construct


title: shRNA2_T08_2__AVG_Signal

description: replicate 2

value: PBK-shRNA construct 2


title: shRNA3_T08_1__AVG_Signal

description: replicate 1


title: shRNA3_T08_3__AVG_Signal

description: replicate 3


title: shRNA2_T08_3__AVG_Signal

description: replicate 3


title: shRNA3_T65_2__AVG_Signal

description: replicate 2


title: OCI-P9a1 [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85152.CEL
C/G Array: a520683-00-805770-070211-4108258-85145.CEL

value: Papillary Serous

value: fresh


title: shRNA3_T65_1__AVG_Signal

description: replicate 1


title: dendritic_cell_ko_control_rep1

tag: strain background

tag: gender

value: male

tag: age

value: 7-8 weeks

tag: genotype/variation

value: bone marrow-derived DC

tag: sample group

value: control

value: CD11C-positive DCs


title: shRNA2_T08_1__AVG_Signal

description: replicate 1


title: M0191.bdl vs M0171.Col-6d-replicate 2

city: saskatoon

first: daoquan

last: xiang

state: SK

address: 110 Gymnasium Place

country: Canada

institute: NRC Saskatoon

hyb_protocol: Hybridized to these slides following the protocol described in http://ag.arizona.edu/microarry.

scan_protocol: ScanArray 4000 laser scanner

data_processing: The image analysis and signal quantification were performed using the QuantArray orogram (GSI Lumonics, Oxford, California)

organism: Arabidopsis thaliana

source_name: 6 days of M0191.bdl

label_protocol: After purification of the aRNA, the NHS-ester dyes were coupled to the modified bases of aRNA in a chemical reaction. The aRNA samples representing four biological replicates from each experiment were labeled (2 cy3 and 2 cy5) following the protocol described inhttp://ag.arizona.edu/microarray.

growth_protocol: Plants were grown under 16h light / 8h dark photoperiod with constant temperature of 220C at 120 μE m-2 s-1 light intensity

extract_protocol:
Total RNA extracted using RNAqueous-Micro kit  following manufacturer's instructions
aRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750).

treatment_protocol: embryos isolated from 6 days of pollination, M0191 is female and bdl is male

tag: ecotype

tag: tissue

value: isolated embryo of M0191Xbdl

tag: stock lines

value: M0191 and bdl

source_name: 6 days M0171.Col-0

treatment_protocol: embryos isolated from 6 days of pollination, M0171 is female and Col-0 is male

value: M0171 and Col-0

value: embryo


title: shRNA2_T65_3__Signal

description: replicate 3

tag: cell type

value: glioblastoma stem-like cell line


title: M0191.bdl vs M0171.Col-6d-replicate 4


title: shRNA2_T65_1_Signal

description: replicate 1


title: OCI-P8p

description: OCI: ovarian-carcinoma-Ince

data_processing: The microarray data were normalized using the quantile normalization method in the Linear Models for Microarray Data package in the R language environment

source_name: OCI ovarian cancer cell line

label_protocol: Biotin-labeled cRNA were prepared with the Illumina TotalPrep RNA Amplivifation Kit (Ambion, Cat#IL1791)

value: Primary

value: Papillary serous

tag: medium

value: OCMI


title: shRNA2_T65_2_Signal

description: replicate 2

tag: cell line


title: RMG-1-HAM-PN-6

description: SOC: standard-ovarian-cell line

source_name: SOC ovarian cancer cell line

value: ascites

value: Clear cell

value: Ham's F12


title: OCI-E2p [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85151.CEL
C/G Array: a520683-00-805770-070211-4108258-85124.CEL

value: Endometrioid

value: fresh


title: OV90-OCMI-PN-4

description: SOC: standard-ovarian-cell line


title: OCI-P2a [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85175.CEL
C/G Array: a520683-00-805770-070211-4108258-85169.CEL

value: Papillary Serous

value: Ascites


title: M0191.bdl vs M0171.Col-3d-replicate 4

source_name: 3 days of M0191.bdl

treatment_protocol: embryos isolated from 3 days of pollination, M0191 is female and bdl is male

source_name: 3 days M0171.Col-0

treatment_protocol: embryos isolated from 3 days of pollination,  M0171 is female and Col-0 is male


title: OV90-BASE15-PN-4

description: SOC: standard-ovarian-cell line


title: M0191.bdl vs M0171.Col-6d-replicate 3


title: OCI-C3x [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85160.CEL
C/G Array: a520683-00-805770-070211-4108258-85135.CEL

value: Xenograft


title: M0191.bdl vs M0171.Col-3d-replicate 3


title: M0191.bdl vs M0171.Col-3d-replicate 2


title: TOV-112D-BASE15-PN-5

description: SOC: standard-ovarian-cell line

value: primary


title: OCI-E1p [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85148.CEL
C/G Array: a520683-00-805769-070211-4108258-84999.CEL


title: RMG-L-OCMI-PN-8

description: SOC: standard-ovarian-cell line

value: Mucinous


title: TOV-112D-OCMI-PN-5

description: SOC: standard-ovarian-cell line


title: FCI-P2p [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85161.CEL
C/G Array: a520683-00-805770-070211-4108258-85120.CEL


title: M0191.bdl vs M0171.Col-3d-replicate 1

value: isolated embryo of M0191Xbdl

value: M0191 and bdl


title: OCI-P9a2

description: OCI: ovarian-carcinoma-Ince


title: OCI-C2p

description: OCI: ovarian-carcinoma-Ince

value: frozen


title: RMG-L DF-PN-8

description: SOC: standard-ovarian-cell line


title: OCI-C5x [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85189.CEL
C/G Array: a520683-00-805770-070211-4108258-85123.CEL


title: A2780-OCMI-P14

description: SOC: standard-ovarian-cell line

value: Adenocarcinoma NOS


title: SKOV3-McCOY-PN-11

description: SOC: standard-ovarian-cell line

value: McCoy's 5A


title: OCI-P5x

description: OCI: ovarian-carcinoma-Ince

value: Papillary serous


title: OCI-P6p

description: OCI: ovarian-carcinoma-Ince

value: Primary

value: OCMI


title: OCI-P1a

description: OCI: ovarian-carcinoma-Ince


title: M0191.bdl vs M0171.Col-6d-replicate 1

value: M0171 and Col-0

value: embryo


title: OCI-P3a

description: OCI: ovarian-carcinoma-Ince


title: FCI-P1p

description: OCI: ovarian-carcinoma-Ince


title: OCI-M1p [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85153.CEL
C/G Array: a520683-00-805770-070211-4108258-85132.CEL


title: OCI-C4p [MIP]

description:
A/T Array: a520683-00-805770-070211-4108258-85156.CEL
C/G Array: a520683-00-805769-070211-4108258-85013.CEL

value: Clear cell


title: A2780-RPMI-P14

description: SOC: standard-ovarian-cell line

value: RPMI


title: OCI-CSp

description: OCI: ovarian-carcinoma-Ince

value: Carcinosarcoma

value: fresh


title: OCI-EP1p

description: OCI: ovarian-carcinoma-Ince

value: Mixed Endometrioid and Pap. serous


title: OCI-P7a

description: OCI: ovarian-carcinoma-Ince

value: Ascites


title: OCI-C1p

description: OCI: ovarian-carcinoma-Ince


title: OCI-P4p

description: OCI: ovarian-carcinoma-Ince


title: OCI-E1p

description: OCI: Ovarian-Carcinoma-Ince

value: Endometrioid


title: OCI D1p

description: OCI: ovarian-carcinoma-Ince

value: Dysgerminoma


title: OCI-P2a

description: OCI: Ovarian-Carcinoma-Ince


title: OCI-E2p

description: OCI: ovarian-carcinoma-Ince


title: OCI-E3x

description: OCI: ovarian-carcinoma-Ince

value: Xenograft


title: OCI-U1a

description: OCI: ovarian-carcinoma-Ince

value: Mullerian NOS


title: OCI-P9a1

description: OCI: ovarian-carcinoma-Ince


title: OCI-C5x

description: OCI: ovarian-carcinoma-Ince

value: frozen


title: OCI-C3x

description: OCI: ovarian-carcinoma-Ince


title: FCI-P2p

description: OCI: ovarian-carcinoma-Ince


title: OCI-C4p

description: OCI: ovarian-carcinoma-Ince


title: OCI-C5x [250K_Sty]

description: Ovarian cancer cell line-250KSty

hyb_protocol: The biotinylated fragments are added to a hybridization solution containing a biotinylated control oligonucletide (for quality control), and hybridized to a microarray chip overnight at 49°C.

scan_protocol: The chips are then transferred to a fluidics instrument that performs washes to remove DNA that has not hybridized to its complementary oligonucleotide probe. The bound DNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE) followed by biotinylated anti-streptavidin, followed by SAPE. Each DNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Invariant set normalization was performed as described in Lee and Wong, Genome Biology 2001, 2(8).

source_name: Ovarian cancer cell line

label_protocol: The fragmented PCR products are labeled with a single biotin at each free 3'OH using terminal deoxynucleotidyl transferase and a dideoxy biotinylated nucleoside triphosphate.

extract_protocol: Cell monolayers were lysed directly in RLT+ buffer and homogenized with Qiashredder columns (Qiagen Allprep kit).  Frozen tissues were homogenized by rotor-stator directly in RLT+.


title: OCI-U1a [250K_Sty]

description: Ovarian cancer cell line-250KSty


title: SKOV3-OCMI-PN-11

description: SOC: standard-ovarian-cell line

value: ascites

value: Adenocarcinoma NOS


title: OV90 [250K_Sty]

description: Standard ovarian cancer cell line-250KSty

source_name: Standard ovarian cancer cell line

value: Papillary serous


title: Caov-4 [250K_Sty]

value: Metastatic site:fallopian tube


title: T-U1a [250K_Sty]

description: Ovarian tumor tissue-250KSty

source_name: Ovarian tumor tissue


title: RMG-1-OCMI-PN-6

description: SOC: standard-ovarian-cell line

value: OCMI


title: A2780 [250K_Sty]


title: Caov-3 [250K_Sty]


title: SKOV3 [250K_Sty]


title: T-E3x [250K_Sty]

description: Ovarian tumor tissue-250KSty


title: COLO704 [250K_Sty]

value: Unknown


title: T-P4p [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Primary


title: TOV-112D [250K_Sty]


title: ES2 [250K_Sty]

value: Clear cell


title: T-P2a [250K_Sty]

description: Ovarian tumor tissue-250KSty


title: T-M1p [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Mucinous


title: T-C1p [250K_Sty]

description: Ovarian tumor tissue-250KSty


title: T-E1p [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: fresh


title: T-P1a [250K_Sty]

description: Ovarian tumor tissue-250KSty


title: T-EP1p [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Mixed Endometrioid and Pap. serous


title: L

city: Yahaba-Cho, Shiwa-Gun

first: Wataru

last: Habano

state: Iwate

address: 2-1-1 Nishitokuta

department: Pharmacodynamics and Molecular Genetics

institute: Iwate Medical University

hyb_protocol: After fragmentation, Cy3-labelled cRNA was hybridized on SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) using Hybridization Gasket Slide Kit and Gene Expression Hybridization Kit.  After hybridization, microarrays were washed by using Gene Expression Wash Buffer Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C using one color scan setting (Dye channel Green, TIFF file dynamic range 20bit, Scan Resolution 3um, R/G PMT gain 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software version 12.6.0 (Agilent) using the conditions (Grit template 039494_D_F_20120628, FE protocol GE１_1010_Sep10, QC Metric GE１_QCMT_Sep10).

source_name: liver adult

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions.

growth_protocol: The 3 hepatoma cells were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total cellular RNA was isolated using RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: The 3 hepatoma cells were cultured with DMEM medium supplemented with 10% heat-inactivated fetal bovine serum. The cells were treated with or without 5μM of DAC for 72hr..

value: liver

value: Male


title: OCI-M1p

description: OCI: ovarian-carcinoma-Ince


title: L_1

hyb_protocol: Human Infinium HD Methylation Assay, Manual Protocol RevA (standard Illumina Protocol)

scan_protocol: iScan Reader (illumina) (standard recommended Illumina scanner setting)

data_processing: GenomeStudio V2011.1/Methylation Module v1.9.0

label: Alexa555 and Alexa647

source_name: liver tissue, adult

extract_protocol: genomic DNA was extracted and purified from tissues by standard proteinaseK/SDS and phenol/chloroform method.

value: 64 years old

value: Liver

tag: disease state

value: Normal


title: SI

source_name: small intestine, adult

value: small intestine


title: L_2

label_protocol: Human Infinium HD Methylation Assay, Manual Protocol RevA (standard Illumina Protocol)


title: NLA

description: Sample name: BA0002_06_a

extract_protocol: genomic DNA was extracted and purified from tissues and cultured cells by standard proteinaseK/SDS and phenol/chloroform method.

treatment_protocol: The 3 hepatoma cells were cultured with DMEM medium supplemented with 10% heat-inactivated fetal bovine serum. The cells were treated with or without trichostatin A for 24hr.

value: 38 years old


title: T-P9a [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Ascites


title: SI_2

source_name: small intestine tissue, adult

value: 25 years old

value: Small intestine


title: 3D

description: Gene expression after treatment of DAC

source_name: JHH1, treated with DAC

tag: treatment

value: DAC


title: 3C

description: Gene expression without treatment


title: T-C5x [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Xenograft

value: frozen


title: NLF

description: Sample name: BA0002_07_a

source_name: liver tissue, fetal

value: 18 weeks old

value: LIver


title: 2D

description: Gene expression after treatment of DAC

source_name: HuH7, treated with DAC


title: SI_1


title: T-C3x [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Clear cell

value: fresh


title: T-P7a [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Papillary serous


title: T-D1p [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Primary

value: Dysgerminoma


title: T-P5x [250K_Sty]

description: Ovarian tumor tissue-250KSty


title: 2C

description: Gene expression without treatment

value: liver


title: 1C

description: Gene expression without treatment


title: 1D

description: Gene expression after treatment of DAC

source_name: Hepg2, treated with DAC


title: Capan-1 cells 24h after siRNA transfection control_2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
gene expression data from Capan-1 cells 24h after siRNA transfection
NC_8

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of HG-U133_Plus_2 -type from Affymetrix. A Custom CDF Version 14 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Capan-1 human pancreatic cancer cell line with unspecific siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown in DMEM High Glucose Pyruvate with glutamine (Gibco, #41966) with 10% FBS (Gibco, #10270) and 1% Pen/Strep (Gibco, #15140) and subcultured twice a week by trypsinization

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Cells were transfected with siRNA against human TBL1X (Qiagen, SI04329514) using Lipofectamine 2000 (Invitrogen) according to manufacturer's instructions

value: control group (unspecific siRNA)


title: Capan-1 cells 24h after siRNA transfection control_1

description:
gene expression data from Capan-1 cells 24h after siRNA transfection
NC_9


title: Capan-1 cells 24h after siRNA transfection_3

description:
gene expression data from Capan-1 cells 24h after siRNA transfection
TBL1_10

source_name: Capan-1 human pancreatic cancer cell line with TBL1_siRNA

value: siRNA-mediated knockdown of TBL1X


title: JHH1_T

description: Sample name: BA0002_05_a

source_name: JHH1, TSA treated

value: Liver

tag: agent

value: TSA

value: Cancer


title: OVCAR3 [250K_Sty]

value: Ascites

tag: histology

value: Adenocarcinoma NOS


title: HepG2_T

description: Sample name: BA0002_02_a

source_name: HepG2, TSA treated


title: OCI-P1a [250K_Sty]

description: Ovarian cancer cell line-250KSty

tag: sample origin


title: OCI-C1p [250K_Sty]

description: Ovarian cancer cell line-250KSty

tag: sample type


title: JHH1_C

description: Sample name: BA0002_04_a


title: green-00001: New8kPr111_C221601m30

status: Public on Jun 15 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: reference

tag: tissue name

value: prostate

tag: cell line name

value: low grade prostatic intraepithelial neoplasia

tag: Sex

value: M

tag: genotype

tag: tumor location

value: PR111 cells injected s.c in C3(1)/Tag mice develop occassionally small adenocarcinomas

value: lung metastasis

value: lung


title: OCI-E3x [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Xenograft

value: Endometrioid

value: frozen


title: green-00001: New8kPr111_C221601m29

scan_protocol: See mage-tab files linked to series entry for additional details

value: prostae


title: Capan-1 cells 24h after siRNA transfection_1

description:
gene expression data from Capan-1 cells 24h after siRNA transfection
TBL1_12


title: green-00001: New8kPr111_C221601m31

data_processing: See mage-tab files linked to series entry for additional details


title: Capan-1 cells 24h after siRNA transfection_2

description:
gene expression data from Capan-1 cells 24h after siRNA transfection
TBL1_11


title: green-00001: VG_8k4New111_C14401m81

label_protocol: See mage-tab files linked to series entry for additional details

value: PR14C1 cells injected s.c in C3(1)/Tag mice develop adenocarcinomas which show nests of cells surrounded by fibrous stroma


title: green-00001: VG_8k3New111_C14401m80

extract_protocol: See mage-tab files linked to series entry for additional details


title: green-00001: 8KReverNewC2_111_4601_m86


title: green-00001: VG_8k1New111_C14401m79


title: green-00001: VG_1New8k111_C14401m78


title: green-00001: G_New8k111C131501m73


title: green-00001: 8kNewPr111_14v1p4m13

value: primary invasive carcinoma


title: green-00001: 8kNewPr111_14v1p4m11

value: PR14 cells injected s.c in C3(1)/Tag mice develop adenocarcinomas with well-differentiated glandular pattern


title: T-C2p [250K_Sty]

description: Ovarian tumor tissue-250KSty

value: Primary

value: Clear cell


title: Capan-1 cells 24h after siRNA transfection control_3

description:
gene expression data from Capan-1 cells 24h after siRNA transfection
NC_7

value: control group (unspecific siRNA)


title: green-00001: 8kNew111_14v1p4m12


title: green-00001: 8kNew111_14_4601_m84


title: OCI-P9a [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Ascites

value: Papillary serous

value: fresh


title: green-00001: 8kReversNew17_111_4601_m83

value: prostate

value: high grade prostatic intraepithelial neoplasia

value: M

value: low grade prostatic intraepithelial neoplasia


title: OCI-P2a [250K_Sty]

description: Ovarian cancer cell line-250KSty


title: HuH7_C

description: Sample name: BA0002_03_a

value: Liver

value: Cancer


title: green-00001: 8kPr111_17M62103100p1090600

value: PR111 cells injected s.c in C3(1)/Tag mice develop occassionally small adenocarcinomas


title: green-00001: 8kNewPr111_1712701m37


title: green-00001: 8kNew111_17m12701m36


title: OCI-M1p [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Mucinous


title: OCI-P4p [250K_Sty]

description: Ovarian cancer cell line-250KSty


title: OCI-D1p [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Dysgerminoma

value: frozen


title: green-00001: 8kNew111_17_4601_m82


title: HepG2_C

description: Sample name: BA0002_01_a


title: OCI-P7a [250K_Sty]

description: Ovarian cancer cell line-250KSty


title: OCI-C3x [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Xenograft


title: green-00001: 8kNewPr111_14v1p4m14

value: primary invasive carcinoma


title: OCI-P5x [250K_Sty]

description: Ovarian cancer cell line-250KSty


title: OCI-E1p [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Primary

value: Endometrioid


title: 24103.L

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

hyb_protocol: The labelled and purified reference samples were mixed and divided into aliquots before combining it with a labelled sample. Each of the 36 labelled samples were co-hybridized with an aliquot of the labelled reference sample and a hybridization blocker containing polydA (Invitrogen Corporation, CA, USA) and Yeast tRNA (Invitrogen Corporation, CA, USA) to 27k pig oligonucleotide microarrays (GEO accession: GPL5972) using a Discovery XT hybridisation station (Ventana Discovery Systems, Tucson, AZ, USA). Chip Prep-2 was transferred from 4 ºC to room temperature 1 hour before use. ChipSpread was prepared by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) followed by incubation at room temperature for 1 hour before use. Labels were printed, trimmed and placed on the slides. The Chip Map reagents (Chip Prep-1, -2 and - 3) were mixed by inversion; the caps were removed and the reagents were placed in the Discovery. The slides were placed in the machine and the run was initiated. The slides were covered with 2.5 mL ChipSpread when the message appeared and the machine used app. 1.5 hours for pre-hybridization of the slides. The Chiphybe80 was mixed and 200 µL were added to the sample (<20 µL) followed by careful mixing. The sample mixtures were heated at 90°C for 3 minutes in a PCR machine carefully mixed by pipetting. The "button" on the machine was pressed to prepare the slides for hybridization. When prompted to, the samples were applied to the slides which were hybridized at 48 ºC for 6 hours. Oil was wiped from the backside of the slides using a clean-room napkin and the slides were placed in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, an equal number of slides were placed in two slide-holders and continued in parallel. The slide-holder was transferred to a HTW filled with RiboWash and washed for 2 min with magnetic stirring at 700 rpm. The HTW was refilled with RiboWash and the wash was repeated. The slide-holder was dipped in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). The slide-holder was then transferred to a HTW filled with 2x SSC and washed for 2 min with magnetic stirring at 700 rpm followed by refill of the HTW with 2x SSC and repetition of the wash. The slide-holder was dipped 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and the holder was left submerged in 0.1x SSC. The slides were transferred to a mBox slide holder placed in a mTub filled with Elga H2O. Arrays were dried by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.27, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = MorphologicalClosingFollowedByOpening

data_processing: Statistical analysis was carried out in the R computing environment (version 2.9.0 for Linux) using the package Linear Models for Microarray Analysis (Limma, version 2.18.0) which is part of the Bioconductor project. The log2-transformed median intensity ratios of Alexa-647 to Alexa-555 (not background corrected) were first normalized within-slide using the loess method and subsequently normalized between arrays using the scale method, both as implemented in Limma. The individual spots were weighted by a spot binary weight matrix where spots flagged by GenePix as non-detectable were given a weight of zero and a sum of the spot weights were calculated for each probe across the 27 microarrays in the two groups (high and low skatole). Probes with a sum of 10 or less in either of the two groups were excluded from further analysis together with the control spots. A linear model including array quality weights was fitted to the normalized data set which subsequently was subjected to an empirical Bayes method to determine differentially expressed genes between the samples of high skatole level and samples of low skatole level. The false discovery rate (FDR) was taken into consideration using the method of Benjamini and Hochberg as implemented in Limma and an adjusted P-value below 0.05 was considered significant.

organism: Sus scrofa

label_protocol: Total-RNA was extracted from each sample and DNase treated using RNeasy Maxi Kit (Qiagen) following the enclosed protocols. Quantities were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE, USA) and qualities were examined by the 28S:18S rRNA ratio using the RNA 6000 Nano LabChip Kit on 2100 Bioanalyzer (Agilent Technologies, CA, USA). Alexa Flour-labeled cDNA was synthesized from 20 µg of total-RNA using Superscript Plus Direct cDNA Labeling System (Invitrogen) and purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. "Green" spike-in RNA was added to the common reference samples and "red" spike-in RNA was added to the samples.

growth_protocol: The animals were raised on the same farm under identical conditions.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen).

tag: breed

value: Danish Landrace

tag: gender

value: boar, uncastrated

tag: weight

value: approx. 80 kg

value: liver

tag: animal id

tag: skatole level

value: low

value: DLY X Hampshire

value: female

tag: animal

tag: project

value: RN


title: 38337.H

tag: tissue

value: high


title: 37133.H


title: 44338.L


title: 32326.L


title: 36102.L


title: 34333.L


title: OCI-EP1p [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Mixed Endometrioid and Pap. serous

value: fresh


title: 44336.H


title: OCI-C2p [250K_Sty]

description: Ovarian cancer cell line-250KSty

value: Clear cell


title: 19311.H


title: 31329.L


title: 36111.H


title: 46303.H


title: 33137.L


title: 34130.L


title: 17128.H


title: 34107.L


title: 39134.L


title: 22138.L


title: 36302.H


title: Subject 26, Clean Air

city: San Francisco

first: Mehrdad

last: Arjomandi

state: CA

address: 4150 Clement St, 3A-20

institute: UCSF

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134875_HUGENE-1_0-ST-V1_HOLO.262-2-10.rma-gene-default-Signal

hyb_protocol: Hybridization was performed using 5 ug of biotinylated target, which was incubated with GeneChip Human Gene 1.0 ST array at 45 C for 16-20 hours. Following hybridization, non-specifically bound material was removed by washing. Detection of specifically bound target was performed using GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G and raw data was extracted from the scanned images

data_processing: The Data were analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method

source_name: BAL_Clean Air_4hrs

label_protocol: Biotin-labeled target was prepared using 100 ng of total RNA of each sample. cDNA was synthesized using the GeneChip WT Sense Target Labeling and Conttrol Reagents kit. Sense cDNA was fragmented by UDG and APE 1 using the GeneChip WT Terminal Labelling Kit.

growth_protocol: BAL cells were collected via bronchoscopy 20 hours after exposure to clean air, 100 ppb ozone, or 200 ppb ozone.

extract_protocol: RNA was extracted from BAL cells stored in Buffer RLT using the Rneasy kit (Qiagen), and concentration and quality were assessed using the Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: BAL cell pellets were stored in Buffer RLT prior to RNA extraction

tag: subject id

value: Subject 26

value: male

tag: ozone exposure (ppb)

tag: cell type

value: bronchoalveolar lavage (BAL) cells


title: 23312.L


title: Subject 26, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134874_HUGENE-1_0-ST-V1_HOLO.2612-15-09.rma-gene-default-Signal

source_name: BAL_200 ppb Ozone_4hrs


title: 34132.L


title: Subject 24, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134872_HUGENE-1_0-ST-V1_HOLO2411-17-09RLT.rma-gene-default-Signal

value: Subject 24


title: Subject 24, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134871_HUGENE-1_0-ST-V1_HOLO2409-29-09RLT.rma-gene-default-Signal

source_name: BAL_100 ppb Ozone_4hrs


title: 32334.H


title: Subject 15, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134865_HUGENE-1_0-ST-V1_HOLO1504-04-09RLT.rma-gene-default-Signal

value: Subject 15


title: Subject 13, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134863_HUGENE-1_0-ST-V1_HOLO1305-05-09RLT.rma-gene-default-Signal

value: Subject 13


title: Subject 20, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134869_HUGENE-1_0-ST-V1_HOLO2010-20-09RLT.rma-gene-default-Signal

value: Subject 20


title: Subject 26, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134873_HUGENE-1_0-ST-V1_HOLO.2611-3-09.rma-gene-default-Signal


title: 34104.L

value: Danish Landrace

value: boar, uncastrated

value: approx. 80 kg


title: Glycerol 24 h_rep3

type: mixed

city: Dublin 4

first: Sarah

last: Finn

address: University College Dublin

institute: Centre for Food Safety

hyb_protocol: 1)Prepared Cy 5 labelled gDNA (6 µl) was added to Cy3 labelled cDNA (18 µl) for a total volume of 24 µl. 2) To each sample, 6µl of blocking solution (Agilent 5188-5973) and 30 µl of :hybridisation buffer (Agilent 5188-6420) were added. 3) Samples were boiled for 2 min at 95oC and centrifuged for 1 min at 13000 rpm. 4) The gasket slide was placed in hybridization chamber rubber and 50 µl of sample placed directly into centre of gasket slide. 5) When all samples were dispensed the array slide was inserted into the hybridisation chamber, sealed and placed in pre-heated hybridisation over (65˚C) at 10 rpm overnight. 6) Slides were removed from chamber washed according to manufacturer’s instructions (http://www.chem.agilent.com/Library/usermanuals/Public/G2534-90004_HybridizationChamber_User.pdf). 7) Array slides were cleaned with inert gas before measurement.

scan_protocol: Scans were carried out using an Agilent DNA Microarray Scanner, Model G2565, at at 5 µm resolution with Green and Red PMT values set to 100 % and an XDR value of 0.1.  Images generated were saved as multi-image .tiff files.

data_processing: Agilent Feature extraction software was used to process the scanned images of the arrays.  The data generated was then analysed using GeneSpring version 7.3 (Agilent Technologies, Santa Clara, California) based on the log ratio of median Cy3/Cy5 signal normalised to the 50th percentile.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: Salmonella exposed to Glycerol for 24 h

label_protocol: 1)Random priming reactions were set up in 1.5 ml microfuge tubes. Total RNA (10 µg) and 5 µg of random hexamers (Invitrogen, Cat: 48190011) were added to a final volume of 9.4 µl in RNase free water. 2) Samples incubated at 70 ˚C for 5 min and chilled on ice for 10 min. 3) RT reaction mix prepared by using the Stratagene AffinityScript multi-temperature Reverse Transcriptase by adding the following to each tube: 2 µl of 10 X RT buffer; 2 µl of 0.1 M DDT; 0.6 µl of 50 X dNTP’s (25 mM dATP, dGTP, dTTP and 10 mM dCTP[GE Healthcare Lifesciences, Cat: 27-2035-02]); 2 µl of Cy3 dCTP (1 mM stock, GE Healthcare Lifesciences, Cat: PA55321); 4 µl of reverse transcriptase. 4) Samples were vortexed to mix and incubated shaking at 25 ˚C for 10 min. 5) Samples then incubated overnight at 42 ˚C. 6) Freshly prepared 0.1 M NaOH (15 µl) was added and the RNA hydrolysed at 70 ˚C for 10 min. Freshly prepared 0.1 M HCl (15 µl) was added to neutralise the alkali. Samples were placed on ice to cool to room temperature.  7) Qia-quick PCR purification kit (Qiagen, Cat: 28104) was used to remove unincorporated/quenched cy dyes.  Samples eluted into 40 µl RNase free water and dried-down on speed vac to 18 µl.

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 10% Glycerol and incubated statically at 24˚C for 24 h

extract_protocol: 1)Cultures exposed to 10% Glycerol (10 ml) for 24 h were harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions

tag: agent

value: Glycerol

tag: time point

tag: strain

tag: biological replicate

source_name: Reference genomic DNA

label_protocol: 1) Chromosomal DNA (2 µg) added to sterile microfuge tube and brought to 21 µl with RNase free water (Sigma, W4502-1L). 2) 20 µl each of 2.5 X Random primer/reaction buffer mix from the Invitrogen BioPrime® DNA Labelling System (18094011) was added to sample and boiled for 5 min, then put on ice for 5 min. 3) On ice, 5 µl of 10X dNTP mix (10X dNTP mix: 1.2 mM each dATP, dGTP, dTTP; 0.6 mM dCTP; 10 mM Tris pH 8.0; 1 mM EDTA;); 3 µl of Cy5 dCTP (1 mM stock, GE Helathcare Lifesciences, Cat: PA55321); and 1 µl Klenow enzyme from the kit were added. 4) Samples were spun briefly and the reaction mix incubated at 37 ˚C overnight. 5) A Qia-quick PCR purification kit (Qiagen Cat: 28104) was used to remove unincorporated/quenched Cy dyes.  Samples were eluted into 80 µl of RNase free water.  This protocol supplies sufficient labelled DNA for 9 hybridisations.  Samples adjusted to a volume of 50 µl using speed vac.

growth_protocol: Salmonella enterica serovar Typhimurium 4/74 grown to stationary phase at 37˚C

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns).

tag: reference

value: stationary phase at 37˚C


title: 32130.L

value: liver

value: low

value: DLY X Hampshire

value: female

value: RN


title: 33338.H

value: high


title: Subject 38, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134858_HUGENE-1_0-ST-V1_HOLO3807-16-10.rma-gene-default-Signal

value: Subject 38


title: Subject 38, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134857_HUGENE-1_0-ST-V1_HOLO3804-30-10.rma-gene-default-Signal

value: bronchoalveolar lavage (BAL) cells


title: 36327.H


title: 18465.L


title: Subject 1, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134860_HUGENE-1_0-ST-V1_HOL0105-06-08RLT.rma-gene-default-Signal

value: Subject 1


title: Subject 15, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134864_HUGENE-1_0-ST-V1_HOLO1503-07-09RLT.rma-gene-default-Signal

value: Subject 15


title: Subject 1, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134859_HUGENE-1_0-ST-V1_HOL0104-08-08RLT.rma-gene-default-Signal


title: 34108.L


title: Subject 15, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134866_HUGENE-1_0-ST-V1_HOLO1505-09-09RLT.rma-gene-default-Signal


title: Subject 20, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134868_HUGENE-1_0-ST-V1_HOLO2009-15-09RLT.rma-gene-default-Signal

value: male


title: Subject 13, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134861_HUGENE-1_0-ST-V1_HOLO.131-28-09.rma-gene-default-Signal

value: Subject 13


title: Subject 20, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134867_HUGENE-1_0-ST-V1_HOLO2008-13-09RLT.rma-gene-default-Signal

value: Subject 20


title: Subject 38, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134856_HUGENE-1_0-ST-V1_HOLO3806-04-10.rma-gene-default-Signal


title: Subject 24, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134870_HUGENE-1_0-ST-V1_HOLO2408-18-09RLT.rma-gene-default-Signal

value: Subject 24


title: 18462.H

value: Danish Landrace

value: boar, uncastrated

value: approx. 80 kg


title: Subject 13, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134862_HUGENE-1_0-ST-V1_HOLO1303-24-09RLT.rma-gene-default-Signal


title: 37328.L

value: liver


title: 38312.H


title: Glycerol 24 h_rep2

value: Glycerol

value: stationary phase at 37˚C


title: 46111.H

value: DLY X Hampshire

value: female


title: Subject 37, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134855_HUGENE-1_0-ST-V1_HOLO3707-30-10.rma-gene-default-Signal

value: Subject 37


title: Glycerol 6 h_rep2

source_name: Salmonella exposed to Glycerol for 6 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 10% Glycerol and incubated statically at 24˚C for 6 h

value: 6 h


title: Glycerol 24 h_rep1


title: Subject 35, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134851_HUGENE-1_0-ST-V1_HOLO3507-13-10.rma-gene-default-Signal

value: Subject 35

value: bronchoalveolar lavage (BAL) cells


title: Glycerol 6 h_rep1


title: 36137.H

value: high

value: RN


title: 17103.L

value: low


title: Subject 37, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134854_HUGENE-1_0-ST-V1_HOLO3709-10-10.rma-gene-default-Signal

value: male


title: Subject 37, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134853_HUGENE-1_0-ST-V1_HOLO3706-11-10.rma-gene-default-Signal


title: Subject 35, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134852_HUGENE-1_0-ST-V1_HOLO3505-25-10.rma-gene-default-Signal


title: Subject 33, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134845_HUGENE-1_0-ST-V1_HOLO3311-22-09.rma-gene-default-Signal

value: Subject 33


title: Glycerol 1 h_rep2

source_name: Salmonella exposed to Glycerol for 1 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 10% Glycerol and incubated statically at 24˚C for 1 h

value: 1 h


title: Subject 34, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134849_HUGENE-1_0-ST-V1_HOLO3403-09-10.rma-gene-default-Signal

value: Subject 34


title: Glycerol 1 h_rep3


title: Glycerol 6 h_rep3


title: Subject 35, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134850_HUGENE-1_0-ST-V1_HOLO3504-14-10.rma-gene-default-Signal


title: 36130.L

value: Danish Landrace

value: boar, uncastrated

value: approx. 80 kg


title: 22127.H

value: liver


title: Subject 33, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134844_HUGENE-1_0-ST-V1_HOLO3301-10-10.rma-gene-default-Signal


title: Subject 34, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134848_HUGENE-1_0-ST-V1_HOLO3406-29-10.rma-gene-default-Signal