title: Combination, biological rep3

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

institute: IDIBAPS-HOSPITAL CLINIC

description: Gene expression data cells treated with acadesine plus rituximab

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm of the BioConductor Affy Package.

source_name: Tumor xenograft of JEKO-1cell line treated with acadesine-rituximab

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: CB17 mice xenotransplanted with  JEKO-1 cell line receiving acadesine 400 mg /kg daily, rituximab 10 mg/kg weekly, combination or vehicle.

extract_protocol: Total RNA was extracted, using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Tumors were collected and snap frozen in Tissue-Tek® O.C.T. medium.

value: JEKO-1 tumor xenograft

value: acadesine 400 mg/kg daily and rituximab 10 mg/kg weekly


title: Acadesine, biological rep 3

status: Public on Jun 13 2013

type: RNA

country: Spain

description: Gene expression data cells treated with acadesine

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Tumor xenograft of JEKO-1cell line treated with acadesine

tag: cell line

tag: treatment

value: acadesine 400 mg/kg daily


title: Combination, biological rep2


title: Rituximab, biological rep 1

description: Gene expression data cells treated with rituximab

source_name: Tumor xenograft of JEKO-1cell line treated with rituximab

value: rituximab 10 mg/kg weekly


title: Acadesine, biological rep 2


title: Combination, biological rep1


title: LLC Tumor_Middle-Aged, rep2

city: Boston

first: christine

middle: elaine

last: briggs

state: MA

address: 736 Cambridge Street

department: Center for Cancer Systems Biology

country: USA

institute: christine briggs

description: Old 0Gy Fe LLC (713)

hyb_protocol: Following hybridization at 55C, the chips were washed.

scan_protocol: Standard Illumina scanning protocol using Illumina iScan.

data_processing: The data was checked with GenomeStudio (Illumina) for quality control. In GenomeStudio, data was background subtracted and rank invariant normalization was applied.

organism: Mus musculus

source_name: Middle-Aged 0Gy Fe LLC tumor tissue

label_protocol: Total RNA of 500ng per sample was amplified using Ambion TotalPrep (Ambion), and 1.5µg of the product was loaded onto the chips.

extract_protocol: RNA was isolated from mouse tumor tissue. Tumor chunks of 1 to 2mm in diameter were placed in TRIzol (Invitrogen, Carlsbad, CA) and homogenized using a Tissue Lyser II (Qiagen, Valencia, CA). Tissue with TRIzol was centrifuged at 1200g and 0.2ml of chloroform was added for 5min. Samples were centrifuged at 10,000g for 15min at 4°C. The aqueous phase with RNA was transferred to a 1.5ml eppendorf tube. Isopropyl alcohol (0.5ml) was added to each sample (room temperature) for 10min and samples were centrifuged at 10,000g for 10min at 4°C. RNA pellets were washed once with 75% ethanol and resuspended in 100μl RNase-free water. Quality and quantity of RNA were measured by an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

tag: tissue

value: Lewis lung carcinoma (LLC)  tumor

tag: gender

value: male

tag: age

value: middle-age


title: Acadesine, biological rep 1


title: LLC Tumor_Middle-Aged, rep4

description: Old 0Gy Fe LLC (716)


title: Rituximab, biological rep 3


title: LLC Tumor_Middle-Aged_0.2Gyx5Fe, rep5

description: Old 0.2Gyx5 Fe LLC (596)

source_name: Middle-Aged 0.2Gyx5 Fe LLC tumor tissue

value: 0.2Gyx5 56Fe irradiation


title: LLC Tumor_Middle-Aged_0.2Gyx5Fe, rep3

description: Old 0.2Gyx5 Fe LLC (599)


title: Control, biological rep3

description: Gene expression data control cells

source_name: Tumor xenograft of JEKO-1cell line treated with vehicle


title: LLC Tumor_Middle-Aged_0.2Gyx5Fe, rep2

description: Old 0.2Gyx5 Fe LLC (593)


title: LLC Tumor_Middle-Aged_0.2Gyx5Fe, rep1

description: Old 0.2Gyx5 Fe LLC (591)


title: Rituximab, biological rep 2


title: Control, biological rep2

description: Gene expression data control cells


title: MSK921

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: Gene expression data from baseline, before treatment

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

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

data_processing: The data were analyzed Affymetrix Power Tools (APT) using RMA  as normalization method.

source_name: HNSCC cell line

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

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

tag: cell type

value: Human head and neck squamous cell carcinomas (HNSCC) cells

tag: phenotype

value: resistant to Rigosertib


title: UMSCC19


title: MSK922

value: sensitive to Rigosertib


title: UMSCC2


title: UMSCC8

value: intermediate sensitive to Rigosertib


title: SCC25


title: HN4


title: Control, biological rep1

description: Gene expression data control cells


title: MDA1586


title: Tu167


title: HN12


title: Torpedo-stage Fe-1 embryo, biological rep 3

city: Urrbrae

first: Matthew

middle: R

last: Tucker

state: SA

address: Hartley Grove, Waite Campus

department: Centre of Excellence in Plant Cell Walls

country: Australia

institute: University of Adelaide

description:
Fe-1_3
Embryo gene expression data from an accession that depends upon ZLL/AGO10 function for shoot stem cell maintenance.

hyb_protocol: A standard Affymetrix hybridisation protocol was used at ATLAS Biolabs, Berlin, Germany.

scan_protocol: A Hewlett-Packard scanner was used at ATLAS Biolabs, Berlin, Germany.

data_processing: Expression analysis and normalisation was performed in R using the RMA package following a previously established pipeline (D'Onofrio et al. Funct Plant Biol 2009).

organism: Arabidopsis thaliana

source_name: Torpedo-stage embryos harvested from maturing seeds collected in PBS on ice, Fe-1

label_protocol: Samples were labelled according to the Small Sample Labelling Protocol according to ATLAS Biolabs (Berlin, Germany) and Affymetrix instructions (http://rtsf.msu.edu/small_sample_labeling.pdf).

growth_protocol: Wild type plants were grown under standard laboratory conditions according to Laux et al. 1996, Development.

extract_protocol: Total RNA was extracted using the Plant RNeasy Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Embryos were extracted fom seeds using syringe tips in an eyeglass containing 1xPBS, above an ice-filled petri dish. Samples were left on ice for less than 1 hr before snap freezing in liquid nitrogen.

tag: accession

tag: genotype

value: wild type

tag: zll dependency

value: dependent

tag: developmental stage

value: torpedo-stage embryo

value: whole body


title: Torpedo-stage Bay-0 embryo, biological rep 1

description:
Bay-0
Embryo gene expression data from an accession that depends upon ZLL/AGO10 function for shoot stem cell maintenance.

source_name: Torpedo-stage embryos harvested from maturing seeds collected in PBS on ice, Bay-0


title: HN11


title: Torpedo-stage Ler-0 embryo, biological rep 1

description:
Ler-0
Embryo gene expression data from an accession that depends upon ZLL/AGO10 function for shoot stem cell maintenance.

source_name: Torpedo-stage embryos harvested from maturing seeds collected in PBS on ice, Ler-1

value: Landsberg erecta-0


title: HN31


title: Torpedo-stage Van-0 embryo, biological rep 1

description:
Van-0
Embryo gene expression data from an accession that does not depend upon ZLL/AGO10 function for shoot stem cell maintenance.

source_name: Torpedo-stage embryos harvested from maturing seeds collected in PBS on ice, Van-0

value: independent


title: Torpedo-stage Col-0 embryo, biological rep 1

description:
Col-0_1
Embryo gene expression data from an accession that does not depend upon ZLL/AGO10 function for shoot stem cell maintenance.

source_name: Torpedo-stage embryos harvested from maturing seeds collected in PBS on ice, Col-0


title: Detroit562


title: Torpedo-stage Fe-1 embryo, biological rep 2

description:
Fe-1_2
Embryo gene expression data from an accession that depends upon ZLL/AGO10 function for shoot stem cell maintenance.


title: Torpedo-stage Fe-1 embryo, biological rep 1

description:
Fe-1_1
Embryo gene expression data from an accession that depends upon ZLL/AGO10 function for shoot stem cell maintenance.


title: Torpedo-stage Ts-1 embryo, biological rep 1

description:
Ts-1
Embryo gene expression data from an accession that does not depend upon ZLL/AGO10 function for shoot stem cell maintenance.

source_name: Torpedo-stage embryos harvested from maturing seeds collected in PBS on ice, Ts-1

value: Tossa del Mar-0


title: Torpedo-stage Nw-0 embryo, biological rep 1

description:
Nw-0
Embryo gene expression data from an accession that depends upon ZLL/AGO10 function for shoot stem cell maintenance.

source_name: Torpedo-stage embryos harvested from maturing seeds collected in PBS on ice, Nw-0


title: Torpedo-stage Col-0 embryo, biological rep 2

description:
Col-0_2
Embryo gene expression data from an accession that does not depend upon ZLL/AGO10 function for shoot stem cell maintenance.


title: Cal27


title: HN6


title: 584


title: MN1 del(12-228)

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on a HT MG-430 PM Genome Array. GeneChip plate arrays were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: Gene array plates were scanned using the Affymetrix GeneTitan system.

data_processing: The data were analyzed with the Affymetrix Expression Console software v1.1. RMA normalization and summarization was performed using the default settings in the software.

source_name: Common Myeloid Progenitor (CMP) cells transduced with MN1 deletion construct (d12-228) expression vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix eukaryote two-cycle expression protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004-2009, Affymetrix).

growth_protocol: MACS-sorted lineage negative mouse bone marrow cells were transduced with retroviral vectors that expressed full-length or truncated forms of MN1 protein. Cells were cultured total 5 days (including the transduction period), and CMP+/GFP+ cells were FACS-sorted 2 days after the first transduction.

treatment_protocol: Linage negative mouse bone marrow cells were cultured for a total of 5 days (including the transduction period) in growth medium which contains IMDM+glutamine (2mM)+penicillin/streptomycin (each 100 U/mL)+10% heat inactivated fetal bovine serum+50ng/ml mouse SCF+ 10ng/ml mouse IL3+ 10ng/ml mouse IL6.

tag: strain


title: Leukemia #934

source_name: Leukemia cells arising from mouse bone marrow cells transduced with MN1 full-length expression vector (animal #934)


title: Torpedo-stage Col-0 embryo, biological rep 3

description:
Col-0_3
Embryo gene expression data from an accession that does not depend upon ZLL/AGO10 function for shoot stem cell maintenance.


title: MN1 del(18-458)

source_name: Common Myeloid Progenitor (CMP) cells transduced with MN1 deletion construct (d18-458) expression vector


title: iRAS 0.5% FBS 3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: Microarray data processing and analysis was carried out at EMBL. All analyses were carried out in R (v.2.13.0). Microarray data were normalized using Robust Multichip Average (RMA) and differentially expressed genes were identified using Linear Models for MicroArrays (LIMMA). A cut-off of a Benjamini-Hochberg false discovery rate (BH) <0.05 was used to identify significant genes.

source_name: IMR90-ER:RAS cells grown in 0.5 % FBS and 200 nM 4OHT

label_protocol: Biotinylated cRNA were prepared from 500 ng total RNA according to theThe Ambion iii ® WT Expression Kit Protocol For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays protocol in conjunction with the Affymetrix® GeneChip® WT Terminal Labeling Kit.

growth_protocol: IMR90 cells were obtained from the ATCC. Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 10% or 0.5% fetal bovine serum (FBS, PAA) and 1% antibiotic-antimycotic solution (Invitrogen). We used 0.02 μm Anopore cell culture inserts (Nunc-Thermo) for Trans-well co-culture experiments.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini kit, using Qiashredder for lysate homogenization.

treatment_protocol: Cells were grown in DMEM suplemented with 0.5 % FBS and 1 % antibiotic-antimycotic solution with 200 nM 4-hydroxytamoxifen (4OHT) (Sigma) during 7 days.

value: primary human diploid fibroblasts

tag: cells analyzed

value: IMR90 ER:RAS cells undergoing OIS


title: Leukemia #10

source_name: Leukemia cells arising from mouse bone marrow cells transduced with MN1 full-length expression vector (animal #10)


title: IMR90 0.5% FBS 2

source_name: IMR90 cells grown in 0.5 % FBS and 200 nM 4OHT

value: parenteral IMR90 cells


title: MCF-10A+rep3

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description: comparison of gene expression levels in MCF10A cells before and after MBD2 overexpression

hyb_protocol: One ug of poly(A)+RNA was annealed to oligo(dT) and transcribed using SurperScript II reverse transcriptase (Invitrogen, Carlsbad, CA).

scan_protocol: Signal scan on the microarrays were performed according to the manufacturer's instructions (One-Cycle Target Labeling Assay, Affymetrix).

data_processing: Microarrays were normalized using RMA as implemented by the affy R/Bioconductor package and then quantile normalized.

label_protocol: Labeling were performed according to the manufacturer's instructions (One-Cycle Target Labeling Assay, Affymetrix).

growth_protocol: Nontransformed immortalized breast epithelial cells MCF-10A were purchased from American Type Culture Collection (ATCC, Manassas, Virginia). Cells were cultured in Mammary Epithelial Basal Media (MEGM®; Lonza/Clonetics Corporation, CC-3150) supplemented with the BulletKit® provided by the manufacturer. The GA-1000 (gentamycine-amphotericin B mix) from the BulletKit® was not added to the media as recommended by ATCC.

extract_protocol: Total RNA (1ug) was extracted using Trizol according to manufacturer's instructions (Invitrogen, 15596-026).

treatment_protocol: Lentiviral infection was performed by cultering 3x106 HEK293 cells for 24 hours before being transfected with 5ug of pMD2G-VSVG, 5ug of pCMV-R8.91 and 5ug of MBD2-lenti plasmid (Open Biosystems) using Fugene (Roche). Cells were washed with PBS and incubated 48hours with DMEM (Invitrogen).  Supernatant was collected and filtered with 0.45um disk filter and used to infect MCF-10A cells (plated at 500,000 cells 24 hours prior to infection).

value: MBD2 transfection

tag: growth

value: Mammary Epithelial Basal Media


title: IMR90/iCherry 3

source_name: IMR90 cells cocultured in transwell with IMR90-vector cells on the top in 0.5 % FBS and 200 nM 4OHT

value: parenteral IMR90 cells cocultured with IMR90-vector normal cells


title: MN1 full construct

source_name: Common Myeloid Progenitor (CMP) cells transduced with full-length MN1 expression vector


title: MCF-10A+rep2


title: IMR90 0.5% FBS 3


title: IMR90/iRAS 3

source_name: IMR90 cells cocultured in transwell with IMR90-ER:RAS cells on the top in 0.5 % FBS and 200 nM 4OHT

value: parenteral IMR90 cells cocultured with IMR90-ER:RAS cells undergoing OIS


title: iRAS 0.5% FBS 2


title: MCF-10A-rep3

value: control


title: MCF-10A-rep2


title: MCF-10A+rep1


title: IMR90/iRAS 2


title: IMR90/iCherry 2


title: GFP vector only

source_name: Common Myeloid Progenitor (CMP) cells transduced with vector only


title: MCF-10A-rep1


title: IMR90/iRAS 1


title: iRAS 0.5% FBS 1


title: HMEC 8 with EPCAM expression

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
EPCAM_8
human mammary epithelial cells from donor 8 with EPCAM over-expression

hyb_protocol: Following RNA purification, 20 μg of cRNA were fragmented at 95° using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to the GeneChips (Human Genome 133 plus 2.0).

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: Data preprocessing was performed in R using Bioconductor's (version 2.15.0) GCRMA package (version 2.28.0).

label_protocol: 500 ng total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: Human mammary epithelial cells were grown under standard culture conditions.

extract_protocol: RNA was extracted using TRI-reagent (Sigma) according to manufacturer's protocol.

treatment_protocol: Human mammary epithelial cells were transfected with EPCAM or GFP adenoviruses with multiplicity of infection (MOI=100). RNA was extracted 24 hours after transfection.

tag: donor

value: mammary epithelial cell

tag: genotype/variation

value: EPCAM over-expression


title: IMR90 0.5% FBS 1


title: MCF-10A-.rep-3

type: genomic

description: comparison of promoter methylation levels of MCF10A cells before and after MBD2 overexpression

hyb_protocol: All the steps of hybridization and washing were performed following the Agilent protocol for chip-on-chip analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The value is background subtracted and log2-quantile normalized using the limma Bioconductor package.

molecule: genomic DNA

label_protocol: 2ug of each of the input and bound fractions were labeled for the microarray hybridization. Cy3-dUTP and Cy5-dUTP (Perkin Elmer) were used to label the input and the bound fractions respectively. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive elements.

growth_protocol: Mammary Epithelial Basal Media

extract_protocol: DNA was extracted with Wizard® Genomic DNA Purification kit (Promega) following the manufacturer's protocol. At least 2 µg DNA were sonicated. Methylated DNA was immunoprecipitated with 10 µg of anti-5methylCytosine (Calbiochem). The DNA-antibody complex was immunoprecipitated with 5 mg protein A and the methylated DNA was eluted with 150 µl of TE at 1.5% SDS. The input and bound fractions were then purified and amplified in triplicate using the Whole Genome Amplification kit (Sigma).

treatment_protocol: control

tag: chip antibody

value: anti-5 methylcytosine antibody (Calbiochem, Cat. #NA81, Lot:D00048001)


title: IMR90/iCherry 1

tag: cell line


title: MCF-10A-.rep-1

tag: treatment


title: HMEC 6 with EPCAM expression

description:
EPCAM_6
human mammary epithelial cells from donor 6 with EPCAM over-expression


title: MCF-10A-.rep-2


title: HMEC 6 with GFP expression

description:
GFP_6
human mammary epithelial cells from donor 6 with GFP over-expression

value: CTRL


title: MCF-10A+.rep-1

treatment_protocol: MBD2 transfection


title: MCF-10A+.rep-2


title: MCF-10A+.rep-3


title: Gastric cancer tissue 3-1

status: Public on Jun 12 2013

city: Ningbo

first: Junming

last: Guo

address: 818 Fenghua Road

department: Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology

country: China

institute: Ningbo University

description: This sample is cancer tissue from a patient with gastric cancer

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 µm/pixel resolution using a GenePix 4000B scanner piloted by GenePix Pro 6.0 software (Axon Instruments, Union City, CA). Scanned images were then imported into NimbleScan software (version 2.5) for grid alignment and raw intensity extraction.

data_processing: The raw microarray data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.Raw signal intensities were normalized in RMA method by NimbleScan v2.5, and low intensity lncRNAs were filtered (lncRNAs that at least 3 out of 6 samples have values >= lower cut-off: 100.0 were chosen for further analysis). 20450 probes passed QA.

source_name: Gastric cancer tissue

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using SuperScript ds-cDNA synthesis kit (Life Technologies, Inc., Carlsbad, CA, USA) in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

extract_protocol: Total RNA was extracted by using TRIzol (Life Technologies, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrohoresis.

tag: tissue

value: Gastric cancer tissue


title: Paracancerous tissue 1-2

description: This sample is paired paracancerous tissue from a patient with gastric cancer

source_name: Paracancerous tissue

value: Paracancerous tissue


title: Paracancerous tissue 3-2


title: Mouse Saliva tumor 6

city: Los Angeles

first: Tristan

last: Grogan

state: CA

address: 911 Broxton Ave, 3rd floor

institute: UCLA

hyb_protocol: The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.  The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.

source_name: Tumor mouse

label_protocol: After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).

extract_protocol: For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.

tag: strain background

value: saliva supernatant

tag: sample group

value: mice with pancreatic tumor


title: Mouse Saliva tumor 3


title: Mouse Saliva healthy 6

source_name: Healthy mouse

value: healthy mice


title: Paracancerous tissue 2-2


title: Mouse Saliva healthy 3


title: Mouse Saliva healthy 2


title: HMEC 8 with GFP expression

description:
GFP_8
human mammary epithelial cells from donor 8 with GFP over-expression

tag: cell type


title: Mouse Saliva healthy 4


title: Gastric cancer tissue 2-1


title: Mouse Saliva tumor 1


title: Mouse Saliva healthy 5


title: Mouse Saliva tumor 4


title: Mouse Saliva tumor 5


title: obese macrophage at T24, replicate 3

city: boston

first: Salomon

last: Amar

state: ma

address: 650 albany street

department: perio-oral bio

institute: boston university

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 4h
Obese_BMM_T24-3

hyb_protocol: Hybridization was conducted according to the Affymetrix GeneChip Manual.

scan_protocol: Scanning was conducted on a GeneChip Scanner 3000 7G scanner.

data_processing:
The data were analyzed withBioconductor, part of the software package R. Quantile normalization was used to reduce variability from three replicates at each time point. Loess normalization was employed to reduce system noise between time points.
Log2 of the normalized probe intensities. Expression values were obtained with the expresso function of the affy library of Bioconductor.

source_name: Bone marrow macrophage from obese mice exposed to P.gingivalis for 24h

label_protocol: Labeling was conducted according to the Affymetrix GeneChip Manual.

growth_protocol: For 16 weeks, C57BL/6J mice were fed a high fat diet to induce obesity. Control (lean) mice were maintained for the same period on standard laboratory chow. Obese and lean mice were euthanized via isofluorane exposure. The femurs and tibulas were dissected from mice and bone marrow cells were flushed from medullar cavity of the bones with PBS and then cultured in 30% L-929 conditioned RPMI media at a density of 106 cells/ml. After one week at 37ºC, cells differentiated into bone marrow macrophages and cell culture medium was changed with fresh RPMI-1640 media 1 h before experiment.

extract_protocol: RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: Cultured P. gingivalis were added to the bone marrow macrophages (BMMΦ) cultures at 20 times the concentration of BMMΦ (MOI = 20:1). BMMΦ incubated with P. gingivalis for three different lengths of time: 1 h, 4 h, and 24 h.

tag: disease state

value: obesity

value: Bone marrrow

value: macrophage

tag: infection

tag: time


title: Mouse Saliva healthy 1


title: obese macrophage at T24, replicate 1

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 24h
Obese_BMM_T24-1


title: obese macrophage at T4, replicate 1

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 4h
Obese_BMM_T4-1

source_name: Bone marrow macrophage from obese mice exposed to P.gingivalis for 4h


title: obese macrophage at T1, replicate 3

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 1h
Obese_BMM_T1-3

source_name: Bone marrow macrophage from obese mice exposed to P.gingivalis for 1h


title: Gastric cancer tissue 1-1


title: obese macrophage at T24, replicate 2

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 4h
Obese_BMM_T24-2


title: obese macrophage at T1, replicate 2

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 1h
Obese_BMM_T1-2


title: Mouse Saliva tumor 2


title: obese macrophage at T4, replicate 3

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 4h
Obese_BMM_T4-3


title: lean macrophage at T24, replicate 1

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 24h
Lean_BMM_T24-1

source_name: Bone marrow macrophage from lean mice exposed to P.gingivalis for 24h

value: control (lean)


title: lean macrophage at T24, replicate 3

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 4h
Lean_BMM_T24-3


title: lean macrophage at T24, replicate 2

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 4h
Lean_BMM_T24-2


title: lean macrophage at T4, replicate 2

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 4h
Lean_BMM_T4-2

source_name: Bone marrow macrophage from lean mice exposed to P.gingivalis for 4h


title: lean macrophage at T1, replicate 1

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 1h
Lean_BMM_T1-1

source_name: Bone marrow macrophage from lean mice exposed to P.gingivalis for 1h


title: lean macrophage at T1, replicate 2

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 1h
Lean_BMM_T1-2


title: lean macrophage at T1, replicate 3

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 1h
Lean_BMM_T1-3


title: lean macrophage at T4, replicate 3

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 4h
Lean_BMM_T4-3


title: lean macrophage at T4, replicate 1

description:
Gene expression from bone marrow macrophage derived from lean mice after being exposed to live P.gingivalis for 4h
Lean_BMM_T4-1


title: obese macrophage at T1, replicate 1

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 1h
Obese_BMM_T1-1


title: Yeast_Control_1h_rep3

city: Sydney

first: Patrick

middle: John

last: O'Doherty

state: NSW

address: Goldsmith Ave

institute: University of Western Sydney

description: Yeast (OD600 1.0), grown from a single colony, were treated with either methanol or LoaOOH at an arresting concentration (75 µM) for 1 h. At 1h total RNA was isolated. Affymetrix Yeast_2 microarrays were used to probe changes in gene expression.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 h at 45 oC on GeneChip Yeast Genome 2.0 Arrays, Affymetrix. GeneChips were washed and stained with streptavidin-phycoerythrin conjugate in the Affymetrix FS450 fluidics station.

scan_protocol: Yeast_2 GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: Collected fluorescent intensity data (CEL files) were imported into the Partek® Genomic Suite™ version 6.5 (Partek inc.) with processing that included RMA normalisation and masking of all non-S. cerevisiae probes present on the Affymetrix Yeast_2 arrays.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: exp growing S. cer treated with solvent (MeOH)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 3, Affymetrix).

growth_protocol: S. cerevisiae (BY4743) was grown in minimal medium, 30 oC, 150 rpm, from a single colony to an optical density of 1.0 (OD600 1.0). Six cultures were prepared in total, three biological replicates each for control and oxidant conditions.

extract_protocol: Frozen cells were lysed with 1 mL cold (4 oC) TRIzol® reagent (Invitrogen) and mechanically disrupted with 0.75 g of acid washed glass beads (425-600 µm, Sigma) using a bead mill. Total RNA was then isolated according to the manufacturer’s instructions. Total RNA was further purified using a Qiagen Rneasy column purification kit according to the manufacturer's protocol.

treatment_protocol: Yeast cultures at OD600 1.0 were treated with an arresting concentration of LoaOOH (75 µM) or an equivalent volume of methanol (absolute). Growth was then allowed to resume at 30 oC, with orbital shaking (150 rpm) for a further 60 min. A 50 mL aliquot for each replicate was centrifuged twice at 5000 g for 3 min, at room temperature. Cell pellets were snap-frozen in liquid nitrogen and stored at -80 °C until extraction.

tag: growth phase

value: Exponential (OD600 1.0)


title: obese macrophage at T4, replicate 2

description:
Gene expression from bone marrow macrophage derived from obese mice after being exposed to live P.gingivalis for 4h
Obese_BMM_T4-2


title: Yeast_LoaOOH-treated_1h_rep1

source_name: exp growing S. cer treated with oxidant (LoaOOH)


title: Yeast_LoaOOH-treated_1h_rep2


title: Yeast_Control_1h_rep2


title: GenoXRQ_ABA_Grp1-A with array type SUNFLOWER from Affymetrix

city: evry

first: caius

last: jose

state: essonne

address: 2 rue gaston cremieux

department: URGV

country: France

institute: transcriptomic platform

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

hyb_protocol: labelled extract quantity: 5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002). We take a subset of probes because we want the results only for Helianthus annuus specific probes.

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, total RNA  .

growth_protocol: aerial - Seeds are surface-sterilized and place 2 days in soaked filter paper at 28°C. Plantlets are then transferred in 20 litre boxes (48 plantlets per box) filled with a complete hydroponic medium and grown during 15 days until treatment and harvesting. Growth chamber 14h day light at 23°C and 65% humidity, 10h night at 18°C and 65% humidity

treatment_protocol: Name:ABA_Sunflower - compound based treatment - compound addition,aba:quantity 0.5uM time 6hour . ABA was prepared in DMS0 at a concentration of 20 mM. 500 µl were added to 20 litres of hydroponic medium (ref Massoneau 2001 Planta). 500 µl DMS0 were added to controls. Leaves of 1 plantlet per box were harvested after 6 hours and 3 plantlets (each repeat of a genotype) were pooled as one sample.

value: XRQ

tag: agent

value: ABA

tag: group

tag: age

tag: developmental stage (boyes et al. plant cell 2001)

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: GenoXRQ_Ctl_Grp1-A with array type SUNFLOWER from Affymetrix

treatment_protocol: no treatment

value: Ctl


title: Yeast_LoaOOH-treated_1h_rep3

tag: strain


title: GenoXRQ_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

tag: genotype/variation


title: GenoPSC8_Ctl_Grp3-A with array type SUNFLOWER from Affymetrix


title: GenoINEDI_Ctl_Grp1-A with array type SUNFLOWER from Affymetrix

value: INEDI


title: GenoPSC8_ABA_Grp2-A with array type SUNFLOWER from Affymetrix


title: Geno262_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoXRQ_ABA_Grp3-A with array type SUNFLOWER from Affymetrix

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.


title: GenoINEDI_Ctl_Grp2-AA with array type SUNFLOWER from Affymetrix


title: Geno235_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno235_Ctl_Grp3 with array type SUNFLOWER from Affymetrix

hyb_protocol: labelled extract quantity: 4ug


title: GenoINEDI_ABA_Grp1-A with array type SUNFLOWER from Affymetrix


title: GenoPSC8_ABA_Grp3-A with array type SUNFLOWER from Affymetrix


title: Geno240_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoXRQ_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno263_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_Ctl_Grp2-A with array type SUNFLOWER from Affymetrix


title: GenoXRQ_ABA_Grp2-A with array type SUNFLOWER from Affymetrix


title: Geno217_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno151_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

hyb_protocol: labelled extract quantity: 5ng


title: Geno241_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno208_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno240_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno209_ABA_Grp3-A with array type SUNFLOWER from Affymetrix


title: Geno231_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoINEDI_Ctl_Grp2-A with array type SUNFLOWER from Affymetrix


title: Geno241_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoINEDI_Ctl_Grp3-A with array type SUNFLOWER from Affymetrix


title: Geno231_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno152_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Yeast_Control_1h_rep1


title: Geno149_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno166_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno171_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno151_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: GenoINEDI_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno177_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno163_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno168_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno156_Ctl_grp2 with array type SUNFLOWER from Affymetrix


title: Geno270_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno267_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno272_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_ABA_Grp1-A with array type SUNFLOWER from Affymetrix


title: GenoINEDI_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno269_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno267_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno202_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno200_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno189_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno270_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno198_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno148_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno146_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno143_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno196_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno143_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno141_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno130_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno148_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno141_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno142_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno142_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno130_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno7_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno158_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno136_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno107_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno43_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno10_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno88_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno149_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno144_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno1_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno140_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno145_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: GenoXRQ_ABA_Grp3bis with array type SUNFLOWER from Affymetrix


title: Geno1_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno209_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno111_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: GenoXRQ_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoXRQ_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno278_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoXRQ_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno190_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno14_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno278_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno272_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno217_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno200_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno212_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno7_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno186_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno10_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno181_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: GenoXRQ_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno198_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno215_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno2_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno5_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno185_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno11_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno8_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno185_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno14_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno11_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno208_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno26_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno144_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno262_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoINEDI_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: GenoPSC8_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno275_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno214_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno216_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno216_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: CTRL_CBM_06

first: Sally

last: Lambert

address: Blizard Institute, 4 Newark Street

department: Centre for Cutaneous Research

institute: Queen Mary, University of London

description: Normal control, Cerebellum, 18 weeks, Male, N/A, N/A

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Data analysis was performed using GenomeStudio 2011.1 (methylationmodule 1.9.0) and anootation 1.2. The methylation analysis was performed as recommended by Illumina, with no background subtraction and normalisation to internal controls.

label: Biotin/DNP

source_name: Normal cerebellum (commercial source)

label_protocol: standard Illumina protocol

extract_protocol: High molecular weight DNA was extracted by use of a salting-out method or by ultracentrifugation over cesium chloride

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

value: normal cerebellum

tag: brain location

value: Cerebellum

tag: age at diagnosis

value: 18 weeks

tag: gender

value: Male

tag: dna methylation subgroup

tag: mapk hit


title: CTRL_CBM_01

description: Normal control, Cerebellum, 29 weeks, Male, N/A, N/A

tag: tissue

value: 29 weeks


title: Geno214_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: PA_60

description: Pilocytic astrocytoma, Cerebellum, 8, Female, 2, KIAA1549:BRAF fusion_16:9

source_name: Frozen pilocytic astrocytoma tumor tissue

value: Pilocytic astrocytoma tumor

value: 8 y

value: Female

value: KIAA1549:BRAF fusion_16:9


title: PA_61

description: Pilocytic astrocytoma, Diencephalon, 12, Male, 1, KIAA1549:BRAF fusion_16:9

value: Diencephalon


title: CTRL_CBM_03

description: Normal control, Cerebellum, 37 weeks, Female, N/A, N/A

value: 37 weeks


title: CTRL_CBM_02

description: Normal control, Cerebellum, 22 weeks, Female, N/A, N/A

value: 22 weeks


title: PA_58

description: Pilocytic astrocytoma, Cerebellum, 3, Male, 2, KIAA1549:BRAF fusion_16:9

value: 3 y


title: Geno210_ABA_Grp2 with array type SUNFLOWER from Affymetrix

value: ABA

value: vegetative


title: PA_60

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 580

department: Pediatric Neuro Oncology

country: Germany

institute: German Cancer Research Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

value: Pilocytic astrocytoma

tag: age at diagnosis (years)


title: CTRL_CBM_04

description: Normal control, Cerebellum, 33, Male, N/A, N/A


title: PA_61


title: PA_51

description: Pilocytic astrocytoma, Optic nerve, 1, Male, 1, KIAA1549:BRAF fusion_15:9

value: Optic nerve

value: 1 y

value: KIAA1549:BRAF fusion_15:9


title: PA_54

description: Pilocytic astrocytoma, Cerebellum, 3, Female, 2, KIAA1549:BRAF fusion_16:9

value: Cerebellum


title: PA_53


title: PA_59

description: Pilocytic astrocytoma, Optic nerve, 3, Female, 1, BRAF V600E

value: BRAF V600E


title: Geno201_ABA_Grp3 with array type SUNFLOWER from Affymetrix

value: Leaves from the 15-day-old-plantlets


title: Geno210_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

value: Ctl


title: PA_59

value: Pilocytic astrocytoma:BRAF V600E


title: PA_56

description: Pilocytic astrocytoma, Cerebellum, 11, Female, 2, KIAA1549:BRAF fusion_16:9

value: Pilocytic astrocytoma tumor

value: Female


title: PA_48

description: Pilocytic astrocytoma, Third ventricle, 2, Male, 1, KIAA1549:BRAF fusion_16:9

value: Third ventricle

value: 2 y

value: Male

value: KIAA1549:BRAF fusion_16:9


title: PA_52

description: Pilocytic astrocytoma, Cerebellum, 9, Male, 1, KIAA1549:BRAF fusion_16:9

value: 9 y


title: PA_55

description: Pilocytic astrocytoma, Cerebellum, 8, Male, 2, KIAA1549:BRAF fusion_16:9

value: 8 y


title: PA_57

description: Pilocytic astrocytoma, Cerebellum, 9, Female, 2, KIAA1549:BRAF fusion_16:9


title: PA_50

description: Pilocytic astrocytoma, Optic nerve, 0.5, Male, 1 KIAA1549:BRAF fusion_15:9


title: PA_47

description: Pilocytic astrocytoma, Cerebellum, 4, Male, 2, KIAA1549:BRAF fusion_16:9

value: 4 y


title: Geno190_ABA_Grp3 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: ABA

value: vegetative


title: PA_46

description: Pilocytic astrocytoma, Cerebellum, 13, Female, 1, None identified

value: None identified


title: PA_45

description: Pilocytic astrocytoma, Optic nerve, 10, Male, 1, BRAF V600E

value: Optic nerve


title: PA_42

description: Pilocytic astrocytoma, Cerebellum, 6, Male, 2, SRGAP3:RAF1 fusion_12:10

value: Cerebellum

value: 6 y

value: SRGAP3:RAF1 fusion_12:10


title: PA_58

value: Pilocytic astrocytoma


title: PA_49

description: Pilocytic astrocytoma, Optic nerve, 4, Male, 1, KIAA1549:BRAF fusion_15:9

value: Pilocytic astrocytoma tumor

value: KIAA1549:BRAF fusion_15:9


title: PA_44

description: Pilocytic astrocytoma, Fourth Ventricle, 9, Male, 1, KIAA1549:BRAF fusion_16:9

value: Fourth Ventricle


title: PA_57

value: Female


title: Geno189_ABA_Grp3 with array type SUNFLOWER from Affymetrix

value: Leaves from the 15-day-old-plantlets


title: Geno187_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: PA_43

description: Pilocytic astrocytoma, Fourth Ventricle, 5, Female, 2, KIAA1549:BRAF fusion_16:9

value: 5 y

value: KIAA1549:BRAF fusion_16:9


title: PA_39

description: Pilocytic astrocytoma, Cerebellum, 5, Male, 2, KIAA1549:BRAF fusion_16:9

value: Male


title: Geno187_Ctl_Grp3 with array type SUNFLOWER from Affymetrix

value: Ctl


title: PA_41

description: Pilocytic astrocytoma, Diencephalon, 1, Male, 1, None identified

value: Diencephalon

value: 1 y


title: PA_37

description: Pilocytic astrocytoma, Cerebellum, 6, Female, 2, KIAA1549:BRAF fusion_16:9


title: PA_56


title: PA_40

description: Pilocytic astrocytoma, Cerebellum, 14, Female, 2, None identified

value: None identified


title: PA_54


title: PA_38

description: Pilocytic astrocytoma, Cerebellum, 17, Female, 2, BRAF ins598T

value: BRAF ins598T


title: PA_68

value: Cerebellum


title: Geno215_ABA_Grp3 with array type SUNFLOWER from Affymetrix

value: ABA

value: vegetative


title: Geno183_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: PA_34

description: Pilocytic astrocytoma, Cerebellum, 6, Male, 2, KIAA1549:BRAF fusion_15:9

value: 6 y


title: PA_36

value: Pilocytic astrocytoma tumor

value: 4 y


title: PA_33

description: Pilocytic astrocytoma, Cerebellum, 7, Female, 2, KIAA1549:BRAF fusion_15:9

value: 7 y

value: KIAA1549:BRAF fusion_15:9


title: Geno183_ABA_Grp2 with array type SUNFLOWER from Affymetrix

value: Leaves from the 15-day-old-plantlets


title: PA_70

value: Pilocytic astrocytoma

value: Female


title: PA_29

value: 5 y

value: Male

value: KIAA1549:BRAF fusion_16:9


title: Geno179_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: PA_27


title: Geno181_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: PA_67


title: Geno178_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

value: Ctl


title: PA_26

description: Pilocytic astrocytoma, Cerebellum, 2, Male, 2, KIAA1549:BRAF fusion_16:9

value: 2 y


title: CTRL_CBM_05

description: Normal control, Cerebellum, 87, Female, N/A, N/A

value: normal cerebellum


title: PA_66

value: Cerebellum


title: PA_24

description: Pilocytic astrocytoma, Cerebellum, 10, Male, 2, KIAA1549:BRAF fusion_16:9


title: PA_32

description: Pilocytic astrocytoma, Cerebral hemisphere, 8, Female, 1, KIAA1549:BRAF fusion_15:9

value: Cerebral hemisphere

value: 8 y


title: PA_35

description: Pilocytic astrocytoma, Cerebellum, 10, Female, 2, None identified

value: None identified


title: Geno184_ABA_Grp3 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: ABA

value: vegetative


title: Geno275_Ctl_Grp3 with array type SUNFLOWER from Affymetrix


title: PA_23

description: Pilocytic astrocytoma, Cerebellum, 11, Female, 2, KRAS E63K

value: Pilocytic astrocytoma tumor

value: KRAS E63K


title: PA_65


title: PA_25

description: Pilocytic astrocytoma, Diencephalon, 3, Female, 1, BRAF V600E

value: Diencephalon

value: 3 y

value: BRAF V600E


title: PA_69

value: Pilocytic astrocytoma

value: Left frontal lobe

value: Female

value: Pilocytic astrocytoma:NF1


title: PA_20

description: Pilocytic astrocytoma, Diencephalon, 12, Female, 1, KIAA1549:BRAF fusion_16:9

value: KIAA1549:BRAF fusion_16:9


title: PA_30

description: Pilocytic astrocytoma, Cerebral hemisphere, 14, Male, 1, KIAA1549:BRAF fusion_15:9

value: Male

value: KIAA1549:BRAF fusion_15:9


title: PA_47

value: Cerebellum


title: PA_28

description: Pilocytic astrocytoma, Cerebellum, 6, Male, 2, KIAA1549:BRAF fusion_16:9

value: 6 y


title: PA_64


title: Geno26_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: Leaves from the 15-day-old-plantlets


title: Geno202_Ctl_Grp3 with array type SUNFLOWER from Affymetrix

value: Ctl


title: PA_31

description: Pilocytic astrocytoma, Brainstem, 7, Male, 1, KIAA1549:BRAF fusion_15:9

value: Brainstem

value: 7 y


title: Geno209_ABA_Grp3 with array type SUNFLOWER from Affymetrix

value: ABA

value: vegetative


title: PA_18

description: Pilocytic astrocytoma, Diencephalon, 3, Female, 1, NF1; KIAA1549:BRAF fusion_15:9; BRAF V600E

value: Pilocytic astrocytoma tumor

value: Diencephalon

value: 3 y


title: PA_21

description: Pilocytic astrocytoma, Diencephalon, 4, Female, 1, BRAF V600E

value: 4 y

value: BRAF V600E


title: PA_40

value: Pilocytic astrocytoma

value: Female

value: Pilocytic astrocytoma:None identified


title: PA_37


title: PA_19

description: Pilocytic astrocytoma, Cerebellum, 17, Female, 2, BRAF ins598T

value: BRAF ins598T


title: PA_22

description: Pilocytic astrocytoma, Cerebellum, 22, Female, 2, KIAA1549:BRAF fusion_16:9

value: Cerebellum

value: KIAA1549:BRAF fusion_16:9


title: Geno201_Ctl_Grp3 with array type SUNFLOWER from Affymetrix

value: Leaves from the 15-day-old-plantlets


title: PA_32

value: Cerebral hemisphere


title: PA_36

value: Male


title: Geno197_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Geno175_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: PA_44

value: Fourth Ventricle


title: Geno199_ABA_Grp3 with array type SUNFLOWER from Affymetrix

value: ABA


title: PA_31

value: Brainstem


title: Liver_45d

city: Beijing

first: Pengfei

last: Cai

address: #9 Dong Dan San Tiao

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences

hyb_protocol: Cy3-labeled cDNA was hybridized overnight at 42°C to mus musculus 12x135K Array (Roche NimbleGen)

scan_protocol: Arrays were scanned with the Axon GenePix 4000B microarray scanner

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).

source_name: liver, infected, 45d

label_protocol: cDNA synthesis followed by Cy3-labeling

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: background strain

value: BALB/c

value: female

value: liver

tag: infectious agent

value: Schistosoma japonicum


title: Liver_30d

source_name: liver, infected, 30d


title: PA_12

description: Pilocytic astrocytoma, Cerebellum, 10, Male, 2, KIAA1549:BRAF fusion_15:9

value: Pilocytic astrocytoma tumor

value: KIAA1549:BRAF fusion_15:9


title: PA_29

value: Pilocytic astrocytoma


title: Liver_15d

source_name: liver, infected, 15d


title: PA_15

description: Pilocytic astrocytoma, Diencephalon, 3, Male, 1, NF1; KIAA1549:BRAF fusion_breakpoint not determined

value: Diencephalon

value: 3 y


title: PA_11

description: Pilocytic astrocytoma, Diencephalon, 2, Female, 1, KIAA1549:BRAF fusion_breakpoint not determined

value: 2 y

value: Female


title: PA_28

value: Cerebellum


title: PA_27


title: Geno167_ABA_Grp2 with array type SUNFLOWER from Affymetrix

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Geno167_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

value: Ctl


title: Geno166_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_WY_300_14D_rep2

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description:
SAMPLE 107
Gene expression following 14.0 days exposure to the PPARalpha ligand Wy-14643

hyb_protocol: Hybridization was performed according the the Agilent manual G4140-90040 v. 5.7.

scan_protocol: Immediately after washing, microarrays were scannedusing a GenePix 4000B microarray scanner (Molecular Devices, Union City, CA) at 532 nm with a scan resultion of 5um.

data_processing:
Feature signal intensities and flagged features were determined using GenePix Pro 6.0 (Molecular Devices, Union City, CA).
Signal intensities normalized using a semi-parametric approach (Eckel, J. E., Gennings, C., Therneau, T. M., Burgoon, L. D., Boverhof, D. R. and Zacharewski, T. R. (2005). Bioinformatics 21(7), 1078-83.). These normalized signal intensities were then analyzed using an empirical Bayes analysis (Eckel, J. E., Gennings, C., Chinchilli, V. M., Burgoon, L. D., and Zacharewski, T. R., 2004. J Biopharm Stat 14, 647-670.) resulting in a final dataset with blank values where n ≤ 2 for a probe at each time-point.

label_protocol: Cy3 Labeling was performed according to the Agilent manual G4140-90040 v. 5.7.

extract_protocol: Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified spectrophotometrically (A260) and purity was assessed using the A260/A280 ratio and visual inspection on a denaturing gel.

treatment_protocol: Female ovariectomized C57BL/6 mice were gavaged daily with 300 mg/kg Clofibrate, Wy-14,643 or sesame oil vehicle control. Mice were sacrificed 2, 4, 8, 12, 18, and 24h post-dose following a single dose or 1, 4 and 14d post initial dose following daily dosing.

tag: treatment

tag: time-point

value: 14 days post initial dose following daily dosing

tag: replicate


title: PA_17

description: Pilocytic astrocytoma, Cerebellum, 11, Male, 2, KIAA1549:BRAF fusion_16:11

value: Male

value: KIAA1549:BRAF fusion_16:11


title: PA_10

description: Pilocytic astrocytoma, Cerebral hemisphere, 14, Male, 1, BRAF V600E

value: Cerebral hemisphere

value: BRAF V600E


title: PA_16

description: Pilocytic astrocytoma, Cerebellum, 19, Male, 2, KIAA1549:BRAF fusion_15:9


title: Mmu_liver_TC_WY_300_14D_rep1

description:
SAMPLE 106
Gene expression following 14.0 days exposure to the PPARalpha ligand Wy-14643

value: female

value: liver


title: Geno161_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

tag: agent

tag: group


title: PA_04

description: Pilocytic astrocytoma, Cerebral hemisphere, 16, Male, 1, FAM131B:BRAF fusion

value: Pilocytic astrocytoma tumor

value: FAM131B:BRAF fusion


title: Geno175_Ctl_Grp3 with array type SUNFLOWER from Affymetrix

tag: age

tag: developmental stage (boyes et al. plant cell 2001)


title: PA_08

description: Pilocytic astrocytoma, Cerebellum, 4, Male, 2, KIAA1549:BRAF fusion_16:9

value: 4 y

value: KIAA1549:BRAF fusion_16:9


title: PA_13

description: Pilocytic astrocytoma, Cerebellum, 13, Male, 2, KIAA1549:BRAF fusion_16:9


title: PA_09

description: Pilocytic astrocytoma, Cerebellum, 16, Male, 2, KIAA1549:BRAF fusion_16:9


title: Mmu_liver_TC_WY_VEH_0_14D_rep3

description:
SAMPLE 105
Gene expression following 14.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_14D

tag: strain

value: sesame oil (vehicle contrrol)


title: Mmu_liver_TC_WY_VEH_0_14D_rep1

description:
SAMPLE 103
Gene expression following 14.0 days exposure to the vehicle control sesame oil


title: Mmu_liver_TC_WY_VEH_0_14D_rep2

description:
SAMPLE 104
Gene expression following 14.0 days exposure to the vehicle control sesame oil


title: PA_24

value: Pilocytic astrocytoma

tag: brain location


title: PA_25

value: Diencephalon

value: Female

value: Pilocytic astrocytoma:BRAF V600E


title: PA_05

description: Pilocytic astrocytoma, Cerebellum, 2, Male, 2, KIAA1549:BRAF fusion_15:9

value: Cerebellum

tag: age at diagnosis

value: 2 y

value: KIAA1549:BRAF fusion_15:9


title: Mmu_liver_TC_WY_300_14D_rep3

description:
SAMPLE 108
Gene expression following 14.0 days exposure to the PPARalpha ligand Wy-14643

tag: gender

value: 14 days post initial dose following daily dosing


title: PA_03

description: Pilocytic astrocytoma, Cerebellum, 5, Female, 2, KIAA1549:BRAF fusion_16:9

value: 5 y

tag: dna methylation subgroup


title: Liver_0d

source_name: liver, uninfected

value: BALB/c

value: n/a (uninfected)


title: Geno160_ABA_Grp2 with array type SUNFLOWER from Affymetrix

tag: genotype/variation

value: ABA

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Mmu_liver_TC_WY_300_4D_rep3

description:
SAMPLE 102
Gene expression following 4.0 days exposure to the PPARalpha ligand Wy-14643

value: female

tag: tissue

value: liver

value: 4 days post initial dose following daily dosing


title: PA_02

description: Pilocytic astrocytoma, Cerebellum, 4, Female, 2, KIAA1549:BRAF fusion_16:9

value: Pilocytic astrocytoma tumor

value: 4 y

tag: mapk hit

value: KIAA1549:BRAF fusion_16:9


title: PA_26

value: Pilocytic astrocytoma

tag: age at diagnosis (years)

value: Male


title: PA_14

description: Pilocytic astrocytoma, Brainstem, 6, Male, 2, KIAA1549:BRAF fusion_16:9

value: Brainstem

value: 6 y


title: PA_06

description: Pilocytic astrocytoma, Cerebellum, 11, Female, 2, KIAA1549:BRAF fusion_15:9

value: Cerebellum

value: Female

value: KIAA1549:BRAF fusion_15:9


title: PA_01

description: Pilocytic astrocytoma, Cerebellum, 9, Male, 2, KIAA1549:BRAF fusion_16:9

value: 9 y


title: PA_23

value: Pilocytic astrocytoma:KRAS E63K


title: Mmu_liver_TC_WY_VEH_0_4D_rep3

description:
SAMPLE 99
Gene expression following 4.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_4D

value: sesame oil (vehicle contrrol)


title: PA_22


title: PA_20

value: Diencephalon


title: PA_07

description: Pilocytic astrocytoma, Cerebellum, 18, Male, 2, KIAA1549:BRAF fusion_16:9


title: Mmu_liver_TC_WY_300_1D_rep1

description:
SAMPLE 94
Gene expression following 1.0 days exposure to the PPARalpha ligand Wy-14643

value: female

value: 1 day post initial dose


title: Geno138_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: Ctl

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Mmu_liver_TC_WY_300_1D_rep2

description:
SAMPLE 95
Gene expression following 1.0 days exposure to the PPARalpha ligand Wy-14643

value: liver


title: Mmu_liver_TC_WY_300_1D_rep3

description:
SAMPLE 96
Gene expression following 1.0 days exposure to the PPARalpha ligand Wy-14643


title: Geno137_ABA_Grp2 with array type SUNFLOWER from Affymetrix

value: ABA


title: Mmu_liver_TC_WY_VEH_0_4D_rep2

description:
SAMPLE 98
Gene expression following 4.0 days exposure to the vehicle control sesame oil

value: 4 days post initial dose following daily dosing


title: Mmu_liver_TC_WY_VEH_0_4D_rep1

description:
SAMPLE 97
Gene expression following 4.0 days exposure to the vehicle control sesame oil


title: PA_19

value: Pilocytic astrocytoma

value: Pilocytic astrocytoma:BRAF ins598T


title: Mmu_liver_TC_WY_VEH_0_1D_rep3

description:
SAMPLE 93
Gene expression following 1.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_1D


title: Geno137_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: PA_17

value: Cerebellum

value: Male


title: Mmu_liver_TC_WY_VEH_0_1D_rep1

description:
SAMPLE 91
Gene expression following 1.0 days exposure to the vehicle control sesame oil


title: Geno140_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: PA_16


title: Geno136_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_WY_300_4D_rep1

description:
SAMPLE 100
Gene expression following 4.0 days exposure to the PPARalpha ligand Wy-14643


title: PA_18

value: Female

value: Pilocytic astrocytoma:NF1; KIAA1549:BRAF fusion_15:9; BRAF V600E


title: Mmu_liver_TC_WY_VEH_0_24H_rep3

description:
SAMPLE 87
Gene expression following 24.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_24H

value: 24 hrs post-dose following a single dose


title: PA_15

value: Pilocytic astrocytoma:NF1; KIAA1549:BRAF fusion_breakpoint not determined


title: Mmu_liver_TC_WY_300_24H_rep2

description:
SAMPLE 89
Gene expression following 24.0 hours exposure to the PPARalpha ligand Wy-14643


title: Geno128_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_WY_300_24H_rep1

description:
SAMPLE 88
Gene expression following 24.0 hours exposure to the PPARalpha ligand Wy-14643


title: Mmu_liver_TC_WY_VEH_0_1D_rep2

description:
SAMPLE 92
Gene expression following 1.0 days exposure to the vehicle control sesame oil

value: sesame oil (vehicle contrrol)


title: Geno127_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno127_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_WY_300_24H_rep3

description:
SAMPLE 90
Gene expression following 24.0 hours exposure to the PPARalpha ligand Wy-14643

value: female


title: Mmu_liver_TC_WY_300_18H_rep3

description:
SAMPLE 84
Gene expression following 18.0 hours exposure to the PPARalpha ligand Wy-14643

value: 18 hrs post-dose following a single dose


title: Mmu_liver_TC_WY_VEH_0_18H_rep3

description:
SAMPLE 81
Gene expression following 18.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_18H


title: Mmu_liver_TC_WY_300_18H_rep1

description:
SAMPLE 82
Gene expression following 18.0 hours exposure to the PPARalpha ligand Wy-14643


title: Geno128_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno125_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: PA_11

value: Diencephalon

value: Pilocytic astrocytoma:KIAA1549:BRAF fusion_breakpoint not determined


title: Mmu_liver_TC_WY_300_12H_rep3

description:
SAMPLE 78
Gene expression following 12.0 hours exposure to the PPARalpha ligand Wy-14643

value: 12 hrs post-dose following a single dose


title: PA_10

value: Cerebral hemisphere

value: Pilocytic astrocytoma:BRAF V600E


title: PA_12


title: Mmu_liver_TC_WY_VEH_0_24H_rep2

description:
SAMPLE 86
Gene expression following 24.0 hours exposure to the vehicle control sesame oil

value: liver


title: Geno178_ABA_Grp2 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: ABA

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: PA_13

value: Pilocytic astrocytoma

value: Cerebellum

value: Male


title: Mmu_liver_TC_WY_300_4D_rep2

description:
SAMPLE 101
Gene expression following 4.0 days exposure to the PPARalpha ligand Wy-14643

value: 4 days post initial dose following daily dosing


title: Mmu_liver_TC_WY_300_18H_rep2

description:
SAMPLE 83
Gene expression following 18.0 hours exposure to the PPARalpha ligand Wy-14643


title: Mmu_liver_TC_WY_VEH_0_18H_rep1

description:
SAMPLE 79
Gene expression following 18.0 hours exposure to the vehicle control sesame oil


title: Mmu_liver_TC_WY_VEH_0_12H_rep2

description:
SAMPLE 74
Gene expression following 12.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_12H


title: Mmu_liver_TC_WY_VEH_0_24H_rep1

description:
SAMPLE 85
Gene expression following 24.0 hours exposure to the vehicle control sesame oil

value: 24 hrs post-dose following a single dose


title: GenoINEDI_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: INEDI


title: PA_09


title: Mmu_liver_TC_WY_300_12H_rep1

description:
SAMPLE 76
Gene expression following 12.0 hours exposure to the PPARalpha ligand Wy-14643

value: female


title: PA_08


title: PA_06

value: Female


title: Mmu_liver_TC_WY_VEH_0_18H_rep2

description:
SAMPLE 80
Gene expression following 18.0 hours exposure to the vehicle control sesame oil

value: sesame oil (vehicle contrrol)

value: 18 hrs post-dose following a single dose


title: Mmu_liver_TC_WY_300_8H_rep1

description:
SAMPLE 70
Gene expression following 8.0 hours exposure to the PPARalpha ligand Wy-14643

value: 8 hrs post-dose following a single dose


title: Mmu_liver_TC_WY_300_8H_rep2

description:
SAMPLE 71
Gene expression following 8.0 hours exposure to the PPARalpha ligand Wy-14643


title: Mmu_liver_TC_WY_VEH_0_12H_rep3

description:
SAMPLE 75
Gene expression following 12.0 hours exposure to the vehicle control sesame oil

value: 12 hrs post-dose following a single dose


title: Geno263_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: PA_05


title: Geno117_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno199_Ctl_Grp3 with array type SUNFLOWER from Affymetrix

value: Ctl


title: Geno17_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: PA_03


title: Mmu_liver_TC_WY_VEH_0_4H_rep1

description:
SAMPLE 61
Gene expression following 4.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_4H

value: liver

value: 4 hrs post-dose following a single dose


title: Geno196_ABA_Grp3 with array type SUNFLOWER from Affymetrix

value: ABA

value: vegetative


title: Mmu_liver_TC_WY_300_4H_rep2

description:
SAMPLE 65
Gene expression following 4.0 hours exposure to the PPARalpha ligand Wy-14643


title: Mmu_liver_TC_WY_300_8H_rep3

description:
SAMPLE 72
Gene expression following 8.0 hours exposure to the PPARalpha ligand Wy-14643


title: PA_04

value: Pilocytic astrocytoma

value: Cerebral hemisphere


title: Mmu_liver_TC_WY_300_4H_rep1

description:
SAMPLE 64
Gene expression following 4.0 hours exposure to the PPARalpha ligand Wy-14643


title: Mmu_liver_TC_WY_300_2H_rep3

description:
SAMPLE 60
Gene expression following 2.0 hours exposure to the PPARalpha ligand Wy-14643

value: 2 hrs post-dose following a single dose


title: Mmu_liver_TC_WY_VEH_0_8H_rep2

description:
SAMPLE 68
Gene expression following 8.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_8H


title: Geno269_ABA_Grp3 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: Leaves from the 15-day-old-plantlets


title: Geno15_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

hyb_protocol: labelled extract quantity: 10ug


title: Mmu_liver_TC_WY_VEH_0_12H_rep1

description:
SAMPLE 73
Gene expression following 12.0 hours exposure to the vehicle control sesame oil


title: Mmu_liver_TC_WY_300_12H_rep2

description:
SAMPLE 77
Gene expression following 12.0 hours exposure to the PPARalpha ligand Wy-14643


title: GenoINEDI_ABA_Grp3 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_WY_300_4H_rep3

description:
SAMPLE 66
Gene expression following 4.0 hours exposure to the PPARalpha ligand Wy-14643


title: Geno42_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno72_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: PA_62

value: Cerebellum

value: Male

value: Pilocytic astrocytoma:None identified


title: Geno40_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: PA_01


title: Mmu_liver_TC_WY_VEH_0_4H_rep3

description:
SAMPLE 63
Gene expression following 4.0 hours exposure to the vehicle control sesame oil

value: female


title: Mmu_liver_TC_WY_VEH_0_2H_rep3

description:
SAMPLE 57
Gene expression following 2.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_2H

value: sesame oil (vehicle contrrol)


title: PA_02

value: Female


title: Mmu_liver_TC_WY_300_2H_rep2

description:
SAMPLE 59
Gene expression following 2.0 hours exposure to the PPARalpha ligand Wy-14643


title: PA_63


title: Mmu_liver_TC_WY_VEH_0_8H_rep3

description:
SAMPLE 69
Gene expression following 8.0 hours exposure to the vehicle control sesame oil

value: 8 hrs post-dose following a single dose


title: Mmu_liver_TC_WY_VEH_0_2H_rep1

description:
SAMPLE 55
Gene expression following 2.0 hours exposure to the vehicle control sesame oil


title: Mmu_liver_TC_WY_VEH_0_8H_rep1

description:
SAMPLE 67
Gene expression following 8.0 hours exposure to the vehicle control sesame oil


title: Mmu_liver_TC_CLF_VEH_0_4H_rep3

description:
SAMPLE 51
Gene expression following 4.0 hours exposure to the vehicle control sesame oil


title: Mmu_liver_TC_CLF_VEH_0_12H_rep3

description:
SAMPLE 53
Gene expression following 12.0 hours exposure to the vehicle control sesame oil

value: 12 hrs post-dose following a single dose


title: Mmu_liver_TC_WY_VEH_0_4H_rep2

description:
SAMPLE 62
Gene expression following 4.0 hours exposure to the vehicle control sesame oil


title: Mmu_liver_TC_CLF_300_8H_rep3

description:
SAMPLE 54
Gene expression following 8.0 hours exposure to the PPARalpha ligand Clofibrate

value: Clofibrate


title: Mmu_liver_TC_WY_300_2H_rep1

description:
SAMPLE 58
Gene expression following 2.0 hours exposure to the PPARalpha ligand Wy-14643

value: liver


title: Geno41_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_WY_VEH_0_2H_rep2

description:
SAMPLE 56
Gene expression following 2.0 hours exposure to the vehicle control sesame oil


title: SAEC

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

description: Normal small airway epithelial cell

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: Normal small airway epithelial cell_SAEC

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

value: Normal small airway epithelial cell


title: DMS53

description: Small lung cancer cell line

source_name: Small lung cancer cell line_DMS53

value: Small lung cancer cell

tag: cell line


title: Mmu_liver_TC_CLF_VEH_0_8H_rep3

description:
SAMPLE 52
Gene expression following 8.0 hours exposure to the vehicle control sesame oil

tag: treatment


title: Mmu_liver_TC_CLF_300_4H_rep3

description:
SAMPLE 50
Gene expression following 4.0 hours exposure to the PPARalpha ligand Clofibrate

tag: time-point

value: 4 hrs post-dose following a single dose


title: Mmu_liver_TC_CLF_300_2H_rep3

description:
SAMPLE 48
Gene expression following 2.0 hours exposure to the PPARalpha ligand Clofibrate

tag: replicate


title: Geno37_ABA_Grp1 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

tag: agent

value: ABA

value: vegetative


title: H209

description: Small lung cancer cell line

source_name: Small lung cancer cell line_H209


title: Mmu_liver_TC_CLF_VEH_0_4D_rep2

description:
SAMPLE 44
Gene expression following 4.0 days exposure to the vehicle control sesame oil

value: 4 days post initial dose following daily dosing


title: Geno71_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

value: Ctl

tag: group

value: Leaves from the 15-day-old-plantlets


title: SCLC251

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC251

value: Small cell lung carcinoma


title: Mmu_liver_TC_CLF_300_24H_rep1

description:
SAMPLE 43
Gene expression following 24.0 hours exposure to the PPARalpha ligand Clofibrate

value: 24 hrs post-dose following a single dose


title: Geno40_ABA_Grp1 with array type SUNFLOWER from Affymetrix

tag: age


title: Geno41_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

tag: developmental stage (boyes et al. plant cell 2001)


title: Mmu_liver_TC_CLF_300_14D_rep2

description:
SAMPLE 47
Gene expression following 14.0 days exposure to the PPARalpha ligand Clofibrate

tag: strain

value: female

value: 14 days post initial dose following daily dosing


title: SCLC255

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC255


title: Geno125_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Geno17_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: SCLC253

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC253


title: Mmu_liver_TC_CLF_VEH_0_14D_rep2

description:
SAMPLE 46
Gene expression following 14.0 days exposure to the vehicle control sesame oil

value: sesame oil (vehicle contrrol)


title: Geno37_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: SCLC257

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC257


title: Mmu_liver_TC_CLF_VEH_0_24H_rep1

description:
SAMPLE 42
Gene expression following 24.0 hours exposure to the vehicle control sesame oil


title: Mmu_liver_TC_CLF_VEH_0_2H_rep3

description:
SAMPLE 49
Gene expression following 2.0 hours exposure to the vehicle control sesame oil

value: 2 hrs post-dose following a single dose


title: Mmu_liver_TC_CLF_300_4D_rep2

description:
SAMPLE 45
Gene expression following 4.0 days exposure to the PPARalpha ligand Clofibrate


title: Mmu_liver_TC_CLF_VEH_0_12H_rep1

description:
SAMPLE 39
Gene expression following 12.0 hours exposure to the vehicle control sesame oil

value: 12 hrs post-dose following a single dose


title: Geno62_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_VEH_0_18H_rep1

description:
SAMPLE 40
Gene expression following 18.0 hours exposure to the vehicle control sesame oil

value: 18 hrs post-dose following a single dose


title: SCLC241

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC241


title: SCLC249

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC249


title: Mmu_liver_TC_CLF_300_18H_rep1

description:
SAMPLE 41
Gene expression following 18.0 hours exposure to the PPARalpha ligand Clofibrate

value: Clofibrate

value: liver


title: SCLC247

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC247


title: Geno62_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_300_12H_rep1

description:
SAMPLE 38
Gene expression following 12.0 hours exposure to the PPARalpha ligand Clofibrate


title: SCLC245

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC245


title: Geno59_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: SCLC239

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC239


title: Geno103_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_VEH_0_8H_rep1

description:
SAMPLE 37
Gene expression following 8.0 hours exposure to the vehicle control sesame oil

value: 8 hrs post-dose following a single dose


title: SCLC233

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC233


title: SCLC237

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC237


title: SCLC243

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC243


title: siCtrl_Hydrocortisone (vi)

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description:
vi_siC_HC
Gene expression data from adult human adipose stem cells treated with a synthetic glucocorticoid.

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in the GeneChip WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1.

data_processing: RMA (Robust Multiarray Average) signal extraction using Affymetrix Expression Console Version 1.1.

source_name: human preadipocytes from VAT tissue + siCtrl oligo + hydrocortisone

label_protocol: 100ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA).

growth_protocol: Human adipose stem cells were grown in DMEM and antibiotics.

extract_protocol: RNeasy mini kit (Qiagen).

treatment_protocol: Matched human adipose stem cells isolated from either SAT (sc) or VAT (vi) from a pool of 3 donors were transfected with a control siRNA (siCtrl) or a siRNA oligo targeting the gene LIM domain only 3 (siLMO3). 40hrs later, the transfected human adipose stem cells were treated with vehicle (veh) or 100nM Hydrocortisone (HC) in serum-free medium, and RNA was isolated 24hrs later.

value: visceral adipose tissue (VAT)

tag: cell type

value: preadipocytes

tag: sirna

value: siCtrl

value: hydrocortisone


title: Mmu_liver_TC_CLF_300_8H_rep1

description:
SAMPLE 36
Gene expression following 8.0 hours exposure to the PPARalpha ligand Clofibrate

tag: gender


title: siLMO3_Hydrocortisone (vi)

description:
vi_siL_HC
Gene expression data from adult human adipose stem cells treated with a synthetic glucocorticoid.

source_name: human preadipocytes from VAT tissue + siLMO3 oligo + hydrocortisone


title: Mmu_liver_TC_CLF_VEH_0_2H_rep1

description:
SAMPLE 34
Gene expression following 2.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_2H


title: Geno98_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: Ctl

value: vegetative


title: siLMO3_vehicle (vi)

description:
vi_siL_veh
Gene expression data from adult human adipose stem cells not treated with a synthetic glucocorticoid.

source_name: human preadipocytes from VAT tissue + siLMO3 oligo + vehicle

value: vehicle


title: Geno4_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: ABA

value: Leaves from the 15-day-old-plantlets


title: Geno84_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_300_4H_rep1

description:
SAMPLE 35
Gene expression following 4.0 hours exposure to the PPARalpha ligand Clofibrate

value: female

value: 4 hrs post-dose following a single dose


title: siLMO3_Hydrocortisone (sc)

description:
sc_siL_HC
Gene expression data from adult human adipose stem cells treated with a synthetic glucocorticoid.

source_name: human preadipocytes from SAT tissue + siLMO3 oligo + hydrocortisone

value: subcutaneous adipose tissue (SAT)


title: Mmu_liver_TC_CLF_300_1D_rep2

description:
SAMPLE 31
Gene expression following 1.0 days exposure to the PPARalpha ligand Clofibrate

value: 1 day post initial dose


title: SCLC231

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC231

value: Small cell lung carcinoma


title: Geno59_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno8_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: SCLC229

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC229


title: SCLC235

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC235


title: Geno56_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_VEH_0_1D_rep2

description:
SAMPLE 32
Gene expression following 1.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_1D

value: sesame oil (vehicle contrrol)


title: SCLC219

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC219


title: siCtrl_vehicle (vi)

description:
vi_siC_veh
Gene expression data from adult human adipose stem cells not treated with a synthetic glucocorticoid.

source_name: human preadipocytes from VAT tissue + siCtrl oligo + vehicle


title: Mmu_liver_TC_CLF_300_2H_rep1

description:
SAMPLE 33
Gene expression following 2.0 hours exposure to the PPARalpha ligand Clofibrate

value: Clofibrate

value: liver

value: 2 hrs post-dose following a single dose


title: Mmu_liver_TC_CLF_VEH_0_24H_rep2

description:
SAMPLE 30
Gene expression following 24.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_24H

value: 24 hrs post-dose following a single dose


title: Geno36_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: SCLC227

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC227


title: siCtrl_Hydrocortisone (sc)

description:
sc_siC_HC
Gene expression data from adult human adipose stem cells treated with a synthetic glucocorticoid.

source_name: human preadipocytes from SAT tissue + siCtrl oligo + hydrocortisone

value: preadipocytes

value: siCtrl


title: siCtrl_vehicle (sc)

description:
sc_siC_veh
Gene expression data from adult human adipose stem cells not treated with a synthetic glucocorticoid.

source_name: human preadipocytes from SAT tissue + siCtrl oligo + vehicle


title: siLMO3_vehicle (sc)

description:
sc_siL_veh
Gene expression data from adult human adipose stem cells not treated with a synthetic glucocorticoid.

source_name: human preadipocytes from SAT tissue + siLMO3 oligo + vehicle


title: Geno104_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_300_24H_rep2

description:
SAMPLE 29
Gene expression following 24.0 hours exposure to the PPARalpha ligand Clofibrate


title: Geno35_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_300_18H_rep2

description:
SAMPLE 28
Gene expression following 18.0 hours exposure to the PPARalpha ligand Clofibrate

value: 18 hrs post-dose following a single dose


title: Geno33_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: vegetative


title: Geno36_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: SCLC215

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC215


title: SCLC207

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC207


title: SCLC209

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC209


title: Geno35_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

value: Ctl


title: Geno56_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: siCtrl_FM_rep2

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: human preadipocytes+siCtrl_day6_rep2

label_protocol: Biotin

growth_protocol: human adipose stem cells were grown in DMEM + FBS (10%) and antibiotics

extract_protocol: Rneasy mini kit (Qiagen)

treatment_protocol: human adipose stem cells were transfected with a control siRNA (siCtrl) or two different siRNA oligos targeting the gene LMO3 (siLMO3_oligo1 or siLMO3_oligo2). 40Hrs later, the transfected human adipose stem cells were induced to differentiate into mature adipocytes with a adipogenic cocktail (FullMix) and RNA isolated at day 0 or day6 after induction of differentiation.

value: white adipose tissue


title: SCLC213

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC213


title: siLMO3_oligo1_FM_rep1

source_name: human preadipocytes+oligo1_day6_rep1


title: Ovary

description: Normal ovary

source_name: Normal ovary

value: Normal ovary


title: Mmu_liver_TC_CLF_VEH_0_8H_rep2

description:
SAMPLE 24
Gene expression following 8.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_8H

value: female

value: 8 hrs post-dose following a single dose


title: Mmu_liver_TC_CLF_300_12H_rep2

description:
SAMPLE 26
Gene expression following 12.0 hours exposure to the PPARalpha ligand Clofibrate

value: 12 hrs post-dose following a single dose


title: siLMO3_oligo2_FM_rep1

source_name: human preadipocytes+oligo2_day6_rep1


title: Geno30_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

value: Leaves from the 15-day-old-plantlets


title: siLMO3_oligo2_0_rep2

source_name: human preadipocytes+oligo2_day0_rep2


title: SCLC211

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC211

value: Small cell lung carcinoma


title: siCtrl_FM_rep1

source_name: human preadipocytes+siCtrl_day6_rep1


title: Geno78_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: ABA


title: Uterus

description: Normal uterus

source_name: Normal uterus

value: Normal uterus


title: Mmu_liver_TC_CLF_VEH_0_4H_rep2

description:
SAMPLE 22
Gene expression following 4.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_4H

value: sesame oil (vehicle contrrol)

value: liver

value: 4 hrs post-dose following a single dose


title: Mmu_liver_TC_CLF_VEH_0_12H_rep2

description:
SAMPLE 25
Gene expression following 12.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_12H


title: SCLC205

description: Small cell lung carcinoma

source_name: Small cell lung carcinoma_SCLC205


title: Mmu_liver_TC_CLF_300_8H_rep2

description:
SAMPLE 23
Gene expression following 8.0 hours exposure to the PPARalpha ligand Clofibrate

value: Clofibrate


title: siLMO3_oligo2_0_rep1

source_name: human preadipocytes+oligo2_day0_rep1

value: preadipocytes


title: Mmu_liver_TC_CLF_VEH_0_18H_rep2

description:
SAMPLE 27
Gene expression following 18.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_18H

value: 18 hrs post-dose following a single dose


title: Breast

description: Normal breast

source_name: Normal breast

value: Normal breast


title: Mmu_liver_TC_CLF_300_4H_rep2

description:
SAMPLE 21
Gene expression following 4.0 hours exposure to the PPARalpha ligand Clofibrate


title: siLMO3_oligo1_0_rep1

source_name: human preadipocytes+oligo1_day0_rep1


title: Geno23_ABA_Grp1 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: vegetative


title: Mmu_liver_TC_CLF_300_2H_rep2

description:
SAMPLE 20
Gene expression following 2.0 hours exposure to the PPARalpha ligand Clofibrate

value: 2 hrs post-dose following a single dose


title: siCtrl_0_rep1

source_name: human preadipocytes+siCtrl_day0_rep1

value: white adipose tissue


title: siLMO3_oligo2_FM_rep2

source_name: human preadipocytes+oligo2_day6_rep2


title: Seminal_vesicle

description: Normal seminal vesicle

source_name: Normal seminal vesicle

value: Normal seminal vesicle


title: Geno105_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

value: Ctl


title: Testis

description: Normal testis

source_name: Normal testis

value: Normal testis


title: Mmu_liver_TC_CLF_300_14D_rep1

description:
SAMPLE 18
Gene expression following 14.0 days exposure to the PPARalpha ligand Clofibrate

value: female

value: 14 days post initial dose following daily dosing


title: siCtrl_0_rep2

source_name: human preadipocytes+siCtrl_day0_rep2


title: Mmu_liver_TC_CLF_VEH_0_4D_rep1

description:
SAMPLE 16
Gene expression following 4.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_4D

value: 4 days post initial dose following daily dosing


title: Monocyte

description: Normal monocyte

source_name: Normal monocyte

value: Normal monocyte


title: Mmu_liver_TC_CLF_VEH_0_14D_rep1

description:
SAMPLE 17
Gene expression following 14.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_14D

value: sesame oil (vehicle contrrol)


title: Macrophage

description: Normal macrophage

source_name: Normal macrophage

value: Normal macrophage


title: siLMO3_oligo1_FM_rep2

source_name: human preadipocytes+oligo1_day6_rep2