title: peripheral blood-Case3_4


title: peripheral blood-Case3_3

status: Public on Feb 20 2014

type: RNA

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (cat. no 901530).

scan_protocol: GeneTitan MC Instrument was used to hybridize, wash, stain and scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control GeneTitan hybridization process and in summarizing probe cell intensity data (.CEL file generation).

data_processing: Sample T1DControl7_4 was excluded from the final analysis as an outlier.  The CEL file and a readme for T1DControl7_4 containing the Metadata are provided as supplementary files on the Series record. The intensities were RMA normalized and log2-transformed using R/Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: 50 ng of total RNA was processed to cDNA with Nugen Ovation RNA Amplification System V2 (cat. no 3100-60) and subsequently biotin-labelled and fragmented with Nugen Encore Biotin Module (cat. no 4200-A01) according to manufacture’s protocol.

growth_protocol: 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70C until analyzed.

extract_protocol: Total whole-blood RNA was extracted from the samples using PAX gene RNA Blood RNA kit (Qiagen, Germany) according to manufacturer's instructions. RNA quality and quantity was determined using Nano Drop ND-1000 (Nano Drop Technologies, USA) and Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).

tag: case/control pair

tag: age at sample (months)

tag: time from seroconversion (months)

tag: time from t1d diagnosis (months)

tag: gender

value: female

tag: hla-dqb1 genotype


title: peripheral blood-Case3_5

hyb_protocol: 1.5 ug each sample was hybridized to Illumina Sentrix Human-6 V2 Expression Bead Chips at 58 °C overnight (18 h) according to Illumina 11225598_WGGEX_IntelliHyb_Seal_SystemManual_RevA.pdf. Hybridizations were detected with 1 ug/ml Cyanine3-streptavidine (Amersham Biosciences cat. no 146065)

scan_protocol: Chips were scanned with Illumina Bead Array Reader. Numerical results were extracted with Bead Studio v2.3.41 without any normalization or background subtraction.

data_processing: The intensities were quantile normalized and log2-transformed using R/Bioconductor.

source_name: peripheral blood-Case3

label_protocol: 500 ng total RNA was amplified and reverse transcribed with RiboAmp OA 1 round RNA amplification kit (Arcturus, cat. no KIT0209). cRNA was biotinylated during the overnight (14 h) IVT reaction with Illumina Total Prep RNA Amplification Kit (Ambion, cat. no L1791). cRNA was purified with RiboAmp OA 1 Round RNA Amplification Kit.

growth_protocol: 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70 °C until analyzed.

tag: tissue

value: peripheral blood


title: peripheral blood-Case3_4


title: mouse_liver_Wfs1_wt_VPA_replicate_3

city: Tartu

first: Anton

last: Terasmaa

address: Ravila 19

department: Faculty of Medicine, Institute of Bio- and Translational Medicine

country: Estonia

institute: University of Tartu

hyb_protocol: Samples were hybridized on Affymetrix Mouse Gene 1.0 st arrays

scan_protocol: standard Affymetrix protocol

data_processing: Images were processed and cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (Affymetrix). Cel files were  processed using Expression Console v.1.1.2800.28061 to yield RMA summarized Log2 transformed expression values for probesets (CHP files). Normalized expression data (chp files) were further analysed using ANOVA in R (genotype x treatment) using R package Bioconductor.

organism: Mus musculus

source_name: Wfs1_WT_mouse_liver_VPA_12 wks_ip

label_protocol: 300 nanograms of total RNA were processed to produce fragmented biotin-labeled cRNA using the Ambion WT expression kit according to manufacturer's instructions.

growth_protocol: Mice were housed under standard laboratory conditions on a 12-h light/dark cycle (lights on at 07:00 AM) with free access to regular chow diet (R70 Lantmännen, Sweden) and water.  Male wild type and Wfs1 mutant mice were used throughout this study, they were 4 to 6 weeks old at the beginning of the experiment.  Mice were treated for three months with valproic acid (VPA, Sigma Aldrich, 300 mg/kg i.p. daily) or vehicle (0.9% saline 10 mL/kg i.p.). A glucose tolerance test (2 g/kg i.p.) was performed 24 hours after the last VPA injection and mice were killed 24 hours after the glucose tolerance test.  Mice were 16 to 18 weeks old when killed. Each experimental group consisted of 8 animals.

extract_protocol: Total liver RNA was extracted using Trizol reagent. Integrity of total RNA was evaluated using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and was within RNA integrity number (RIN) 7 to 9.

treatment_protocol: mice were killed, the liver was dissected out, snap frozen in liquid nitrogen and stored at -80°C until further analysis.

tag: genotype/variation

value: male

tag: age

value: 16-18 weeks

tag: treated with

value: valproic acid (300 mg/kg/day i.p.) for 12 weeks

value: liver


title: peripheral blood-Case3_3


title: HSA8

type: genomic

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: MeDIP of genomic DNA from HSA8 brain sample, technical replicate 1 and 2

hyb_protocol: Samples were hybridized to microarrays for 16 h at 42°C using default instrument settings.

scan_protocol: Microarrays were scanned with a MS200 scanner (Illumina); image gridding and intensity read-out was performed with Nimblescan version 2.6.

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages Starr and IRanges; MeDIP and input sample pairs were within-sample loess normalized followed by calculation of log2 (MeDIP/input) signal ratios and between-sample quantiles normalization; technical replicates were summarized and smoothed by application of a 400 bp sliding window along the genomically ordered data using the function „computeRunningMedians“ implemented in the „Starr“ package; data were then weighted by the number of CpGs with a maximum distance of 400 bp away from each probe position using an adaption of the „MEDIPS“ CpG density normalization [PMID: 24227674] to microarray data.

molecule: genomic DNA

label_protocol: MeDIP and input DNAs were amplified with the GenomePlex Complete Whole Genome Amplification 2 kit (Sigma-Aldrich) and purified using the QIAquick PCR Purification kit (Qiagen); 1 µg of amplified DNA was denatured and labelled via primer extension with Cy dyes attached to 9-mer primers using the two color protocol (NimbleGen Roche).

extract_protocol: Genomic DNA was extracted using the Precellys Tissue DNA kit (PEQLAB) following the manufacturer's instructions and sheared with a Bioruptor (Diagenode) to fragment sizes from 100 bp to 600 bp; MeDIP samples were generated by overnight incubation of ca. 1.5 µg sheared DNA with monoclonal anti-5-methylcytosine antibody (Diagenode) at 4°C and subsequent magnetic bead-based enrichment of antibody-bound DNA; input samples consisted of untreated sheared DNA.

treatment_protocol: MeDIP

value: brain, frontal cortex tissue area A10

tag: Sex

source_name: Input of genomic DNA from HSA8 brain sample

treatment_protocol: input


title: mouse_liver_Wfs1_wt_VPA_replicate_2


title: HSA7

description: MeDIP of genomic DNA from HSA7 brain sample, technical replicate 1

source_name: Input of genomic DNA from HSA7 brain sample


title: peripheral blood-Case3_1


title: mouse_liver_Wfs1_ko_SAL_replicate_8

source_name: Wfs1_KO_mouse_liver_SAL_12 wks_ip

value: vehicle (saline, 10ml/kg i.p.) for 12 weeks


title: peripheral blood-Control2_4

source_name: peripheral blood-Control2

value: no seroconversion

value: no T1D diagnosis


title: peripheral blood-Case3_2


title: mouse_liver_Wfs1_wt_VPA_replicate_1


title: peripheral blood-Control2_4


title: peripheral blood-Control2_3


title: peripheral blood-Case3_1


title: peripheral blood-Control2_3


title: mouse_liver_Wfs1_ko_SAL_replicate_6


title: peripheral blood-Control2_2


title: peripheral blood-Case2_7


title: peripheral blood-Control2_1


title: peripheral blood-Control2_1


title: peripheral blood-Case2_7

source_name: peripheral blood-Case2


title: peripheral blood-Case2_6


title: peripheral blood-Control2_2


title: mouse_liver_Wfs1_ko_SAL_replicate_7


title: mouse_liver_Wfs1_ko_SAL_replicate_3


title: peripheral blood-Case2_6


title: peripheral blood-Case2_5


title: mouse_liver_Wfs1_ko_SAL_replicate_4


title: mouse_liver_Wfs1_ko_SAL_replicate_5


title: peripheral blood-Case2_5


title: mouse_liver_Wfs1_ko_SAL_replicate_2


title: peripheral blood-Case3_2


title: peripheral blood-Case2_3


title: peripheral blood-Case2_4


title: peripheral blood-Case2_2


title: mouse_liver_Wfs1_hz_SAL_replicate_7

source_name: Wfs1_HZ_mouse_liver_SAL_12 wks_ip


title: peripheral blood-Case2_1


title: peripheral blood-Case2_3


title: peripheral blood-Case2_4


title: peripheral blood-Case2_2


title: peripheral blood-Control1_4


title: peripheral blood-Control1_5


title: mouse_liver_Wfs1_hz_SAL_replicate_8


title: peripheral blood-Control1_1

source_name: peripheral blood-Control1


title: mouse_liver_Wfs1_hz_SAL_replicate_6


title: peripheral blood-Control1_2


title: mouse_liver_Wfs1_ko_SAL_replicate_1


title: peripheral blood-Control1_4


title: peripheral blood-Control1_5


title: mouse_liver_Wfs1_hz_SAL_replicate_4


title: peripheral blood-Case2_1


title: peripheral blood-Control1_3


title: peripheral blood-Case1_8


title: peripheral blood-Control1_1


title: peripheral blood-Control1_2


title: mouse_liver_Wfs1_hz_SAL_replicate_3


title: mouse_liver_Wfs1_hz_SAL_replicate_1


title: peripheral blood-Control1_3


title: mouse_liver_Wfs1_hz_SAL_replicate_5


title: peripheral blood-Case1_7


title: mouse_liver_Wfs1_wt_SAL_replicate_8

source_name: Wfs1_WT_mouse_liver_SAL_12 wks_ip


title: mouse_liver_Wfs1_hz_SAL_replicate_2


title: peripheral blood-Case1_6


title: peripheral blood-Case1_8

source_name: peripheral blood-Case1


title: mouse_liver_Wfs1_wt_VPA_replicate_4


title: peripheral blood-Case1_7


title: peripheral blood-Case1_6


title: mouse_liver_Wfs1_wt_SAL_replicate_7


title: mouse_liver_Wfs1_wt_SAL_replicate_6


title: mouse_liver_Wfs1_wt_SAL_replicate_5


title: peripheral blood-Case1_3


title: peripheral blood-Case1_5


title: peripheral blood-Case1_5


title: peripheral blood-Case1_4


title: peripheral blood-Case1_1


title: peripheral blood-Case1_2


title: peripheral blood-Case1_4


title: mouse_liver_Wfs1_wt_SAL_replicate_2


title: peripheral blood-Case1_3


title: mouse_liver_Wfs1_wt_SAL_replicate_1


title: peripheral blood-Case1_1


title: mouse_liver_Wfs1_wt_SAL_replicate_3


title: peripheral blood-Case1_2


title: mouse_liver_Wfs1_wt_SAL_replicate_4


title: placenta-rep52

status: Public on Feb 19 2014

city: Charlestown

first: Martin

last: Aryee

state: MA

address: 149 13th Street

department: Pathology

country: USA

institute: Massachusetts General Hospital

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: minfi, Bioconductor, R

label: Cy3 and Cy5

source_name: placenta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

value: placenta


title: placenta-rep45


title: placenta-rep48


title: placenta-rep50


title: placenta-rep47


title: placenta-rep53


title: placenta-rep32


title: placenta-rep56


title: placenta-rep35


title: placenta-rep54


title: placenta-rep42


title: placenta-rep30


title: placenta-rep31


title: placenta-rep51


title: placenta-rep33


title: placenta-rep37


title: placenta-rep40


title: placenta-rep41


title: placenta-rep28


title: placenta-rep39


title: placenta-rep36


title: placenta-rep34


title: placenta-rep44


title: placenta-rep49


title: placenta-rep43


title: placenta-rep29


title: placenta-rep38


title: placenta-rep27


title: placenta-rep25


title: placenta-rep20


title: placenta-rep21


title: placenta-rep24


title: placenta-rep26


title: placenta-rep46


title: placenta-rep16


title: placenta-rep22


title: placenta-rep18


title: placenta-rep15


title: placenta-rep13


title: placenta-rep6


title: placenta-rep12


title: placenta-rep17


title: placenta-rep7


title: placenta-rep19


title: placenta-rep9


title: liver-rep69

source_name: liver


title: placenta-rep4


title: placenta-rep23


title: placenta-rep3


title: placenta-rep10


title: placenta-rep14


title: placenta-rep11


title: liver-rep70


title: placenta-rep1


title: liver-rep68


title: placenta-rep5


title: placenta-rep55


title: liver-rep67


title: liver-rep66


title: placenta-rep8


title: liver-rep65


title: liver-rep61


title: liver-rep63


title: liver-rep60


title: liver-rep58


title: liver-rep59


title: liver-rep44


title: liver-rep52


title: RKO, biological rep2

city: Seoul

first: Gi Hoon

last: Son

state: select a state

address: Inchon-ro 73

department: Department of Legal Medicine

country: South Korea

institute: Korea University

description: Gene expression data from ventral midbrain of RKO mice

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS software using Affymetrix default analysis settings and normalized by RMA (Robust Multi-array Average) method.

source_name: Ventral midbrain from RKO mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Male RKO and WT mice (10-15 weeks of age) were maintained in a C57BL/6J background. Mice were housed in temperature-controlled (22-23ºC) quarters under a 12-h light-dark (LD) photoperiod (lights on at 8:00 a.m.).

extract_protocol: Total RNA was isolated by the single-step acid guanidinium thiocyanate-phenol-chloroform method.

treatment_protocol: After entrainment for >10 days under LD conditions, mice were kept in constant darkness (DD) for 2 days starting at lights-off time. On the third day, mice were sacrificed at indicated time points by cervical dislocation. Tissue was rapidly removed and frozen in liquid nitrogen.

value: Ventral midbrain

tag: genotype

value: Rev-erba knock-out

value: 10-15 weeks

tag: genetic background


title: liver-rep62


title: liver-rep55


title: liver-rep57


title: liver-rep56


title: liver-rep47


title: liver-rep51


title: liver-rep49


title: RKO, biological rep1


title: liver-rep48


title: liver-rep46


title: liver-rep40


title: liver-rep45


title: liver-rep39


title: liver-rep38


title: liver-rep42


title: liver-rep41


title: WT, biological rep2

description: Gene expression data from ventral midbrain of WT mice

source_name: Ventral midbrain from WT mice

value: Wild-type


title: liver-rep54


title: liver-rep37


title: WT, biological rep1


title: PBS-7 days 1

city: Saint Louis

first: laura

last: schuettpelz

state: MO

address: 660 S. Euclid

institute: washington university

hyb_protocol: MoGene 1.0 ST array

scan_protocol: GeneChip Scanner

data_processing: Data normalized using Robust Multichip Average (RMA) algorithm

source_name: bone marrow

label_protocol: amplified using NuGen Ovation System

extract_protocol: RNA preparation using RNA XS columns (Machery-Nagel)

treatment_protocol: G-CSF 125 mcg/kg twice daily, subcutaneous

tag: cell type

value: KSL SLAM cells (Lineage- c-Kit+ Sca-1+ CD150+ CD48- CD41-)

tag: treatment

value: PBS  7 days


title: PBS-7 days 2


title: G-CSF-36hrs 4

hyb_protocol: Affymetrix MoGene 1.0 ST array

label_protocol: NuGen Ovation amplification

extract_protocol: RNA prepared using RNA XS columns (Macherey-Nagel)

value: G-CSF 36 hours


title: PBS-7 days 3


title: G-CSF-36hrs 3


title: placenta-rep2


title: liver-rep35


title: liver-rep36


title: G-CSF-7 days 1

value: G-CSF 7 days


title: liver-rep64


title: liver-rep43


title: liver-rep34


title: liver-rep50


title: G-CSF-7 days 2


title: G-CSF-7 days 3


title: liver-rep28


title: PBS-36hrs 2

value: PBS 36 hours


title: PBS-36hrs 3


title: G-CSF-36hrs 2


title: PBS-36hrs 1


title: PBS-36hrs 4


title: liver-rep53


title: G-CSF-36hrs 1


title: liver-rep32


title: liver-rep29


title: liver-rep31


title: liver-rep33


title: liver-rep25


title: HPT1_R3

city: Martinsried

first: Milena

last: Dürrbaum

address: Am Klopferspitz 18

department: Maintenance of Genome Stability

institute: Max Planck Institute of Biochemistry

hyb_protocol: Following cRNA clean-up and quantification (NanoDrop ND-1000 Spectrophotometer, peqlab) 1.65 µg (HCT116 3/3 and HCT116 H2B-GFP 5/4) or 0.60 µg (others) of each Cyanin-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent). Each cRNA sample was hybridized at 65 °C for 17 hrs on separate Whole Human Genome Oligo Microarrays (4x44K format) (for HCT116 3/3 and HCT116 H2B-GFP 5/4) or SurePrint G3 Human Gene Expression Arrays (8x60K).

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.1.3. Software (Agilent Technologies) (HCT116 3/3 and HCT116 H2B-GFP 5/4) or Scan Control A.8.4.1. Software (Agilent Technologie) on the Agilent DNA Microarray Scanner.

data_processing: Signal intensities were extracted from the image using Feature Extraction 10.5.1 Software (Agilent Technologies) and the design file 014850_D_F_20090416.xml (HCT116 3/3 and HCT116 H2B-GFP 5/4) or 10.7.3.1 Software and the design file 028004_D_F_20120130.xml (others). Data was background subtracted; log2 transformed and normalized. Medians of replicates were calculated and a ratio of the aneuploid cell line (median) vs the corresponding WT cell line (median) was used for further analysis (indicated in the column header).

source_name: HCT116 cell line, complex aneuploidy, clone1, replicate 3

label_protocol: 500 ng (HCT116 3/3 and HCT116 H2B-GFP 5/4) or 100 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (HCT116 3/3 and HCT116 H2B-GFP 5/4: Quick-Amp Labeling Kit One-Color, Agilent Technologies; all others: Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP according to the manufacturer´s instructions.

growth_protocol: Cell lines were cultered in DMEM with 10% FBS at 5% CO2, 37°C

extract_protocol: Total RNA extraction with the Quiagen mRNeasy Mini Kit

treatment_protocol: No treatment

value: human colon carcinoma cell line

tag: variation

value: complex aneuploidy

tag: cell line


title: HPT2_R1

source_name: HCT116 cell line, complex aneuploidy, clone 2, replicate 1


title: liver-rep30

value: liver


title: HPT2_R3

source_name: HCT116 cell line, complex aneuploidy, clone 2, replicate 3


title: HCT116 H2B-GFP_R2

source_name: HCT116 cell line, diploid, replicate 2

value: diploid


title: HCT116 H2B-GFP_R3

source_name: HCT116 cell line, diploid, replicate 3


title: HPT1_R1

source_name: HCT116 cell line, complex aneuploidy, clone1, replicate 1


title: HPT2_R2

source_name: HCT116 cell line, complex aneuploidy, clone 2, replicate 2


title: HCT116 H2B-GFP_R1

source_name: HCT116 cell line, diploid, replicate 1


title: HPT1_R2

source_name: HCT116 cell line, complex aneuploidy, clone1, replicate 2


title: liver-rep27


title: liver-rep24


title: KARPAS_HIGH_Day6_C

city: Cambridge

first: Yonghong

last: Xiao

address: 400 Technology Square, 4th Floor

department: Biological Sciences

institute: Epizyme Inc.

description: KARPAS_422  treated with EPZ6438 at 10xLCC for 6 days

hyb_protocol: RNA hybridization to Affymetrix HG-U133 Plus 2 arrays was performed by Expression Analysis, Inc. (Durham, NC). Standard Affymetrix protocols were used with the Affymetrix FS450 Fluidics Station and the Affymetrix Hybridization, Washing and Staining kits.

scan_protocol: Microarray scanning and data extraction was perfomed by Expression Analysis, Inc. (Durham, NC). The Affymetrix GeneChip Scanner 3000 7G was used. GeneChip Command Console (Affymetrix) was used to drive the scanners. Expression Console (Affymetrix) was used to extract data from the scanned images.

data_processing: Expression file matrix data was generated using Genepattern Software for the Broad Institute (http://genepattern.broadinstitute.org/gp) with the ExpressionFileCreator Module. GCRMA method was used with quantile normalization.

source_name: KARPAS_422, EPZ6438 at 10xLCC, Day 6

label_protocol: RNA labeling was peformed by Expression Analysis, Inc. (Durham, NC). Total RNA was converted cDNA and in vitro transcribed to biotin-labeled anti-sense RNA, using the Enzo Single Round RNA Amplification and Biotin Labeling System (Enzo # ENZ-42420-10) according to the manufacturer’s protocol.

extract_protocol: RNA isolation was peformed by Expression Analysis, Inc. (Durham, NC). RNA was purified using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol, including the on-column DNase I digestion. RNA integrity and quantity was measured using an Agilent Bioanalyzer 2100.

tag: agent

tag: dose

tag: time

value: 6 days


title: KARPAS_LOW_Day6_B

description: KARPAS_422  treated with EPZ6438 at LCC for 6 days

source_name: KARPAS_422, EPZ6438 at LCC, Day 6

value: LCC


title: KARPAS_HIGH_Day6_B


title: liver-rep22


title: KARPAS_LOW_Day6_C


title: KARPAS_LOW_Day6_A


title: liver-rep19


title: KARPAS_DMSO_Day6_B

description: KARPAS_422 treated with DMSO for 6 days

source_name: KARPAS_422, DMSO, Day 6

value: DMSO

value: control


title: liver-rep17


title: liver-rep23


title: KARPAS_DMSO_Day6_C

description: KARPAS_422 treated with DMSO for 6 days


title: KARPAS_DMSO_Day6_A

description: KARPAS_422 treated with DMSO for 6 days


title: liver-rep20


title: liver-rep21


title: Patient 30 Prog Treated with vemurafenib

city: Westmead

first: Gulietta

last: Pupo

state: NSW

address: Darcy Road

country: Australia

institute: University of Sydney

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using with cubic spline using the Illumina GenomeStudio v2011.1

source_name: Melanoma tumour

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

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

value: BRAF V600E

tag: disease state

value: melanoma

tag: location

value: lung

value: vemurafenib


title: liver-rep18

source_name: liver


title: liver-rep15


title: KARPAS_HIGH_Day6_A


title: SUDHL6_HIGH_Day6_B

description: SUDHL6  treated with EPZ6438 at 10xLCC for 6 days

source_name: SUDHL6, EPZ6438 at 10xLCC, Day 6


title: liver-rep10


title: liver-rep16


title: liver-rep11


title: SUDHL6_HIGH_Day6_C


title: liver-rep14


title: Patient 30 Pre untreated

description: Patient 30 Pre untreated

value: subcutaneous


title: SUDHL6_LOW_Day6_C

description: SUDHL6  treated with EPZ6438 at LCC for 6 days

source_name: SUDHL6, EPZ6438 at LCC, Day 6


title: SUDHL6_LOW_Day6_A


title: Patient 28 Prog 4 Treated with vemurafenib

value: BRAF V600R


title: Patient 28 Prog 3 Treated with vemurafenib


title: liver-rep13


title: SUDHL6_HIGH_Day6_A


title: SUDHL6_DMSO_Day6_C

description: SUDHL6 treated with DMSO for 6 days

source_name: SUDHL6, DMSO, Day 6


title: SUDHL6_DMSO_Day6_A

description: SUDHL6 treated with DMSO for 6 days


title: SUDHL6_DMSO_Day6_B

description: SUDHL6 treated with DMSO for 6 days


title: liver-rep12


title: liver-rep9


title: Patient 28 Prog 2 Treated with vemurafenib


title: liver-rep7


title: SUDHL6_LOW_Day6_B


title: liver-rep8


title: PFEIFFER_LOW_Day6_A

description: PFEIFFER treated with EPZ6438 at LCC for 6 days

source_name: PFEIFFER, EPZ6438 at LCC, Day 6

value: PFEIFFER


title: PFEIFFER_LOW_Day6_C


title: PFEIFFER_HIGH_Day6_C

description: PFEIFFER treated with EPZ6438 at 10xLCC for 6 days

source_name: PFEIFFER, EPZ6438 at 10xLCC, Day 6


title: TBEP_1470_rep2

city: Montreal

first: Maeva

last: Giraudo

state: Quebec

address: 105 McGill street

department: Water Science and Technology Directorate

country: Canada

institute: Environment Canada

description: Gene expression after 21 days exposure to 1470µg/l TBEP, biological replicate 2 of 3

hyb_protocol: Labeled cRNA was hybridized to a custom 15,000 sequence D. magna array using the protocols of Agilent Technologies (Agilent HD 8x15k format, AMADID # 023710) following the One-Color Microarray-Based Gene Expression Analysis Protocol

scan_protocol: Microarrays were scanned using a Surescan High-Resolution Agilent DNA Microarray Scanner with the following settings: Channels: G; Scan Region: 61x21.6mm; Resolution: 5 um; TIFF: 20-bit; G PMT: 100%; no XDR. The images were processed using Agilent Feature Extraction Software version 11.5.1.1.

data_processing: Raw data were analyzed using Agilent Genespring GX Software version 12.0. Quantile normalization was performed to reduce variance between arrays and poor quality/non-detected data points were filtered out. For each experimental condition, statistically significant, differentially expressed genes were selected with fold changes (treated relative to the control values) cut-offs of ±1 according to an ANOVA analysis with post-hoc Tukey’s HSD (p-value ≤ 0.05).

organism: Daphnia magna

source_name: TBEP, 21 days, 1470 µg/L, replicate 2

label_protocol: Agilent Low Input Quick Amp Labeling Kit, one-color

growth_protocol: Environment Canada test method (1990). 20°C, 16 hr light/8 hr dark photoperiod; fed daily on green algae and YCT preparation

extract_protocol: RNEasy Plus Mini kit (Qiagen); Experion Automated Electrophoresis System (BioRad)

treatment_protocol: OECD Guidelines 2008; 21-day exposures

value: TBEP, 21 days, 1470 µg/L

value: whole organism

value: <24h old neonates

value: female

tag: pooling

value: 10 pooled individuals


title: PFEIFFER_DMSO_Day6_C

description: PFEIFFER treated with DMSO for 6 days

source_name: PFEIFFER, DMSO, Day 6


title: PFEIFFER_HIGH_Day6_A


title: PFEIFFER_HIGH_Day6_B


title: liver-rep4

tag: tissue

value: liver


title: TBEP_1470_rep3

description: Gene expression after 21 days exposure to 1470µg/l TBEP, biological replicate 3 of 3

source_name: TBEP, 21 days, 1470 µg/L, replicate 3


title: Patient 28 Prog 1 Treated with vemurafenib


title: Patient 25 Pre untreated

description: Patient 25 Pre untreated

value: BRAF V600K

value: lymph node


title: liver-rep5


title: PFEIFFER_DMSO_Day6_B

description: PFEIFFER treated with DMSO for 6 days

value: DMSO

value: 6 days


title: liver-rep3


title: Patient 25 Prog Treated with vemurafenib


title: Patient 24 Prog Treated with vemurafenib

value: BRAF V600E


title: Patient 24 Pre untreated (replicate)

description: Patient 24 Pre untreated (replicate)

value: melanoma


title: PFEIFFER_DMSO_Day6_A

description: PFEIFFER treated with DMSO for 6 days

value: control


title: Patient 28 Pre untreated

description: Patient 28 Pre untreated


title: WSU_HIGH_Day6_A

description: WSU_DLCL2 treated with EPZ6438 at 10xLCC for 6 days

source_name: WSU_DLCL2, EPZ6438 at 10xLCC, Day 6


title: WSU_HIGH_Day6_C


title: TBEP_147_rep3

description: Gene expression after 21 days exposure to 147µg/l TBEP, biological replicate 3 of 3

source_name: TBEP, 21 days, 147 µg/L, replicate 3

value: TBEP, 21 days, 147 µg/L


title: TBEP_147_rep2

description: Gene expression after 21 days exposure to 147µg/l TBEP, biological replicate 2 of 3

source_name: TBEP, 21 days, 147 µg/L, replicate 2


title: Patient 24 Pre untreated

description: Patient 24 Pre untreated

value: subcutaneous


title: TBEP_14.7_rep3

description: Gene expression after 21 days exposure to 14.7µg/l TBEP, biological replicate 3 of 3

source_name: TBEP, 21 days, 14.7µg/L, replicate 3

value: TBEP, 21 days, 14.7µg/L


title: TBEP_147_rep1

description: Gene expression after 21 days exposure to 147µg/l TBEP, biological replicate 1 of 3

source_name: TBEP, 21 days, 147 µg/L, replicate 1


title: liver-rep6


title: Patient 23 Prog Treated with vemurafenib

value: vemurafenib


title: TBEP_1470_rep1

description: Gene expression after 21 days exposure to 1470µg/l TBEP, biological replicate 1 of 3

source_name: TBEP, 21 days, 1470 µg/L, replicate 1

value: TBEP, 21 days, 1470 µg/L


title: WSU_LOW_Day6_C

description: WSU_DLCL2 treated with EPZ6438 at LCC for 6 days

source_name: WSU_DLCL2, EPZ6438 at LCC, Day 6

value: LCC


title: liver-rep1


title: WSU_LOW_Day6_B


title: WSU_DMSO_Day6_B

description: WSU_DLCL2 treated with DMSO for 6 days

source_name: WSU_DLCL2, DMSO, Day 6


title: WSU_LOW_Day6_A


title: WSU_HIGH_Day6_B


title: WSU_DMSO_Day6_C

description: WSU_DLCL2 treated with DMSO for 6 days


title: KARPAS_HIGH_Day4_C

description: KARPAS_422  treated with EPZ6438 at 10xLCC for 4 days

source_name: KARPAS_422, EPZ6438 at 10xLCC, Day 4

value: 4 days


title: Patient 21 Prog Treated with dabrafenib

description: Patient 21 Prog Treated with dabrafenib

source_name: Melanoma tumour

value: brain

value: dabrafenib


title: TBEP_ctrl_rep3

description: Gene expression after 21 days in unexposed controls, biological replicate 3 of 3

source_name: TBEP, 21 days, control, replicate 3

value: TBEP, 21 days, control

value: whole organism

value: <24h old neonates

value: female

value: 10 pooled individuals


title: liver-rep2

source_name: liver

value: liver


title: Patient 21 Pre untreated

description: Patient 21 Pre untreated

value: BRAF V600E

value: melanoma


title: liver-rep26


title: WSU_DMSO_Day6_A

description: WSU_DLCL2 treated with DMSO for 6 days

value: DMSO

value: control

value: 6 days


title: TBEP_14.7_rep2

description: Gene expression after 21 days exposure to 14.7µg/l TBEP, biological replicate 2 of 3

source_name: TBEP, 21 days, 14.7µg/L, replicate 2

value: TBEP, 21 days, 14.7µg/L


title: KARPAS_LOW_Day4_A

description: KARPAS_422  treated with EPZ6438 at LCC for 4 days

source_name: KARPAS_422, EPZ6438 at LCC, Day 4


title: KARPAS_HIGH_Day4_B


title: TBEP_ctrl_rep2

description: Gene expression after 21 days in unexposed controls, biological replicate 2 of 3

source_name: TBEP, 21 days, control, replicate 2


title: PFEIFFER_LOW_Day6_B

source_name: PFEIFFER, EPZ6438 at LCC, Day 6

value: PFEIFFER


title: KARPAS_HIGH_Day4_A


title: Patient 18 Prog 1 Treated with dabrafenib

value: bowel


title: Patient 18 Pre untreated (replicate)

description: Patient 18 Pre untreated (replicate)

value: subcutaneous


title: KARPAS_LOW_Day4_B

value: LCC

value: 4 days


title: KARPAS_DMSO_Day4_C

description: KARPAS_422 treated with DMSO for 4 days

source_name: KARPAS_422, DMSO, Day 4


title: KARPAS_LOW_Day4_C


title: TBEP_ctrl_rep1

description: Gene expression after 21 days in unexposed controls, biological replicate 1 of 3

source_name: TBEP, 21 days, control, replicate 1

value: TBEP, 21 days, control


title: KARPAS_DMSO_Day4_A

description: KARPAS_422 treated with DMSO for 4 days


title: SUDHL6_HIGH_Day4_A

description: SUDHL6  treated with EPZ6438 at 10xLCC for 4 days

source_name: SUDHL6, EPZ6438 at 10xLCC, Day 4


title: Patient 23 Pre untreated

description: Patient 23 Pre untreated


title: Patient 18 Pre untreated

description: Patient 18 Pre untreated


title: Patient 17 Prog Treated with dabrafenib

description: Patient 17 Prog Treated with dabrafenib

value: lung

value: dabrafenib


title: SUDHL6_HIGH_Day4_C


title: SUDHL6_LOW_Day4_B

description: SUDHL6  treated with EPZ6438 at LCC for 4 days

source_name: SUDHL6, EPZ6438 at LCC, Day 4


title: SUDHL6_LOW_Day4_C


title: Patient 18 Prog 2 Treated with dabrafenib


title: SUDHL6_HIGH_Day4_B


title: KARPAS_DMSO_Day4_B

description: KARPAS_422 treated with DMSO for 4 days


title: TBEP_14.7_rep1

description: Gene expression after 21 days exposure to 14.7µg/l TBEP, biological replicate 1 of 3

source_name: TBEP, 21 days, 14.7µg/L, replicate 1

value: whole organism

value: <24h old neonates

value: female


title: SUDHL6_LOW_Day4_A


title: AGO2_Rep2

type: other

city: Toronto

first: Zhaolei

last: Zhang

state: ONTARIO

address: 160 College St

department: Molecular Genetics, Computer Science

institute: University of Toronto

hyb_protocol: Hybridizations were carried out for 20 hours at 42°C and washed for 30 seconds in 6 x SSPE, 0.005% sarcosine and 30 seconds in 0.06x SPE in a HS4800 Pro Hybridization Station (Tecan).

scan_protocol: Arrays were scanned on an microarray scanner at 5 micron resolution (Axon Instruments GenePix 4000B). Images were quantified using Imagene 3.0.

data_processing: Each batch of experiments was represented with a matrix where rows correspond to probes and columns are the pulldown intensities of the RBPs in that batch. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all the experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

molecule: other

source_name: Pulldown RNA labeled with Cy5

label_protocol: Manufacturer's recommended protocol (Kreatech).

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purifyied by phenol-chloroform extraction followed by ethanol precipitation.

tag: protocol

value: GST-tagged RNA-binding protein pulldown


title: SUDHL6_DMSO_Day4_C

description: SUDHL6 treated with DMSO for 4 days

source_name: SUDHL6, DMSO, Day 4


title: SUDHL6_DMSO_Day4_B

description: SUDHL6 treated with DMSO for 4 days


title: Patient 14 Prog Treated with dabrafenib

description: Patient 14 Prog Treated with dabrafenib

value: BRAF V600K

value: melanoma


title: AGO2_Rep1


title: yeast parent_KA31a_4_600

city: Gifu

first: Kazuki

last: Nomura

address: 1-1, Yanagido

country: Japan

institute: Gufu university

hyb_protocol: Cy5-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 25 ml containing 1x Blocking Agent and 1x  Fragmentation Buffer. On completion of the fragmentation reaction, 2x Hybridization Buffer HI-RPM solution was added to the fragmentation mixture containing 0.6 μg of Cy5-labelled cRNA and hybridized for 17 h, at 65C and 10 rpm. After hybridization, microarrays were washed according to Quick Amp Labeling Kit Protocol (Agilent).

scan_protocol: Slides were scanned immediately after washing on the DNA Microarray Scanner (GenePix 4000B, Axon CNS Co. Ltd.) using one color scan setting for 8x15k array slides. PMT values set to 500-700 in 50 interval. we used 600 and 700 of PMT values in this study.

data_processing: These data were normalized by the quantile methods using Excel.

organism: Saccharomyces cerevisiae

source_name: parent_YPD 48h culture

label_protocol: Fluorescently-labeled cRNA was commissioned by Ecogenomics, Inc. (Fukuoka, Japan). cDNA was synthesized by Quick Amp Labeling Kit (Agilent) using 0.5 μg total RNA as a template. Cyanine-5 (Cy5) labeled cRNA was prepared from cDNA using the T7 RNA polymerase. Cy5-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN, Hilden, Germany), and checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Both strains were gorwn in YPD medium (1.0% yeast extract, 2.0% peptone ; Becton, Dickinson and Co., NJ, USA, and 2.0% glucose, if necessary 1.5% agar; Wako Pure Chemical Industries, Ltd, Osaka, Japan) at 30°C for 48 h.

extract_protocol: The yeast cells after growth were collected by centrifugation of 15,000 rpm for 1.0 min at 4°C. RNA extraction conformed according to partially modified manufacture protocol of Fast RNA ® Pro Red Kit (MP Biomedicals, CA, USA).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

tag: genotype/variation

value: parent strain

tag: time point

value: after 48 h in YPD medium


title: yeast mutant_E1_7_700

source_name: pressure-sensitive mutant_YPD 48h culture

value: pressure-sensitive mutant


title: yeast parent_KA31a_6_600


title: PFEIFFER_HIGH_Day4_C

description: PFEIFFER treated with EPZ6438 at 10xLCC for 4 days

source_name: PFEIFFER, EPZ6438 at 10xLCC, Day 4

value: PFEIFFER


title: Patient 17 Pre untreated

description: Patient 17 Pre untreated

source_name: Melanoma tumour

tag: genotype

value: BRAF V600E

value: brain


title: PFEIFFER_LOW_Day4_B

description: PFEIFFER treated with EPZ6438 at LCC for 4 days

source_name: PFEIFFER, EPZ6438 at LCC, Day 4

value: LCC


title: yeast mutant_E1_5_700


title: Patient 13 Pre untreated (replicate)

description: Patient 13 Pre untreated (replicate)

value: subcutaneous


title: SUDHL6_DMSO_Day4_A

description: SUDHL6 treated with DMSO for 4 days

value: DMSO

value: control

value: 4 days


title: PFEIFFER_LOW_Day4_A


title: yeast parent_KA31a_2_600


title: PFEIFFER_HIGH_Day4_B


title: PFEIFFER_LOW_Day4_C


title: PFEIFFER_HIGH_Day4_A


title: Patient 14 Pre untreated

description: Patient 14 Pre untreated


title: yeast parent_KA31a_8_700


title: Patient 13 Prog Treated with dabrafenib

description: Patient 13 Prog Treated with dabrafenib

value: dabrafenib


title: yeast mutant_E1_3_600


title: Patient 13 Pre untreated

description: Patient 13 Pre untreated


title: PFEIFFER_DMSO_Day4_C

description: PFEIFFER treated with DMSO for 4 days

source_name: PFEIFFER, DMSO, Day 4


title: Patient 12 Pre untreated

description: Patient 12 Pre untreated

value: lymph node


title: yeast mutant_E1_1_600


title: Patient 12 Prog Treated with dabrafenib

description: Patient 12 Prog Treated with dabrafenib


title: PFEIFFER_DMSO_Day4_B

description: PFEIFFER treated with DMSO for 4 days


title: WSU_HIGH_Day4_C

description: WSU_DLCL2 treated with EPZ6438 at 10xLCC for 4 days

source_name: WSU_DLCL2, EPZ6438 at 10xLCC, Day 4


title: PFEIFFER_DMSO_Day4_A

description: PFEIFFER treated with DMSO for 4 days


title: WSU_HIGH_Day4_B


title: Patient 11 Prog 2 Treated with dabrafenib (replicate)


title: WSU_LOW_Day4_C

description: WSU_DLCL2 treated with EPZ6438 at LCC for 4 days

source_name: WSU_DLCL2, EPZ6438 at LCC, Day 4


title: Brain-Old-Female-3

city: ANKARA

first: Ayca

last: Arslan Ergul

state: ÇANKAYA

address: Bilkent Üniversitesi UNAM

department: UNAM

country: Turkey

institute: Bilkent University

description: 31 month old female, fish no: HD42

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw Affymetrix CEL files were processed with RMA normalization method. Probesets were annotated using BioMart (http://www.biomart.org/biomart/martview) with the current Zebrafish Genome Built (Danio rerio Zv9).

label: Biotin

organism: Danio rerio

source_name: old zebrafish, brain, female

label_protocol: RNA was amplified with Ovation RNA Amplification System (NuGen) and biotin-labeled with Encore Biotin Module (NuGen).

growth_protocol: Fish were maintained at a constant temperature of 28°C on a 14L:10D light cycle. All the fish were fed three times daily and kept in a recirculating system at all times. All animals were kept in groups, around 10 animals in a 4L tank.

extract_protocol: RNA isolation was performed with a RNAeasy Mini Kit (Qiagen, Germany). DNase treatment was done with RNase-free DNase Set (Qiagen, Germany).

treatment_protocol: For the brain dissection, fish were anesthetized in Tricaine (Sigma-Aldrich, Germany) and head was separated from the body with a scalpel. The eyes/optic nerves were dissected, brain was dissected away from dorsal surface. Following visualization of the brain, it was removed from the skull. Tissues were weighed in 0.5 ml microtubes, frozen in liquid nitrogen and stored at -80°C until RNA isolation.

value: AB


title: HCT116 H2B-GFP 5/4_R3

source_name: HCT116 cell line, tetrasomic for Chr. 5, replicate 3

value: human colon carcinoma cell line

value: 4x Chr. 5


title: Patient 11 Prog 1 Treated with dabrafenib (replicate)

value: BRAF V600K

value: melanoma


title: Patient 11 Prog 1 Treated with dabrafenib


title: WSU_DMSO_Day4_C

description: WSU_DLCL2 treated with DMSO for 4 days

source_name: WSU_DLCL2, DMSO, Day 4


title: WSU_LOW_Day4_B


title: Brain-Young-Female-3

description: 8.5 month old female, fish no: HD41

source_name: young zebrafish, brain, female


title: Patient 10 Prog 2 Treated with dabrafenib


title: Brain-Young-Female-1

description: 8.5 month old female, fish no: HD47


title: Brain-Old-Female-2

description: 36 month old female, fish no: Vet21


title: Brain-Old-Male-3

description: 36 month old male, fish no: Vet22

source_name: old zebrafish, brain, male


title: WSU_DMSO_Day4_A

description: WSU_DLCL2 treated with DMSO for 4 days


title: Patient 11 Pre untreated

description: Patient 11 Pre untreated


title: HCT116 H2B-GFP 5/4_R2

source_name: HCT116 cell line, tetrasomic for Chr. 5, replicate 2


title: WSU_HIGH_Day4_A


title: Patient 11 Prog 2 Treated with dabrafenib


title: WSU_LOW_Day4_A


title: HCT116 H2B-GFP 5/4_R1

source_name: HCT116 cell line, tetrasomic for Chr. 5, replicate 1


title: WSU_DMSO_Day4_B

description: WSU_DLCL2 treated with DMSO for 4 days


title: Patient 11 Pre untreated (replicate)

description: Patient 11 Pre untreated (replicate)


title: Brain-Old-Male-1

description: 31 month old male, , fish no: HD45


title: Brain-Young-Male-3

description: 8.5 month old male, fish no: HD44

source_name: young zebrafish, brain, male


title: HCT116 3/3_R2

source_name: HCT116 cell line, trisomic for Chr. 3, replicate 2

value: 3x Chr. 3


title: HCT116 3/3_R1

source_name: HCT116 cell line, trisomic for Chr. 3, replicate 1


title: Brain-Young-Female-2

description: 7.5 month old female, fish no: HD84


title: Patient 10 Prog 1 Treated with dabrafenib


title: Patient 10 EDT Treated with dabrafenib

description: Patient 10 EDT Treated with dabrafenib


title: KARPAS_HIGH_Day2_C

description: KARPAS_422  treated with EPZ6438 at 10xLCC for 2 days

source_name: KARPAS_422, EPZ6438 at 10xLCC, day 2

value: 2 days


title: Brain-Young-Male-2

description: 7.5 month old male, fish no: HD82


title: Brain-Old-Male-2

description: 31 month old male, fish no: HD39


title: KARPAS_HIGH_Day2_B


title: long-Con rep1

city: New Haven

first: Andrew

middle: Zhuo

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

hyb_protocol: Following Affymetrix techinical manual.

scan_protocol: Gene Array Scaner (Affymetrix)

data_processing: Analyzed by MAS 5.0 using Affymetrix default settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Hierarchical clustering was performed using cluster software (version 3) and by applied mean centering and normalization of genes and arrays before average linkage clustering. Significantly different genes were identified using a 1-class unpaired significance analysis of microarrays (SAM) and fold change.

source_name: F1 ES Cells

label_protocol: Following Affymetrix techinical manual.

growth_protocol: ES cells were cultured on feeder plates following standard ES cell culture protocol.

extract_protocol: Total RNA was extracted by Trizol following the instruction.

treatment_protocol: Control and Rif1 virus or siRNA were applied and selected for further culture and analysis.

tag: transfection

value: control shRNA

value: Stable F1 Rif1 knockdown ES cells at passage 16

tag: background strain


title: Brain-Old-Female-1

description: 31 month old female, fish no: HD55

value: brain


title: long-Rif1 KD rep1

value: Rif1 shRNA


title: long-Rif1 KD rep2


title: BR-RFcoloniesxBR-Scolonies_day7_rep2

city: Prague

first: Vratislav

last: Stovicek

address: Vinicna 5

department: Genetics and Microbiology

country: Czech Republic

institute: Faculty of Science, Charles University in Prague

description: day7 replicate 2/3, double genome array, dye swap, BR-S(Cy5)/BR-RF(Cy3)

hyb_protocol: Labeled cDNA mixed with hybridization solution (DIG Easy Hyb solution (Roche)), yeast tRNA (10 mg/ml, Invitrogen) and calf thymus DNA (10 mg/ml, Sigma) was applied to Yeast 6.4K Array (Y6.4K) double spotted ORF slides (University Health network, Toronto, Canada) and incubated overnight at 37ºC.

scan_protocol: Images were scanned using an Axon fluorescent scanner and Genepix software, spots quantified and validated using TIGR Spotfinder software (www.tm4.org)

data_processing: LOWESS normalization of medians of total intensities using TIGR MIDAS software (www.tm4.org). Low values replaced by arbitrary value, saturated spots replaced with values obtained from lower intensity scan. In the raw data files, column IA represents channel 1 and column IB represents channel 2

molecule: polyA RNA

source_name: cells from 7-day-old BR-RF colonies

label_protocol: Reverse transcription was performed from 2-4 µg of mRNA with random hexamers (Roche), Oligo(dT) (Invitrogen), dUTP-Cy3 or dUTP-Cy5 (GE Healthcare), dATP, dCTP and dGTP, dTTP (Roche) and Superscript III reverse transcriptase (Invitrogen). After reverse transcription, the two reactions (Cy3 and Cy5) were pooled and purified in a Quiaquick column (Quiagen)

growth_protocol: Yeast colonies were grown on solid media (1% yeast extract, 2% agar, 3% glycerol). Biomass from colonies was harvested 4th and 7th day of growth

extract_protocol: The biomass from colonies was suspended in TES (10mM Tris pH 7.5, 10mM EDTA, 0.5% SDS) buffer. An approximately 200 mg biomass of BR-F and BR-RF colonies and 100 mg biomass of BR-S colonies were used for one isolation procedure. Total RNA from the cells was isolated by the hot phenol method. mRNA was isolated from total RNA by binding to oligo dT cellulose using a Micro-Fast track 2.0 Kit (Invitrogen).

value: BR-RF

source_name: cells from 7-day-old BR-S colonies

value: BR-S


title: Patient 10 Pre untreated

description: Patient 10 Pre untreated

source_name: Melanoma tumour

value: BRAF V600E

value: subcutaneous

tag: treatment


title: BR-RFcoloniesxBR-Scolonies_day7_rep1

description: day7 replicate 1/3, double genome array, BR-RF(Cy5)/BR-S(Cy3)


title: KARPAS_LOW_Day2_C

description: KARPAS_422  treated with EPZ6438 at LCC for 2 days

source_name: KARPAS_422, EPZ6438 at LCC, day 2

value: LCC


title: short-Rif1 KD rep2

source_name: J1 ES Cells

value: J1 ES Cells


title: Patient 9 Pre untreated

description: Patient 9 Pre untreated


title: KARPAS_LOW_Day2_A


title: KARPAS_LOW_Day2_B


title: KARPAS_DMSO_Day2_B

description: KARPAS_422 treated with DMSO for 2 days

source_name: KARPAS_422, DMSO, day 2

value: DMSO

value: control


title: KARPAS_DMSO_Day2_A

description: KARPAS_422 treated with DMSO for 2 days


title: short-Rif1 KD rep1


title: BR-RFcoloniesxBR-Scolonies_day4_rep3

description: day4 replicate 3/3, double genome array, biological replicate, BR-S(Cy5)/BR-RF(Cy3)

source_name: cells from 4-day-old BR-RF colonies

source_name: cells from 4-day-old BR-S colonies


title: Patient 9 Prog Treated with dabrafenib

description: Patient 9 Prog Treated with dabrafenib

value: dabrafenib


title: long-Con rep2


title: Patient 8 Prog 2 Treated with dabrafenib


title: short-Con rep2


title: Patient 8 Pre untreated (replicate)

description: Patient 8 Pre untreated (replicate)


title: KARPAS_DMSO_Day2_C

description: KARPAS_422 treated with DMSO for 2 days


title: Patient 8 Prog 1 Treated with dabrafenib


title: Brain-Young-Male-1

description: 8.5 month old male, fish no: HD38

value: AB


title: short-Con rep1


title: BR-RFcoloniesxBR-Scolonies_day4_rep2

description: day4 replicate 2/3, double genome array, dye swap, BR-RF(Cy5)/BR-S(Cy3)


title: BR-RFcoloniesxBR-Scolonies_day4_rep1

description: day4 replicate 1/3, double genome array, BR-S(Cy5)/BR-RF(Cy3)


title: BR-FcoloniesxBR-Scolonies_day7_rep3

description: day7 replicate 3/3, double genome array, biological replicate BR-S(Cy5)/BR-F(Cy3)

source_name: cells from 7-day-old BR-F colonies

value: BR-F


title: SUDHL6_HIGH_Day2_B

description: SUDHL6  treated with EPZ6438 at 10xLCC for 2 days

source_name: SUDHL6, EPZ6438 at 10xLCC, day 2


title: SUDHL6_HIGH_Day2_C


title: SUDHL6_HIGH_Day2_A


title: BR-RFcoloniesxBR-Scolonies_day7_rep3

description: day7 replicate 3/3, double genome array, biological replicate BR-RF(Cy5)/BR-S(Cy3)


title: GM-LPS-IL4_vs_GM_REP1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: moDCs cultured with GM-CSF in presence of IL4 stimulated with LPS vs moDCs cultured with GM-CSF. Replicate 1

hyb_protocol: RNA was labeled with Cy3 or Cy5 by using the SuperScript indirect cDNA labeling system (invitrogen) as described in the instruction manual.

scan_protocol: Raw GPR files were obtained by Axon's GenePix 4000B scanner and GenePixPro 5.1 software.

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

source_name: moDCs cultured with GM-CSF

label_protocol: RNA was amplified with the MessageAmp aRNA amplification kit from Ambion following the instruction manual. To allow later labeling with Cy fluorophores, aminoallyl UTP (Ambion) was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount and quality of aRNA obtained was assessed as before. The aminoallyl-labeled aRNA (10 µg) was incubated in 1 M Na2CO3 with 8 nmol of dye monofunctional NHS ester (Cy3/Cy5) RPN 5661 (Amersham Biosciences) at room temperature in the dark for 1 h. Then, 35 µL of 0.1 M sodium acetate, pH 5.2, was added and incubated for a further 5 min in the dark. The Cy-labeled aRNA was purified with the Megaclear kit from Ambion and measured with the Nanodrop ND-100 spectrophotometer.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (50) from Qiagen.

tag: cell type

value: monocyte-derived dendritic cells (moDCs)


title: Patient 7 Prog Treated with dabrafenib

description: Patient 7 Prog Treated with dabrafenib

value: melanoma

value: lymph node


title: Patient 5 Prog Treated with dabrafenib

description: Patient 5 Prog Treated with dabrafenib

value: BRAF V600K


title: GM-LPS-IL4_vs_GM_REP2

description: moDCs cultured with GM-CSF in presence of IL4 stimulated with LPS vs moDCs cultured with GM-CSF. Replicate 2


title: BR-FcoloniesxBR-Scolonies_day7_rep2

description: day7 replicate 2/3, double genome array, dye swap, BR-S(Cy5)/BR-F(Cy3)


title: Patient 8 Pre untreated

description: Patient 8 Pre untreated


title: SUDHL6_LOW_Day2_C

description: SUDHL6  treated with EPZ6438 at LCC for 2 days

source_name: SUDHL6, EPZ6438 at LCC, day 2

tag: cell line

value: 2 days


title: Patient 7 Pre untreated

description: Patient 7 Pre untreated


title: BR-FcoloniesxBR-Scolonies_day7_rep1

description: day7 replicate 1/3, double genome array, BR-F(Cy5)/BR-S(Cy3)


title: GM-IL4_vs_GM_REP2

description: moDCs cultured with GM-CSF in presence of IL4 vs moDCs cultured with GM-CSF. Replicate 2

scan_protocol: Raw TXT files were obtained by Agilent's DNA Microarray Scanner and  Feature Extraction Software.

growth_protocol: Differentiation of C-moDCs or IL4-moDCs was achieved by culturing monocytes in 24-well plates in RPMI medium supplemented with 10% FCS and 20 ng/ml GM-CSF for 24 h at 37ºC and 5% CO2, in the absence or presence of 20 ng/ml IL-4; these cultures contained around 90% moDCs; C-moDCs or IL4-moDCs were further purified by immunomagnetic positive selection after incubation with biotin-conjugated anti-CD11c and streptavidin-conjugated microbeads.


title: Patient 5 Pre untreated

description: Patient 5 Pre untreated


title: SUDHL6_LOW_Day2_A

tag: agent


title: GM-LPS_vs_GM_REP1

description: moDCs cultured with GM-CSF stimulated with LPS vs moDCs cultured with GM-CSF. Replicate 1


title: BR-FcoloniesxBR-Scolonies_day4_rep2

description: day4 replicate 2/3, double genome array, dye swap, BR-F(Cy5)/BR-S(Cy3)

source_name: cells from 4-day-old BR-F colonies


title: Patient 4 Prog Treated with dabrafenib

description: Patient 4 Prog Treated with dabrafenib

value: bowel


title: SUDHL6_DMSO_Day2_B

description: SUDHL6 treated with DMSO for 2 days

source_name: SUDHL6, DMSO, day 2

tag: dose


title: GM-IL4_vs_GM_REP1

description: moDCs cultured with GM-CSF in presence of IL4 vs moDCs cultured with GM-CSF. Replicate 1


title: SUDHL6_DMSO_Day2_C

description: SUDHL6 treated with DMSO for 2 days

tag: time


title: BR-FcoloniesxBR-RFcolonies_day7_rep3

description: day7 replicate 3/3, double genome array, biological replicate BR-F(Cy5)/BR-RF(Cy3)

value: BR-RF


title: Patient 5 EDT treated with dabrafenib

description: Patient 5 EDT treated with dabrafenib

tag: disease state


title: Patient 3 Prog 2 Treated with dabrafenib

tag: location


title: BR-FcoloniesxBR-RFcolonies_day7_rep2

description: day7 replicate 2/3, double genome array, dye swap, BR-F(Cy5)/BR-RF(Cy3)


title: BR-FcoloniesxBR-Scolonies_day4_rep1

description: day4 replicate 1/3, double genome array, BR-S(Cy5)/BR-F(Cy3)

value: BR-S


title: SUDHL6_DMSO_Day2_A

description: SUDHL6 treated with DMSO for 2 days


title: GM-LPS_vs_GM_REP2

description: moDCs cultured with GM-CSF stimulated with LPS vs moDCs cultured with GM-CSF. Replicate 2


title: BR-FcoloniesxBR-RFcolonies_day4_rep1

description: day4 replicate 1/3, double genome array, BR-RF(Cy5)/BR-F(Cy3)


title: miR-126-/-_S3

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University

description:
RS-188_07
Genomewide expression profile of miR-126-/-/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.

hyb_protocol: Following cRNA clean-up and quantification, 825 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Each single cRNA sample was hybridized at 65°C for 17 hrs on separate SurePrint G3 Mouse GE Microarrays (8x60K format). The microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 028005_D_F_20101029.xml.

data_processing: The software tools Feature Extraction 10.7.3.1, GeneSpring GX 11.5 and Spotfire Decision Site 9.1.2 were used for quality control, statistical data analysis, Gene ontology annotation and visualization. Quantile normalization was applied to the data set. After normalization, data is returned as log2 transformed values and filtered based on flags.

label_protocol: 100 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP.

extract_protocol: Total RNA was isolated using RNeasy micro Kit (QIAGEN) following the manufacturer's instruction.  The protocol includes tissue lysis, hemogenization, and an on-column DNase digestion. RNA was quantified using a NanoDrop spectrophotometer and quality was measured with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Wire-induced carotid injury was performed in miR-126+/+ApoE-/- (control group) and miR-126-/-ApoE-/- (target group) mice on western-type diet. RNA was isolated after 14 days following vascular injury (n=4 each group) and hybridized to the Agilent mouse microarrays.

tag: gender

value: female

tag: age

value: 6 weeks

value: carotid artery


title: Patient 10 Pre untreated (replicate)

description: Patient 10 Pre untreated (replicate)

value: BRAF V600E

value: subcutaneous


title: BR-FcoloniesxBR-RFcolonies_day4_rep2

description: day4 replicate 2/3, double genome array, dye swap, BR-F(Cy5)/BR-RF(Cy3)


title: KARPAS_HIGH_Day2_A

description: KARPAS_422  treated with EPZ6438 at 10xLCC for 2 days


title: PFEIFFER_HIGH_Day2_B

description: PFEIFFER treated with EPZ6438 at 10xLCC for 2 days

source_name: PFEIFFER, EPZ6438 at 10xLCC, day 2

value: PFEIFFER


title: miR-126-/-_S4

description:
RS-188_09
Genomewide expression profile of miR-126-/-/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.

tag: tissue


title: Patient 2 Pre untreated

description: Patient 2 Pre untreated


title: PFEIFFER_HIGH_Day2_C


title: Patient 3 Prog 1 Treated with dabrafenib

value: dabrafenib


title: SUDHL6_LOW_Day2_B

value: LCC


title: BR-FcoloniesxBR-RFcolonies_day4_rep3

description: day4 replicate 3/3, double genome array, biological replicate, BR-RF(Cy5)/BR-F(Cy3)

tag: strain

value: BR-F


title: PFEIFFER_HIGH_Day2_A


title: BR-FcoloniesxBR-RFcolonies_day7_rep1

description: day7 replicate 1/3, double genome array, BR-RF(Cy5)/BR-F(Cy3)


title: Patient 4 Pre untreated

description: Patient 4 Pre untreated

value: brain


title: PFEIFFER_LOW_Day2_B

description: PFEIFFER treated with EPZ6438 at LCC for 2 days

source_name: PFEIFFER, EPZ6438 at LCC, day 2


title: BR-FcoloniesxBR-Scolonies_day4_rep3

description: day4 replicate 3/3, double genome array, biological replicate, BR-F(Cy5)/BR-S(Cy3)


title: Patient 2 Prog Treated with dabrafenib

description: Patient 2 Prog Treated with dabrafenib

value: melanoma


title: PFEIFFER_LOW_Day2_C


title: miR-126-/-_S1

description:
RS-188_05
Genomewide expression profile of miR-126-/-/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.

tag: genotype/variation


title: Patient 3 Pre untreated

description: Patient 3 Pre untreated


title: miR-126-/-_S2

description:
RS-188_06
Genomewide expression profile of miR-126-/-/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.


title: miR-126+/+_S4

description:
RS-188_04
Genomewide expression profile of miR-126+/+/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.


title: miR-126+/+_S2

description:
RS-188_02
Genomewide expression profile of miR-126+/+/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.


title: Patient 7 Pre untreated (replicate)

description: Patient 7 Pre untreated (replicate)


title: PFEIFFER_DMSO_Day2_C

description: PFEIFFER treated with DMSO for 2 days

source_name: PFEIFFER, DMSO, day 2

value: DMSO

value: control


title: Patient 1 Pre untreated

description: Patient 1 Pre untreated


title: miR-126+/+_S3

description:
RS-188_03
Genomewide expression profile of miR-126+/+/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.


title: Patient 1 Prog Treated with dabrafenib

description: Patient 1 Prog Treated with dabrafenib


title: GIF-14_untreated_rep3

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: replicate 3

hyb_protocol: Incubated at 58oC for 16 hours in Illumina Hyb Chamber with rocker speed at 5

scan_protocol: Standard Illumina scanning protocol using Scan Factor of 3

data_processing: The data were normalised using quantile and average normalisation with Illumina GenomeStudio

label_protocol: Biotinylated cRNA was prepared with Ambion TotalPrep RNA Amplification Kit for Illumina

growth_protocol: Dulbecco’s Modified Eagle Medium with 4500 mg/l glucose supplemented with 10% FBS, 100 units/ml penicillin and 100 µg/ml streptomycin

extract_protocol: RNA was extracted with QIAGEN RNeasy Mini Kit according to manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Recombinant TGF-β1 for 24 h at a final concentration of 2.5 ng/ml

value: Fetal gastric epithelial cells

value: Runx3-/-;p53-/- genotype


title: BC_RPPA_JS_pFoxO3a_S318_S321

status: Public on Feb 18 2014

type: protein

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 24

hyb_protocol: Slides were blocked with 50% blocking buffer for fluorescent applications (Rockland) in TBS containing 5 mM NaF and 1 mM Na3VO4 for 2h at RT, prior to incubation with target specific primary antibodies at 4°C over night. Detection of the primary antibodies was done with Alexa Fluor® 680 F(ab')2 fragments of goat anti-mouse IgG or anti-rabbit IgG in 1:8000 dilution (Life Technologies).

scan_protocol: Images of all slides were obtained at an excitation wavelength of 685 nm and a resolution of 21 µm using the Odyssey Scanner (LI-COR). These 16-bit TIFF-files where then used to quantify the signal intensities for each individual spot with the software GenePixPro 5.0 (Molecular Devices).

data_processing: Representative slides were stained for total protein quantification using the protein dye Fast Green FCF. To account for variation in total protein amount, a normalization factor for each spot was calculated using information obtained form these FCF slides and antibody signals of each spot were normalized accordingly. Each sample was printed in technical replicate on the slide and the median was used for further analyses.

label: Alexa Fluor 680

molecule: protein

label_protocol: Alexa Fluor® 680

extract_protocol: Frozen tumor samples were homogenized using a bead mill (TissueLyser, Qiagen) and tissue protein extraction reagent (T-PER, Thermo Scientific) supplemented with 1 mM EDTA, 5 mM NaF, 2 μM staurosporine, PhosSTOP Phosphatase Inhibitor Cocktail (Roche Applied Science), and Complete Mini Protease Inhibitor Cocktail (Roche Applied Science). Total protein concentration was determined by bicinchoninic acid assay (Pierce). Prior to spotting, tumor lysates were mixed with 4x SDS sample buffer (10% Glycerol, 4% SDS, 10 mM DTT, 125 mM Tris-HCl, pH 6.8), adjusted to 2 µg/µl total protein, and boiled for 5 min at 95°C.

tag: target protein

tag: phospho site

tag: antibody id

tag: antibody manufacturer

value: CST


title: PFEIFFER_DMSO_Day2_A

description: PFEIFFER treated with DMSO for 2 days

value: 2 days


title: GIF-14_TGF-β1_rep1

description: replicate 1

tag: genotype


title: WSU_HIGH_Day2_B

description: WSU_DLCL2 treated with EPZ6438 at 10xLCC for 2 days

source_name: WSU_DLCL2, EPZ6438 at 10xLCC, day 2


title: WSU_HIGH_Day2_C


title: GIF-14_untreated_rep2

description: replicate 2

tag: cell type


title: PFEIFFER_LOW_Day2_A

tag: cell line


title: WSU_HIGH_Day2_A

tag: agent


title: PFEIFFER_DMSO_Day2_B

description: PFEIFFER treated with DMSO for 2 days

tag: dose


title: GIF-14_TGF-β1_rep2

description: replicate 2


title: BC_RPPA_JS_PCNA

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 23

value: PCNA

value: SantaCruz


title: BC_RPPA_JS_PKA

value: PKA


title: WSU_LOW_Day2_C

description: WSU_DLCL2 treated with EPZ6438 at LCC for 2 days

source_name: WSU_DLCL2, EPZ6438 at LCC, day 2

tag: time


title: GIF-14_TGF-β1_rep3

description: replicate 3


title: miR-126+/+_S1

description:
RS-188_01
Genomewide expression profile of miR-126+/+/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.

value: female

value: 6 weeks

value: carotid artery


title: WSU_LOW_Day2_B


title: BC_RPPA_JS_Cyclin_D1

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 22


title: BC_RPPA_JS_Cyclin_B1

value: Epitomics


title: BC_RPPA_JS_bCatenin

value: bCatenin


title: BC_RPPA_JS_pp38_T180_Y182


title: BC_RPPA_JS_pERBB2_Y1112

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 22

value: Millipore


title: BC_RPPA_JS_metadherin

value: metadherin


title: BC_RPPA_JS_P-cadherin

value: P-cadherin


title: HCT116 H2B-GFP bafilo_R3

hyb_protocol: Following cRNA clean-up and quantification (NanoDrop ND-1000 Spectrophotometer, peqlab) 0.60 µg of each Cyanin-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent). Each cRNA sample was hybridized at 65 °C for 17 hrs on one SurePrint G3 Human GE v2 Microarray (8x60K format).

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.1.4. Software (Agilent Technologies) on the Agilent DNA Microarray Scanner.

data_processing: Signal intensities were extracted from the image using Feature Extraction 10.7.3.1 Software and the design file 039494_D_F_20120628. Data was background subtracted; log2 transformed and normalized. Medians of replicates were calculated and a ratio of the aneuploid cell line (median) vs the corresponding WT cell line (median) was used for further analysis (indicated in the column header).

source_name: HCT116 cell line, diploid, replicate 3

label_protocol: 100 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP according to the manufacturer´s instructions.

treatment_protocol: bafilomycin treatment, 10nM, 30h

tag: treatment

value: bafilomycin 10nM, 30h


title: HCT116 H2B-GFP bafilo_R4

source_name: HCT116 cell line, diploid, replicate 4


title: WSU_DMSO_Day2_A

description: WSU_DLCL2 treated with DMSO for 2 days

source_name: WSU_DLCL2, DMSO, day 2

value: DMSO

value: control


title: BC_RPPA_JS_p70S6K


title: BC_RPPA_JS_Acetyl_CoA_Carboxylase


title: BC_RPPA_JS_pCytokeratin_8_S23


title: WSU_DMSO_Day2_C

description: WSU_DLCL2 treated with DMSO for 2 days


title: WSU_DMSO_Day2_B

description: WSU_DLCL2 treated with DMSO for 2 days


title: HCT116 H2B-GFP bafilo_R2

source_name: HCT116 cell line, diploid, replicate 2


title: BC_RPPA_JS_EpCAM

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 21

value: EpCAM


title: BC_RPPA_JS_pAKT_T308

value: pAKT

value: CST


title: WSU_LOW_Day2_A

value: LCC

value: 2 days


title: GIF-14_untreated_rep1

description: replicate 1

value: Fetal gastric epithelial cells

value: Runx3-/-;p53-/- genotype


title: HCT116 H2B-GFP bafilo_R1

source_name: HCT116 cell line, diploid, replicate 1


title: BC_RPPA_JS_cJUN

value: cJUN


title: BC_RPPA_JS_SDHA

value: SDHA

value: SantaCruz


title: BC_RPPA_JS_TOP2A

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 19

value: Uhlen


title: BC_RPPA_JS_MET

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 18

value: MET


title: BC_RPPA_JS_MEK

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 19

value: MEK

value: BD


title: BC_RPPA_JS_PDK1

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 20


title: BC_RPPA_JS_TIE2

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 17


title: BC_RPPA_JS_NFkB

value: NFkB


title: BC_RPPA_JS_Cytokeratin_18

value: Epitomics


title: BC_RPPA_JS_SHP1

value: HPA


title: BC_RPPA_JS_GATA3


title: BC_RPPA_JS_STARD10

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 18


title: BC_RPPA_JS_ERBB3

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 24

value: Neomarkers


title: BC_RPPA_JS_PLCg

value: PLCg

value: Abcam


title: BC_RPPA_JS_pPKCa_S657_Y658

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 17

value: pPKCa


title: BC_RPPA_JS_PKCa

value: PKCa


title: BC_RPPA_JS_CREB

value: CREB

value: CST


title: BC_RPPA_JS_p38


title: BC_RPPA_JS_Vimentin

value: Vimentin


title: BC_RPPA_JS_pcRAF_S259

value: pcRAF


title: BC_RPPA_JS_PAK2


title: BC_RPPA_JS_RKIP

value: RKIP

value: Milipore


title: BC_RPPA_JS_NOTCH3

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 15


title: BC_RPPA_JS_pERBB4_Y1162


title: BC_RPPA_JS_pyruvate_dehydrogenase

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 16


title: BC_RPPA_JS_NDKA

value: NDKA


title: BC_RPPA_JS_GRB2


title: BC_RPPA_JS_pERBB2_Y1248

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 14

value: Millipore


title: BC_RPPA_JS_pp53_Ser15

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 14


title: BC_RPPA_JS_pPTEN_T366_S370

value: pPTEN


title: BC_RPPA_JS_CBL

value: CBL


title: BC_RPPA_JS_pNFkB_S536

value: pNFkB


title: BC_RPPA_JS_PAK1


title: BC_RPPA_JS_SHP2


title: BC_RPPA_JS_p53

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 13

value: SantaCruz


title: BC_RPPA_JS_pbCatenin_S33_S37_T41

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 10

value: pbCatenin


title: BC_RPPA_JS_PARP

value: PARP

value: Calbiochem


title: BC_RPPA_JS_pGSK3B_S9

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 9


title: BC_RPPA_JS_APC

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 11

value: APC


title: BC_RPPA_JS_GSK3B

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 12


title: BC_RPPA_JS_SRC

value: SRC


title: BC_RPPA_JS_ERBB4


title: BC_RPPA_JS_pSRC_Y416

value: pSRC


title: BC_RPPA_JS_SMAD2

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 10

value: CST


title: BC_RPPA_JS_SMAD7

value: Abcam


title: BC_RPPA_JS_SMURF2


title: BC_RPPA_JS_ROCK1


title: BC_RPPA_JS_ROCK2

value: Sigma


title: BC_RPPA_JS_PI3K_p85


title: BC_RPPA_JS_caveolin_1


title: BC_RPPA_JS_NOTCH2


title: BC_RPPA_JS_pSTAT5_Y694_Y699

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 9


title: BC_RPPA_JS_pSTAT1_Y701

value: BD


title: BC_RPPA_JS_BRCA2


title: BC_RPPA_JS_pGSK3A_Y279_pGSK3B_Y216

value: Epitomics


title: BC_RPPA_JS_CDK6

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 7


title: BC_RPPA_JS_ATM

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 6

value: ATM


title: BC_RPPA_JS_ATR

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 5

value: ATR


title: BC_RPPA_JS_CDK2


title: BC_RPPA_JS_p27

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 8


title: BC_RPPA_JS_FIH

value: FIH


title: BC_RPPA_JS_STAT1


title: BC_RPPA_JS_pSTAT3_Y705


title: BC_RPPA_JS_STAT3

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 12


title: BC_RPPA_JS_pRB_S807_S811

value: pRB


title: BC_RPPA_JS_Claudin-3

value: Acris


title: BC_RPPA_JS_Claudin-1


title: BC_RPPA_JS_CDK1


title: BC_RPPA_JS_IntegrinB3


title: BC_RPPA_JS_N-cadherin

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 8

value: N-cadherin


title: BC_RPPA_JS_E-cadherin

value: E-cadherin


title: BC_RPPA_JS_pFAK_S843

value: pFAK


title: BC24_ADN0222_s1h1

city: Paris

first: Jaydutt

middle: D

last: Bhalshankar

address: 26 rue d'Ulm

department: INSERM UNIT 830

country: France

institute: Institut CURIE

description: Hybridized to SNP6.222

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

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 to generate .CEL files for downstream analysis.

data_processing: CEL files and TXT files (generated by Affymetrix Genotyping Console 3.0.1) were processed by GAP (Popova T et al, Genome Biol, 2009) and Partek® GS software version 6.5 build 6.10.1020

source_name: Breast tumoral sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tumor fragments using a standard phenol/chloroform procedure. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: group

value: training set

value: breast cancer tissue


title: BC24_ADN0221_s1h1

description: Hybridized to SNP6.221


title: BC24_ADN0220_s1h1

description: Hybridized to SNP6.220


title: BC24_ADN0219_s2h1

description: Hybridized to SNP6.219


title: BC24_ADN0218_s1h1

description: Hybridized to SNP6.218


title: BC24_ADN0217_s1h1

description: Hybridized to SNP6.217


title: BC_RPPA_JS_BAX

value: BAX


title: BC_RPPA_JS_RB

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 7

value: RB


title: BC24_ADN0215_s1h1

description: Hybridized to SNP6.215


title: BC24_ADN0216_s1h1

description: Hybridized to SNP6.216


title: BC_RPPA_JS_MCL-1

value: CST


title: BC24_ADN0213_s1h1

description: Hybridized to SNP6.213


title: BC24_ADN0211_s1h1

description: Hybridized to SNP6.211


title: BC24_ADN0214_s1h1

description: Hybridized to SNP6.214


title: BC_RPPA_JS_IntegrinB1


title: BC_RPPA_JS_PDI

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 2

value: PDI


title: BC_RPPA_JS_BCL-XL

value: BCL-XL


title: BC_RPPA_JS_COL4A3BP

value: Uhlen


title: BC_RPPA_JS_VEGFR2

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 4


title: BC24_ADN0209_s1h1

description: Hybridized to SNP6.209


title: BC_RPPA_JS_EGFR

value: EGFR


title: BC24_ADN0208_s1h1

description: Hybridized to SNP6.208


title: BC_RPPA_JS_BCL-2


title: BC24_ADN0210_s1h1

description: Hybridized to SNP6.210


title: BC24_ADN0207_s1h1

description: Hybridized to SNP6.207


title: BC_RPPA_JS_LAMB1

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 1

value: Epitomics


title: BC24_ADN0205_s1h1

description: Hybridized to SNP6.205


title: BC_RPPA_JS_GSK3A


title: BC24_ADN0206_s1h1

description: Hybridized to SNP6.206


title: BC_RPPA_JS_pGSK3A_S21

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 3


title: BC_RPPA_JS_pp70S6K_T421_S424


title: BC_RPPA_JS_pAKT_S473

value: pAKT


title: BC24_ADN0203_s1h1

description: Hybridized to SNP6.203


title: BC24_ADN0204_s1h1

description: Hybridized to SNP6.204


title: BC_RPPA_JS_pp70S6K_T389


title: BC24_ADN0202_s1h1

description: Hybridized to SNP6.202


title: BC24_ADN0212_s1h1

description: Hybridized to SNP6.212


title: BC24_ADN0201_s1h1

description: Hybridized to SNP6.201


title: BC_RPPA_JS_PTEN

value: PTEN


title: BC24_ADN0200_s1h1

description: Hybridized to SNP6.200


title: BC24_ADN0199_s1h1

description: Hybridized to SNP6.199


title: BC_RPPA_JS_TSC2


title: BC_RPPA_JS_pTSC2_T1462


title: BC24_ADN0198_s1h1

description: Hybridized to SNP6.198


title: BC24_ADN0196_s1h1

description: Hybridized to SNP6.196


title: BC24_ADN0195_s1h1

description: Hybridized to SNP6.195


title: BC_RPPA_JS_AKT1

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 4

value: BD


title: BC24_ADN0193_s1h1

description: Hybridized to SNP6.193


title: BC24_ADN0194_s1h1

description: Hybridized to SNP6.194


title: BC_RPPA_JS_mTOR

value: mTOR


title: BC_RPPA_JS_AKT2


title: BC24_ADN0192_s1h1

description: Hybridized to SNP6.192


title: BC24_ADN0191_s1h1

description: Hybridized to SNP6.191


title: BC_RPPA_JS_pPDK1_S241


title: BC_RPPA_JS_pmTOR_S2448

value: pmTOR


title: BC24_ADN0190_s1h1

description: Hybridized to SNP6.190


title: BC_RPPA_JS_RPS6


title: BC24_ADN0188_s1h1

description: Hybridized to SNP6.188


title: BC_RPPA_JS_pRPS6_S235_S236


title: BC_RPPA_JS_TSC1


title: BC_RPPA_JS_RSK

value: RSK


title: BC_RPPA_JS_PI3K_p110


title: BC_RPPA_JS_pRPS6_S240_S244


title: BC_RPPA_JS_pPRAS40_T246


title: BC24_ADN0187_s1h1

description: Hybridized to SNP6.187


title: BC_RPPA_JS_pp90RSK_S380


title: BC24_ADN0186_s1h1

description: Hybridized to SNP6.186


title: BC24_ADN0197_s1h1

description: Hybridized to SNP6.197


title: BC_RPPA_JS_MNK1


title: BC24_ADN0185_s1h1

description: Hybridized to SNP6.185


title: BC24_ADN0184_s1h1

description: Hybridized to SNP6.184


title: BC_RPPA_JS_Ki67

value: DAKO


title: BC24_ADN0182_s1h1

description: Hybridized to SNP6.182

value: training set


title: BC24_ADN0165_s1h1

description: Hybridized to SNP6.165

value: breast cancer tissue


title: BC_RPPA_JS_ERBB2

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 2

value: Neomarkers


title: BC_RPPA_JS_ERa

value: ERa

value: DCS


title: BC_RPPA_JS_PRAS40

value: CST


title: BC24_ADN0179_s1h1

description: Hybridized to SNP6.179


title: BC24_ADN0159_s1h1

description: Hybridized to SNP6.159


title: BC24_ADN0148_s1h1

description: Hybridized to SNP6.148


title: BC_RPPA_JS_PR

value: PR


title: BC24_ADN0146_s1h1

description: Hybridized to SNP6.146


title: BC24_ADN0139_s1h1

description: Hybridized to SNP6.139


title: BC24_ADN0144_s1h1

description: Hybridized to SNP6.144


title: BC24_ADN0145_s1h1

description: Hybridized to SNP6.145


title: BC24_ADN0138_s1h1

description: Hybridized to SNP6.138


title: BC24_ADN0140_s1h1

description: Hybridized to SNP6.140


title: BC24_ADN0189_s1h1

description: Hybridized to SNP6.189


title: BC24_ADN0141_s1h1

description: Hybridized to SNP6.141


title: BC24_ADN0142_s1h1

description: Hybridized to SNP6.142


title: BC_RPPA_JS_ERK1

value: RnD


title: BC_RPPA_JS_pMEK_S217_S221

value: pMEK

value: Sigma


title: BC24_ADN0137_s1h1

description: Hybridized to SNP6.137


title: BC_RPPA_JS_pERK1_pERK2_T202_Y204


title: BC24_ADN0147_s1h1

description: Hybridized to SNP6.147


title: BC24_ADN0134_s1h1

description: Hybridized to SNP6.134


title: BC24_ADN0136_s1h1

description: Hybridized to SNP6.136


title: BC24_ADN0135_s1h1

description: Hybridized to SNP6.135


title: BC24_ADN0133_s1h1

description: Hybridized to SNP6.133


title: BC24_ADN0132_s1h1

description: Hybridized to SNP6.132


title: BC24_ADN0131_s1h1

description: Hybridized to SNP6.131


title: BC24_ADN0130_s1h1

description: Hybridized to SNP6.130


title: BC24_ADN0128_s1h1

description: Hybridized to SNP6.128


title: BC24_ADN0127_s1h1

description: Hybridized to SNP6.127


title: BC24_ADN0125_s1h1

description: Hybridized to SNP6.125


title: BC24_ADN0123_s1h1

description: Hybridized to SNP6.123


title: BC24_ADN0121_s1h1

description: Hybridized to SNP6.121


title: BC24_ADN0122_s1h1

description: Hybridized to SNP6.122


title: BC24_ADN0124_s1h1

description: Hybridized to SNP6.124


title: BC24_ADN0118_s1h1

description: Hybridized to SNP6.118


title: BC24_ADN0116_s1h1

description: Hybridized to SNP6.116


title: BC24_ADN0117_s1h1

description: Hybridized to SNP6.117


title: BC24_ADN0115_s1h1

description: Hybridized to SNP6.115


title: BC24_ADN0114_s1h1

description: Hybridized to SNP6.114


title: BC24_ADN0129_s1h1

description: Hybridized to SNP6.129


title: BC24_ADN0113_s1h1

description: Hybridized to SNP6.113


title: BC24_ADN0126_s1h1

description: Hybridized to SNP6.126


title: BC24_ADN0119_s1h1

description: Hybridized to SNP6.119


title: BC24_ADN0112_s1h1

description: Hybridized to SNP6.112


title: BC24_ADN0110_s1h1

description: Hybridized to SNP6.110


title: BC24_ADN0111_s1h1

description: Hybridized to SNP6.111


title: BC24_ADN0109_s1h1

description: Hybridized to SNP6.109


title: BC24_ADN0108_s1h1

description: Hybridized to SNP6.108


title: ein3eil1_4hrAR_Re6_rep1

city: Taipei

first: Kuen-Jin

last: Tsai

address: 128 Academia Road, Section 2, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica, Taiwan

description:
AR_076
Gene expression at reoxygenation 6hr in ein3eil1 (4hr-anoxia)

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Arabidopsis V4 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing the microarrays are scanned with an Agilent microarray scanner G2565CA (Agilent Technologies, USA) at 535 nm for Cy3. The array image was analyzed by the Feature Extraction software version 10.7.1.1 using the default setting.

data_processing:
The raw data of hybridization was imported into the analysis software GeneSpring 11.5 (Agilent Technologies), and the data of normaxia of Col-0 was used as control to normalize all the samples.
threshold raw signals to: 1.0; normalization algorithm: Percentile Shift; Percentile target: 75; no baseline transformation or filtering

organism: Arabidopsis thaliana

source_name: 4hr anoxia-reoxygenated ein3eil1_reoxygenation 6hr

label_protocol: Cy3 labeling (CyDye, Agilent Technologies, USA) was performed  during the in vitro transcription process. 1.65 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes.

growth_protocol: Seeds were sterilized by 0.5% sodium hypochlorite for 20 min and then sown on the plates containing 1/2 Murashige and Skoog (MS) medium (Duchefa Biochemie BV, Haarlem, Netherlands) with 0.55% phytagel and 0.5% sucrose. The plates were further stored at 4°C in the dark for 3 d. After cold stratification, the plates were incubated at 22°C and placed in a vertical position in a growth chamber under long photoperiod with 16 h of light and 8 h of darkness for 5 d. 5-day-old seedlings were then transplanted onto fresh plates for another 2 d before anoxia treatment.

extract_protocol: Total RNA were extracted from treated Arabidopsis seedlings by TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). Based on the manufacturer’s instruction, a 1:2 ratio of sample:TRIZOL reagent was applied to reach higher extraction efficiency. Extracted total RNA were further treated with DNase by using TURBO RNA free kit (Ambion) to remove genomic DNA contamination. For quality control, the integrity of total RNA was determined by Agilent Bioanalyzer 2100. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA)

treatment_protocol: For anoxic treatment, 7-day-old Arabidopsis seedlings were placed into a chamber that was filled with pure nitrogen (100% N2) to replace the air in chamber. To prevent remnant oxygen in the system, anaerobic bags were placed in the chamber to ensure anoxic environment. For re-aeration, air was pumped into the chamber to replace the content in it.  Both anoxic and reoxygenation treatment were carried out in dark condition.

tag: ecotype

value: Columbia

value: 7 days

value: whole seedling


title: ein3eil1_4hrAR_Re6_rep2

description:
AR_077
Gene expression at reoxygenation 6hr in ein3eil1 (4hr-anoxia)

tag: age


title: BC24_ADN0106_s1h1

description: Hybridized to SNP6.106

tag: tissue


title: ein3eil1_4hrAR_Re6_rep3

description:
AR_078
Gene expression at reoxygenation 6hr in ein3eil1 (4hr-anoxia)


title: ein3eil1_4hrAR_Re1_rep2

description:
AR_071
Gene expression at reoxygenation 1hr in ein3eil1 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein3eil1_reoxygenation 1hr


title: ein3eil1_4hrAR_Re3_rep2

description:
AR_074
Gene expression at reoxygenation 3hr in ein3eil1 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein3eil1_reoxygenation 3hr


title: BC24_ADN0104_s1h1

description: Hybridized to SNP6.104


title: BC24_ADN0105_s1h1

description: Hybridized to SNP6.105


title: ein3eil1_4hrAR_Re1_rep1

description:
AR_070
Gene expression at reoxygenation 1hr in ein3eil1 (4hr-anoxia)


title: ein3eil1_4hrAR_Re3_rep1

description:
AR_073
Gene expression at reoxygenation 3hr in ein3eil1 (4hr-anoxia)


title: ein2-5_4hrAR_Re6_rep3

description:
AR_060
Gene expression at reoxygenation 6hr in ein2-5 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein2-5_reoxygenation 6hr


title: ein3eil1_4hrAR_Re0_rep3

description:
AR_066
Gene expression at reoxygenation 0hr in ein3eil1 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein3eil1_reoxygenation 0hr


title: ein3eil1_4hrAR_Re0.5_rep2

description:
AR_068
Gene expression at reoxygenation 0.5hr in ein3eil1 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein3eil1_reoxygenation 0.5hr


title: ein3eil1_4hrAR_Nor_rep2

description:
AR_062
Gene expression under normal condition in ein3eil1 (4hr-anoxia)

source_name: ein3eil1_normal condition_before 4h anoxia


title: ein3eil1_4hrAR_Re0_rep1

description:
AR_064
Gene expression at reoxygenation 0hr in ein3eil1 (4hr-anoxia)


title: ein2-5_4hrAR_Re6_rep2

description:
AR_059
Gene expression at reoxygenation 6hr in ein2-5 (4hr-anoxia)


title: ein3eil1_4hrAR_Re0_rep2

description:
AR_065
Gene expression at reoxygenation 0hr in ein3eil1 (4hr-anoxia)


title: BC24_ADN0107_s1h1

description: Hybridized to SNP6.107


title: ein3eil1_4hrAR_Re3_rep3

description:
AR_075
Gene expression at reoxygenation 3hr in ein3eil1 (4hr-anoxia)


title: ein3eil1_4hrAR_Re0.5_rep3

description:
AR_069
Gene expression at reoxygenation 0.5hr in ein3eil1 (4hr-anoxia)


title: ein3eil1_4hrAR_Re0.5_rep1

description:
AR_067
Gene expression at reoxygenation 0.5hr in ein3eil1 (4hr-anoxia)


title: ein3eil1_4hrAR_Nor_rep1

description:
AR_061
Gene expression under normal condition in ein3eil1 (4hr-anoxia)


title: ein3eil1_4hrAR_Nor_rep3

description:
AR_063
Gene expression under normal condition in ein3eil1 (4hr-anoxia)


title: BC24_ADN0102_s1h1

description: Hybridized to SNP6.102


title: ein2-5_4hrAR_Re3_rep2

description:
AR_056
Gene expression at reoxygenation 3hr in ein2-5 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein2-5_reoxygenation 3hr


title: ein2-5_4hrAR_Re3_rep3

description:
AR_057
Gene expression at reoxygenation 3hr in ein2-5 (4hr-anoxia)


title: BC24_ADN0101_s1h1

description: Hybridized to SNP6.101


title: BC24_ADN0100_s1h1

description: Hybridized to SNP6.100


title: BC24_ADN0099_s1h1

description: Hybridized to SNP6.099


title: BC24_ADN0098_s1h1

description: Hybridized to SNP6.098


title: BC24_ADN0097_s1h1

description: Hybridized to SNP6.097


title: BC24_ADN0095_s1h1

description: Hybridized to SNP6.095


title: BC24_ADN0092_s1h1

description: Hybridized to SNP6.092


title: BC24_ADN0093_s1h1

description: Hybridized to SNP6.093


title: ein2-5_4hrAR_Re6_rep1

description:
AR_058
Gene expression at reoxygenation 6hr in ein2-5 (4hr-anoxia)


title: ein2-5_4hrAR_Re3_rep1

description:
AR_055
Gene expression at reoxygenation 3hr in ein2-5 (4hr-anoxia)


title: BC24_ADN0090_s1h2

description: Hybridized to SNP6.090


title: BC24_ADN0089_s1h1

description: Hybridized to SNP6.089


title: BC24_ADN0084_s2h1

description: Hybridized to SNP6.084


title: BC24_ADN0062_s1h1

description: Hybridized to SNP6.062


title: BC24_ADN0059_s1h1

description: Hybridized to SNP6.059


title: BC24_ADN0049_s1h1

description: Hybridized to SNP6.049


title: ein2-5_4hrAR_Re1_rep2

description:
AR_053
Gene expression at reoxygenation 1hr in ein2-5 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein2-5_reoxygenation 1hr


title: ein3eil1_4hrAR_Re1_rep3

description:
AR_072
Gene expression at reoxygenation 1hr in ein3eil1 (4hr-anoxia)


title: BC24_ADN0039_s1h1

description: Hybridized to SNP6.039


title: ein2-5_4hrAR_Nor_rep3

description:
AR_045
Gene expression under normal condition in ein2-5 (4hr-anoxia)

source_name: ein2-5_normal condition_4hr anoxia


title: BC24_ADN0037_s1h1

description: Hybridized to SNP6.037


title: Col_4hrAR_Re6_rep3

description:
AR_042
Gene expression at reoxygenation 6hr in Col-0 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated WT_reoxygenation 6hr

value: wild type


title: ein2-5_4hrAR_Re1_rep1

description:
AR_052
Gene expression at reoxygenation 1hr in ein2-5 (4hr-anoxia)


title: ein2-5_4hrAR_Re1_rep3

description:
AR_054
Gene expression at reoxygenation 1hr in ein2-5 (4hr-anoxia)


title: ein2-5_4hrAR_Nor_rep2

description:
AR_044
Gene expression under normal condition in ein2-5 (4hr-anoxia)


title: Col_4hrAR_Re6_rep2

description:
AR_041
Gene expression at reoxygenation 6hr in Col-0 (4hr-anoxia)


title: ein2-5_4hrAR_Nor_rep1

description:
AR_043
Gene expression under normal condition in ein2-5 (4hr-anoxia)


title: BC24_ADN0028_s1h1

description: Hybridized to SNP6.028


title: Col_4hrAR_Re6_rep1

description:
AR_040
Gene expression at reoxygenation 6hr in Col-0 (4hr-anoxia)


title: ein2-5_4hrAR_Re0_rep3

description:
AR_048
Gene expression at reoxygenation 0hr in ein2-5 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein2-5_reoxygenation 0hr


title: ein2-5_4hrAR_Re0.5_rep2

description:
AR_050
Gene expression at reoxygenation 0.5hr in ein2-5 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated ein2-5_reoxygenation 0.5hr


title: BC24_ADN0011_s1h1

description: Hybridized to SNP6.011


title: BC24_ADN0013_s1h1

description: Hybridized to SNP6.013


title: ein2-5_4hrAR_Re0.5_rep3

description:
AR_051
Gene expression at reoxygenation 0.5hr in ein2-5 (4hr-anoxia)


title: ein2-5_4hrAR_Re0_rep2

description:
AR_047
Gene expression at reoxygenation 0hr in ein2-5 (4hr-anoxia)


title: Col_4hrAR_Re3_rep3

description:
AR_039
Gene expression at reoxygenation 3hr in Col-0 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated WT_reoxygenation 3hr


title: BC24_ADN0224_s1h1

description: Hybridized to SNP6.224

value: validation set


title: BC24_ADN0181_s1h1

description: Hybridized to SNP6.181


title: ein2-5_4hrAR_Re0_rep1

description:
AR_046
Gene expression at reoxygenation 0hr in ein2-5 (4hr-anoxia)


title: BC24_ADN0180_s1h1

description: Hybridized to SNP6.180


title: Col_4hrAR_Re1_rep1

description:
AR_034
Gene expression at reoxygenation 1hr in Col-0 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated WT_reoxygenation 1hr


title: Col_4hrAR_Re1_rep3

description:
AR_036
Gene expression at reoxygenation 1hr in Col-0 (4hr-anoxia)


title: BC24_ADN0177_s1h1

description: Hybridized to SNP6.177


title: BC24_ADN0178_s1h1

description: Hybridized to SNP6.178


title: ein2-5_4hrAR_Re0.5_rep1

description:
AR_049
Gene expression at reoxygenation 0.5hr in ein2-5 (4hr-anoxia)


title: Col_4hrAR_Re3_rep1

description:
AR_037
Gene expression at reoxygenation 3hr in Col-0 (4hr-anoxia)


title: Col_4hrAR_Re0.5_rep2

description:
AR_032
Gene expression at reoxygenation 0.5hr in Col-0 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated WT_reoxygenation 0.5hr


title: Col_4hrAR_Re3_rep2

description:
AR_038
Gene expression at reoxygenation 3hr in Col-0 (4hr-anoxia)


title: Col_4hrAR_Re0.5_rep3

description:
AR_033
Gene expression at reoxygenation 0.5hr in Col-0 (4hr-anoxia)


title: BC24_ADN0176_s1h1

description: Hybridized to SNP6.176

source_name: Breast tumoral sample


title: BC24_ADN0175_s1h1

description: Hybridized to SNP6.175


title: BC24_ADN0174_s1h1

description: Hybridized to SNP6.174


title: Col_4hrAR_Re1_rep2

description:
AR_035
Gene expression at reoxygenation 1hr in Col-0 (4hr-anoxia)


title: BC24_ADN0173_s1h1

description: Hybridized to SNP6.173


title: BC24_ADN0103_s1h1

description: Hybridized to SNP6.103


title: BC24_ADN0171_s1h1

description: Hybridized to SNP6.171


title: BC24_ADN0170_s1h1

description: Hybridized to SNP6.170


title: Col_4hrAR_Re0_rep2

description:
AR_029
Gene expression at reoxygenation 0hr in Col-0 (4hr-anoxia)

source_name: 4hr anoxia-reoxygenated WT_reoxygenation 0hr


title: BC24_ADN0169_s1h1

description: Hybridized to SNP6.169


title: Col_4hrAR_Re0_rep3

description:
AR_030
Gene expression at reoxygenation 0hr in Col-0 (4hr-anoxia)


title: Col_4hrAR_Re0_rep1

description:
AR_028
Gene expression at reoxygenation 0hr in Col-0 (4hr-anoxia)


title: Col_4hrAR_Nor_rep1

description:
AR_025
Gene expression under normal condition in Col-0 (4hr-anoxia)

source_name: WT_normal condition_before 4hr anoxia


title: Col_4hrAR_Nor_rep2

description:
AR_026
Gene expression under normal condition in Col-0 (4hr-anoxia)


title: BC24_ADN0167_s1h1

description: Hybridized to SNP6.167


title: BC24_ADN0166_s1h1

description: Hybridized to SNP6.166


title: Col_4hrAR_Nor_rep3

description:
AR_027
Gene expression under normal condition in Col-0 (4hr-anoxia)


title: Col_8hrAR_Re6_rep3

description:
AR_023
Gene expression at reoxygenation 6hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 6hr


title: BC24_ADN0164_s1h1

description: Hybridized to SNP6.164


title: BC24_ADN0172_s1h1

description: Hybridized to SNP6.172


title: Col_8hrAR_Re3_rep4

description:
AR_020
Gene expression at reoxygenation 3hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 3hr


title: BC24_ADN0163_s1h1

description: Hybridized to SNP6.163


title: BC24_ADN0168_s1h1

description: Hybridized to SNP6.168


title: Col_8hrAR_Re6_rep1

description:
AR_021
Gene expression at reoxygenation 6hr in Col-0 (8hr-anoxia)


title: BC24_ADN0162_s1h1

description: Hybridized to SNP6.162


title: Col_8hrAR_Re3_rep2

description:
AR_018
Gene expression at reoxygenation 3hr in Col-0 (8hr-anoxia)


title: BC24_ADN0160_s1h1

description: Hybridized to SNP6.160


title: Col_8hrAR_Re1_rep3

description:
AR_015
Gene expression at reoxygenation 1hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 1hr


title: BC24_ADN0156_s1h1

description: Hybridized to SNP6.156


title: Col_4hrAR_Re0.5_rep1

description:
AR_031
Gene expression at reoxygenation 0.5hr in Col-0 (4hr-anoxia)


title: Col_8hrAR_Re6_rep4

description:
AR_024
Gene expression at reoxygenation 6hr in Col-0 (8hr-anoxia)


title: BC24_ADN0155_s1h1

description: Hybridized to SNP6.155