title: Colorectal cancer tissue patient 09/1601 T0 A CL145

description: Colorectal cancer tissue from patient_1_timepoint_T0_replicate_A


title: Normal colon tissue patient 08/14630 T0 A CL091

status: Public on Feb 01 2013

type: RNA

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised using RSN normalisation with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: normal colon mucosa

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.

tag: tissue

value: Normal colon tissue

tag: patient

tag: time point

tag: replicate

value: A

tag: rin (rna integrity number)

tag: disease state

value: colon cancer


title: Normal colon tissue patient 08/14630 T2 A CL095


title: Normal colon tissue patient 08/15000 T3 A CL083


title: Normal colon tissue patient 08/15000 T0 A CL079


title: Normal colon tissue patient 08/14630 T3 A CL096


title: Normal colon tissue patient 08/15000 T2 A CL084


title: Normal colon tissue patient 08/14630 T1 A CL094


title: Normal colon tissue patient 08/14630 T0 B CL092

value: B


title: Normal colon tissue patient 08/15000 T0 C CL081

value: C


title: Normal colon tissue patient 08/15161 T2 A CL046


title: Normal colon tissue patient 08/15161 T3 A CL047


title: Normal colon tissue patient 08/15000 T0 B CL080


title: Normal colon tissue patient 08/15161 T1 A CL048


title: Normal colon tissue patient 08/15161 T0 A CL043


title: Normal colon tissue patient 08/14623 T1 A CL034


title: Normal colon tissue patient 08/14623 T2 A CL035


title: Normal colon tissue patient 08/15161 T0 C CL045


title: Normal colon tissue patient 08/15000 T1 A CL082


title: Normal colon tissue patient 08/14623 T0 A CL031


title: COCs from GnRH+eCG+hCG treated rat 23

city: Columbia

first: Cansu

last: Agca

state: MO

address: 1600 E. Rollins St

department: Veterinary Pathobiology

country: USA

institute: University of Missouri

description:
Sexually mature, female, Sprague Dawley  rat cumulus oocyte complex
RNA amplification

hyb_protocol: Illumina  RatRef-12 Expression BeadChip hybridization protocol, 48oC hybridization temperature

scan_protocol: standard Illumina protocol

data_processing: BeadStudio Expression Analysis Software then normalized in GeneSpring

label: Biotin

organism: Rattus norvegicus

source_name: COCs from GnRH+eCG+hCG treated rat 23

label_protocol: Encore BiotinIL Module (Nugen, San Carlos, CA)

extract_protocol: Arcturus PicoPure RNA Isolation Kit

tag: developmental stage

value: sexually mature

tag: strain

value: Sprague Dawley

tag: gender

value: female

value: cumulus oocyte complex

tag: treatment

value: GnRH + eCG + hCG


title: Normal colon tissue patient 08/14856 T1 A CL022


title: Normal colon tissue patient 08/14856 T3 A CL024


title: Normal colon tissue patient 08/14856 T2 A CL023


title: Normal colon tissue patient 08/14623 T0 C CL033


title: Normal colon tissue patient 08/15161 T0 B CL044


title: COCs from GnRH+eCG+hCG treated rat 24

source_name: COCs from GnRH+eCG+hCG treated rat 24


title: COCs from GnRH+eCG treated rat 21

source_name: COCs from GnRH+eCG treated rat 21

value: GnRH + eCG


title: Normal colon tissue patient 08/14856 T0 B CL020


title: COCs from GnRH+eCG+hCG treated rat 22

source_name: COCs from GnRH+eCG+hCG treated rat 22


title: Normal colon tissue patient 08/14856 T0 A CL019


title: COCs from GnRH+eCG treated rat 20

source_name: COCs from GnRH+eCG treated rat 20


title: COCs from GnRH treated rat 17

source_name: COCs from GnRH treated rat 17

value: GnRH


title: Normal colon tissue patient 08/15607 T3 A CL012


title: Normal colon tissue patient 08/15607 T0 B CL008


title: Normal colon tissue patient 08/15607 T2 A CL010


title: COCs from NC rat 15

source_name: COCs from NC rat 15

value: control


title: COCs from GnRH treated rat 16

source_name: COCs from GnRH treated rat 16


title: COCs from NC rat 13

source_name: COCs from NC rat 13


title: COCs from GnRH treated rat 18

source_name: COCs from GnRH treated rat 18


title: COCs from NC rat 14

source_name: COCs from NC rat 14


title: Normal colon tissue patient 08/15824 T1 A CL072


title: COCs from GnRH+eCG+hCG treated rat 11

source_name: COCs from GnRH+eCG+hCG treated rat 11


title: Normal colon tissue patient 08/15607 T0 C CL009


title: Normal colon tissue patient 08/15607 T1 A CL011


title: Normal colon tissue patient 08/15824 T2 A CL070


title: Normal colon tissue patient 08/15607 T0 A CL007


title: Normal colon tissue patient 08/15824 T3 A CL071


title: Normal colon tissue patient 08/15824 T0 C CL069


title: COCs from GnRH+eCG+hCG treated rat 10

source_name: COCs from GnRH+eCG+hCG treated rat 10


title: Normal colon tissue patient 08/15824 T0 A CL067


title: COCs from GnRH+eCG treated rat 9

source_name: COCs from GnRH+eCG treated rat 9


title: COCs from GnRH+eCG+hCG treated rat 12

source_name: COCs from GnRH+eCG+hCG treated rat 12


title: Normal colon tissue patient 08/15824 T0 B CL068


title: COCs from GnRH treated rat 4

source_name: COCs from GnRH treated rat 4


title: COCs from GnRH treated rat 6

source_name: COCs from GnRH treated rat 6


title: COCs from GnRH+eCG treated rat 7

source_name: COCs from GnRH+eCG treated rat 7


title: Normal colon tissue patient 08/15827 T2 A CL058

source_name: normal colon mucosa


title: Normal colon tissue patient 08/15827 T0 B CL056


title: Normal colon tissue patient 08/14058 T3 A CL180


title: Normal colon tissue patient 08/15827 T3 A CL060


title: Normal colon tissue patient 08/15827 T0 C CL057


title: Normal colon tissue patient 08/15827 T1 A CL059


title: COCs from NC rat 1

source_name: COCs from NC rat 1


title: COCs from GnRH treated rat 5

source_name: COCs from GnRH treated rat 5


title: COCs from NC rat 2

source_name: COCs from NC rat 2


title: Normal colon tissue patient 08/15827 T0 A CL055


title: Normal colon tissue patient 08/14058 T2 A CL179


title: COCs from NC rat 3

source_name: COCs from NC rat 3


title: COCs from GnRH+eCG treated rat 8

source_name: COCs from GnRH+eCG treated rat 8


title: Normal colon tissue patient 08/14058 T0 C CL177


title: Normal colon tissue patient 08/14058 T0 B CL176


title: Normal colon tissue patient 08/14058 T0 A CL175


title: Normal colon tissue patient 08/14058 T1 A CL178


title: Normal colon tissue patient 08/14856 T0 C CL021


title: Normal colon tissue patient 08/15233 T2 A CL108


title: Mutant ureter at E16.5 biological rep1

city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

country: France

institute: CNRS-AMU

description: Gene expression data from E16.5 ureter

hyb_protocol: Labelled-cRNA was fragmented and hybridised to mouse gene 1.0 ST arrays (Affymetrix) following manufacturer’s protocols. Three independent RNA preparations from the four different conditions [wild type and mutant, E14.5 and E16.5] were processed and hybridised on Mouse Gene Arrays.

scan_protocol: Affymetrix Fluidics Station 450 GeneChip® Scanner 3000 7G Image processing software: GeneChip® Command Console® Software (AGCC)

data_processing: Arrays have been quantile-normalize with respect to the probe GC content using the RMA algorithm (GC contend adjustment, RMA background correction and mean probe set summarization). Not or low expressed transcripts have been removed by a maximum expression cutoff < 100.

organism: Mus musculus

source_name: E16.5 mouse embryonic ureter

label_protocol: cRNAs for hybridisation to Affymetrix arrays were prepared from 100 ng total RNA using the wild-type expression kit Affymetrix (Affymetrix, Santa Clara, CA 95051).

extract_protocol: Total RNA was isolated from ureters using TRIsure Reagent (Bioline) according to manufacturer's instructions. The integrity of RNA was assessed using an Agilent 2100 Bioanalyser (Agilent Technology) and RNA concentration determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Rockland, DE).

treatment_protocol: Ureters at E14.5 and E16.5 were microdissected and placed in RNAlater solution (Ambion, Austin, TX) until sufficients samples had been collected to perform the experiments in triplicate for each condition.

value: dissected ureters

tag: age

tag: genotype


title: Normal colon tissue patient 08/14623 T0 B CL032


title: Normal colon tissue patient 08/15233 T3 A CL107


title: Mutant ureter at E16.5 biological rep2

description: Gene expression data from E16.5 ureter


title: Wild type ureter at E16.5 biological rep1

description: Gene expression data from E16.5 ureter

value: Wild type


title: Wild type ureter at E16.5 biological rep2

description: Gene expression data from E16.5 ureter


title: COCs from GnRH+eCG treated rat 19

source_name: COCs from GnRH+eCG treated rat 19


title: Normal colon tissue patient 08/15233 T1 A CL106


title: Normal colon tissue patient 08/15233 T0 A CL103


title: Normal colon tissue patient 08/16477 T2 A CL143


title: Mutant ureter at E16.5 biological rep3

description: Gene expression data from E16.5 ureter


title: Mutant ureter at E14.5 biological rep2

description: Gene expression data from E14.5 ureter

source_name: E14.5 mouse embryonic ureter


title: Normal colon tissue patient 08/15233 T0 C CL105


title: Normal colon tissue patient 08/16477 T1 A CL144


title: Wild type ureter at E16.5 biological rep3

description: Gene expression data from E16.5 ureter


title: Mutant ureter at E14.5 biological rep3

description: Gene expression data from E14.5 ureter


title: 9div A2 0h

city: Tokyo

first: Yukiko

last: Gotoh

address: Bunkyo-ku, Yayoi, 1-1-1

department: IMCB

country: Japan

institute: the Univ. of Tokyo

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were labeled and hybridized for 16 hr at 45C on GeneChip® Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

source_name: Neuroepithelial cells from the neocortex of embryonic day 11.5 mice cultured for 9 days and infected with HMGA2-expressing retrovirus for 3 days

label_protocol: RNA amplification and labeling using Ambion® WT Expression Kit (Life Technologies, California, US) and GeneChip® WT Terminal Labeling and Controls Kit (Affymetrix, California , US)

extract_protocol: Total RNA was extracted using TRIzol® Reagent(Life Technologies, California, U.S.) and purified with RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to manufacture’s instructions.

value: embryonic day 11.5

value: brain

tag: cell type

value: Neuroepithelial cells

tag: culture protocol [pre-infection]

value: cultured as neurospheres for 9 days in vitro in the presence of FGF2 and EGF

tag: infection

value: HMGA2-expressing retrovirus

tag: culture protocol [post-infection]


title: 9div A2 12h

source_name: Neuroepithelial cells from the neocortex of embryonic day 11.5 mice cultured for 9 days and infected with HMGA2-expressing retrovirus for 3 days, followed by culturing in the absence of FGF for 12 h

value: cultured in the absence of FGF for 12 h


title: Wild type ureter at E14.5 biological rep3

description: Gene expression data from E14.5 ureter


title: 9div cont 12h

source_name: Neuroepithelial cells from the neocortex of embryonic day 11.5 mice cultured for 9 days and infected with control retrovirus for 3 days, followed by culturing in the absence of FGF for 12 h

value: control retrovirus


title: Wild type ureter at E14.5 biological rep1

description: Gene expression data from E14.5 ureter


title: Wild type ureter at E14.5 biological rep2

description: Gene expression data from E14.5 ureter


title: Normal colon tissue patient 08/15233 T0 B CL104

value: Normal colon tissue

value: B

value: colon cancer


title: Normal colon tissue patient 08/16477 T0 C CL141

value: C


title: Normal colon tissue patient 08/16477 T0 A CL139

value: A


title: Normal colon tissue patient 08/16477 T3 A CL142


title: Mutant ureter at E14.5 biological rep1

description: Gene expression data from E14.5 ureter


title: 9div cont 0h

source_name: Neuroepithelial cells from the neocortex of embryonic day 11.5 mice cultured for 9 days and infected with control retrovirus for 3 days


title: Normal colon tissue patient 08/16477 T0 B CL140


title: Normal colon tissue patient 09/1056 T2 A CL132


title: Normal colon tissue patient 09/1056 T0 B CL128


title: Normal colon tissue patient 09/1056 T1 A CL131


title: Normal colon tissue patient 09/1056 T0 C CL129


title: Normal colon tissue patient 09/1825 T2 A CL166


title: Normal colon tissue patient 09/1825 T0 B CL164


title: Normal colon tissue patient 09/1825 T0 A CL163


title: Normal colon tissue patient 09/1066 T0 B CL116


title: Normal colon tissue patient 09/1601 T1 A CL154


title: Normal colon tissue patient 09/1601 T2 A CL156


title: Normal colon tissue patient 09/1066 T2 A CL120


title: pupal wing ~80h APF, biological rep3

first: Benjamin

last: Prudhomme

address: Parc scientifique de Luminy case 907

institute: IBDM-CNRS

description: Gene expression data from pupal wings ~80h APF

hyb_protocol: biotin-labeled cRNA was hybridized overnight to D. melanogaster GeneChip in the AFX HybOven480 and post processed on the automated Fluidics450 Station

scan_protocol: GeneChips were scanned on the GC 3000 G7 Scanner

data_processing: The data was analyzed using BioConductor (MAS 5.0 evaluations and RMA calculations)

organism: Drosophila melanogaster

source_name: Drosophila melanogaster pupal wings, ~80h APF

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

growth_protocol: Flies were grown at 25C

extract_protocol: Wings were mechanically discrupted in Trizol using aTissueTearor (to crack the cuticle surrounding the cells) and then processed for RNA extraction according to the manufacturer's instructions

treatment_protocol: Pupae were manually extracted from the pupal case, the pupal membrane surrounding the wings was removed with tweezer and the wings were dissected and directly collected and collected in a small drop of water in a tube on dry ice.

value: Oregon R

value: pupal wings


title: Normal colon tissue patient 09/1056 T3 A CL130


title: pupal wing ~80h APF, biological rep1


title: Normal colon tissue patient 09/1825 T0 C CL165


title: Normal colon tissue patient 09/1601 T0 B CL152


title: siSpt6; CIT(+); Replicate #3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal. The raw Red signal data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.The raw Red signal data　intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. Detected signals for each gene were normalized by global normalization method (the median of the detected signal intensity was adjusted to 30).

source_name: siSpt6; CIT(+)

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: RPMI 1640 supplemented with 10% FCS, 50mM 2-mercaptoethanol, 5% NCTC, 20mM HEPES, 2mM L-glutamine

extract_protocol: Total RNA  was extracted from cells using RNeasy mini kit (Qiagen).

treatment_protocol: Stelth siRNA oligonucleotides (Invitrogen) were introduced to CH12F3-2A cells by Aamaxa electroporation system (Lonza).  The cells were then cultured for 24h, stimulated by CD40L, IL4, TGFb (CIT), and cultured for another 24h.

tag: cell line

tag: cit-induced switch

value: IgA

tag: knockdown

value: CD40L, IL4, TGFb (CIT)


title: Normal colon tissue patient 09/1066 T3 A CL119

tag: tissue

tag: patient

tag: time point


title: pupal wing ~80h APF, biological rep2


title: siSpt6; CIT(+); Replicate #1


title: siSpt6; CIT(+); Replicate #2


title: Normal colon tissue patient 09/1601 T3 A CL155

tag: replicate

tag: rin (rna integrity number)

tag: disease state


title: Normal colon tissue patient 09/1066 T0 A CL115


title: Glioma, clinical trial RT v RT+PCV 62 273.CEL

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

description: Abbreviations: IGS: intrinsic glioma subtype; Trt: treatment; SS: survival in years; C: classical; P: proneural; M: mesenchymal; N:neural

hyb_protocol: Hybridization was performed according to the Affymetrix (Santa Clara, CA) Labelling Assay manual

scan_protocol: Genechip scanner 3000 7G

data_processing: RMA

source_name: Glioma, clinical trial RT v RT+PCV

label_protocol: labelling was performed according to the Affymetrix (Santa Clara, CA) Labelling Assay manual

extract_protocol: Qiagen Rneasy

value: glioma

tag: sample

tag: igs

tag: tissue type

value: FF

tag: idhmut

value: mut

tag: 1p19q loh

value: LOH

tag: egfr

value: amp

tag: mgmt

value: meth

tag: trt

value: RT

tag: ss (y)

tag: event

value: alive

tag: Sex

value: F

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment

value: pt 5


title: Normal colon tissue patient 09/1601 T0 A CL151

tag: tissue

value: Normal colon tissue

tag: patient

tag: time point

tag: replicate

value: colon cancer


title: Normal colon tissue patient 09/1601 T0 C CL153

value: C

tag: rin (rna integrity number)

tag: disease state


title: Glioma, clinical trial RT v RT+PCV 74 048.CEL

tag: sample

tag: igs

tag: tcga classification

value: N

tag: tissue type

value: RT/PCV

value: deceased

tag: age

value: AOA


title: Glioma-EORTC26951 A1488-06.CEL

value: glioma

value: FF

tag: idhmut

value: wt

tag: 1p19q loh

value: no loss

tag: egfr

tag: mgmt

value: unmeth

tag: trt

tag: ss (y)

value: M

value: pt 4


title: PBLs of patient 17 post therapy

city: Tübingen

first: Benita

last: Wolf

address: Quenstedtstrasse 12

department: Medical Clinic 1

country: Germany

institute: University Hospital Tübingen

hyb_protocol: cDNA was hybridized to the GeneChip Human Gene 1.0 ST Array according to Affymetrix guidelines

scan_protocol: the stained array was scanned at 532nm using an Affymetrix GeneCChip Scanner 3000

data_processing: Chip-quality was controled with Affymetrix expression console. CEL files were normalized and summarized using RMA.

source_name: periphereal blood lymphocytes

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 5,5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PBLs were isolated from pheresis product by elutrition fractionation

extract_protocol: total RNA was isolated using RNAeasy kit (Quiagen) according to manufacteurer's protocol

treatment_protocol: immunotherapy consisted of intranodal vaccination of dendritic cells loaded with tumor renal cell carcinoma lysate, intravenous infusion of Interleukin 2 and subcutaneous injections of Interferon-alpha2a

tag: cell type

value: PBLs from leucapheresis product

value: metastatic renal cell carcinoma

tag: group

value: post therapy


title: PBLs of patient 12 post therapy


title: Glioma-EORTC26951 A1488-07.CEL

tag: tissue

value: P

value: FFPE

tag: cimp

value: CIMP+

value: RT

tag: event

tag: Sex

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment


title: PBLs of patient 16 post therapy

tag: disease state


title: PBLs of patient 13 post therapy


title: PBLs of patient 11 post therapy


title: Normal colon tissue patient 09/1825 T3 A CL168

source_name: normal colon mucosa

value: Normal colon tissue

tag: patient

tag: time point

tag: replicate

value: A

tag: rin (rna integrity number)

value: colon cancer


title: Glioma-EORTC26951 A1488-02.CEL

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FF

tag: 1p19q loh

tag: egfr

value: RT/PCV

value: deceased

tag: age


title: PBLs of patient 14 post therapy

tag: cell type

tag: group


title: PBLs of patient 4 post therapy


title: Glioma-EORTC26951 A1488-03.CEL

tag: tissue

value: N

tag: idhmut

value: wt

value: no loss

tag: mgmt

value: unmeth

tag: trt

tag: ss (y)

tag: event

tag: Sex

value: F

tag: original diagnosis

value: pt 4


title: PBLs of patient 5 post therapy

value: PBLs from leucapheresis product

tag: disease state

value: metastatic renal cell carcinoma

value: post therapy


title: Glioma, clinical trial RT v RT+PCV 192 22.CEL

hyb_protocol: HG U133-plus2 microarrays were hybridized overnight with 15 μg biotin-labeled cRNA

scan_protocol: Genechip scanner

label_protocol: cDNA synthesis and cRNA labeling was done using the alternative protocol for one-cycle cDNA synthesis.Biotin-labeled cRNA was generated using the ENZO Highyield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). Affymetrix (Santa Clara, CA)

extract_protocol: Trizol

tag: sample

tag: igs

value: amp

value: M

value: AOD

tag: review diagnosis

tag: experiment

value: pt 3


title: Glioma-EORTC26951 A1488-01.CEL

value: glioma

tag: tcga classification

value: P

tag: tissue type

tag: 1p19q loh

value: RT

value: AOA


title: PBLs of patient 9 post therapy

tag: cell type

tag: group


title: Glioma, clinical trial RT v RT+PCV 171 36.CEL

tag: tissue

value: FF

tag: idhmut

tag: egfr

value: deceased

tag: age


title: Glioma-EORTC26951 A1488-04.CEL

value: no loss

tag: trt

value: RT/PCV

tag: ss (y)

tag: event


title: Glioma, clinical trial RT v RT+PCV 99 15.CEL

value: C

tag: cimp

value: CIMP-

value: wt

tag: mgmt

value: meth

tag: Sex

value: F

tag: original diagnosis


title: PBLs of patient 10 post therapy

value: PBLs from leucapheresis product

tag: disease state

value: metastatic renal cell carcinoma

value: post therapy


title: PBLs of patient 1 post therapy


title: PBLs of patient 2 post therapy


title: PBLs of patient 8 post therapy


title: Ycs.mat_Ycon.pat

city: Cambridge

first: Pan-Pan

last: Jiang

state: MA

address: 16 Divinity Ave c/o Hartl Lab

department: Organismic and Evolutionary Biology

institute: Harvard University

hyb_protocol: Genisphere 3DNA system.

scan_protocol: Axon scanner and GenePix.

data_processing: Ratios were taken from the Limma package after Loess normalization of the raw intensities data originally obtained in GenePix.

source_name: Ycs, maternal transmission

label_protocol: Genisphere 3DNA system.

growth_protocol: 24hr light, humidity controlled, males 3 days old at time of RNA extraction.

extract_protocol: Trizol RNA extraction.

treatment_protocol: Treatment: 2 Y-lineages (Cs or Con) and 2 modes of Y chromosome transmission (paternal or maternal) in every possible pairing.

tag: lineage

value: Cs

value: 3 days

tag: gender

value: male

tag: parent of origin of y chr

value: maternal

source_name: Ycon, paternal transmission

value: Con

value: paternal


title: Glioma, clinical trial RT v RT+PCV 94 17.CEL

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: P

tag: tissue type

value: FF

tag: 1p19q loh

value: unmeth

value: RT

value: deceased

value: M

value: AOD

tag: review diagnosis

tag: experiment

value: pt 3


title: Ycon.pat_Ycs.mat

tag: age


title: PBLs of patient 17 pre therapy

tag: cell type

value: PBLs from leucapheresis product

value: metastatic renal cell carcinoma

tag: group

value: pre therapy


title: PBLs of patient 16 pre therapy


title: Ycs.pat_Ycon.mat

source_name: Ycs, paternal transmission

value: Cs

value: 3 days

source_name: Ycon, maternal transmission


title: Ycon.mat_Ycs.pat

value: male

value: maternal


title: PBLs of patient 13 pre therapy


title: PBLs of patient 14 pre therapy


title: Ycs.pat_Ycs.mat

value: paternal


title: PBLs of patient 10 pre therapy


title: Glioma, clinical trial RT v RT+PCV 80 29.CEL

tag: tissue

value: glioma

value: C

tag: idhmut

value: wt

value: no loss

tag: egfr

value: amp

tag: mgmt

value: meth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: AOA


title: PBLs of patient 18 pre therapy

tag: disease state


title: PBLs of patient 11 pre therapy


title: PBLs of patient 12 pre therapy


title: Glioma-EORTC26951 A1488-05.CEL

tag: sample

tag: igs

value: FF

value: RT

value: deceased

tag: Sex

value: M

tag: original diagnosis

value: GBM/AA

value: pt 4


title: ASBatch3_LPS_B_Nr.19

city: Regensburg

first: Katharina

last: Meyer

address: Josef Engert Street 9

department: Statistical Bioinformatics

institute: Institute for Functional Genomics

hyb_protocol: Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.

label_protocol: Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)

growth_protocol: BL2 cells in RPMI containing 10% FCS

extract_protocol: Qiagen RNA-isolation

treatment_protocol: treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints

tag: cell line

value: Burkitt Lymphoma cells

tag: treated with

value: LPS for 6hrs

tag: biological replicate


title: ASBatch3_Kontrolle_Nr.17

source_name: BL2_none (control)

tag: cell type

value: none (control)


title: ASBatch3_rhIL21_Nr.22

value: rhIL21 for 2hrs


title: Ycon.pat_Ycs.pat

tag: lineage

value: Con

tag: age

value: 3 days

tag: gender

value: male

tag: parent of origin of y chr

value: paternal

value: Cs


title: Glioma, clinical trial RT v RT+PCV 15 47.CEL

tag: tissue

value: glioma

tag: tcga classification

value: P

tag: tissue type

tag: cimp

value: CIMP+

tag: 1p19q loh

value: LOH

tag: egfr

value: wt

tag: mgmt

value: meth

value: RT/PCV

value: alive

value: AOD

tag: review diagnosis

tag: experiment

value: pt 3


title: PBLs of patient 9 pre therapy

value: PBLs from leucapheresis product

tag: disease state

value: metastatic renal cell carcinoma

tag: group

value: pre therapy


title: PBLs of patient 8 pre therapy


title: Ycs.mat_Ycs.pat

value: 3 days

value: maternal


title: PBLs of patient 5 pre therapy


title: PBLs of patient 7 pre therapy


title: ASBatch3_rhCD40L_B_Nr.18

tag: cell line

value: Burkitt Lymphoma cells

tag: treated with

value: rhCD40L for 6hrs

tag: biological replicate


title: PBLs of patient 6 pre therapy

tag: cell type


title: ASBatch3_antiIgM F(ab) fragments_Nr.21

source_name: BL2_antiIgM F(ab) fragments_3hrs

value: antiIgM F(ab) fragments for 3hrs


title: Normal colon tissue patient 09/1066 T0 C CL117

value: Normal colon tissue

tag: patient

tag: time point

tag: replicate

value: C

tag: rin (rna integrity number)

value: colon cancer


title: Ycon.pat_Ycon.mat

tag: lineage

value: Con

tag: age

tag: gender

value: male

tag: parent of origin of y chr

value: paternal


title: Normal colon tissue patient 09/1066 T1 A CL118

tag: tissue

value: A


title: Ycs.pat_Ycon.pat

value: Cs


title: PBLs of patient 3 pre therapy


title: PBLs of healthy control 9

value: healthy

value: control


title: PBLs of healthy control 8

value: PBLs from leucapheresis product


title: PBLs of patient 4 pre therapy

value: metastatic renal cell carcinoma

value: pre therapy


title: Normal colon tissue patient 09/1056 T0 A CL127


title: PBLs of patient 2 pre therapy


title: Ycon.mat_Ycs.mat

value: 3 days

value: maternal


title: ASBatch3_rhBAFF_B_Nr.20

value: Burkitt Lymphoma cells

value: rhBAFF for 9hrs


title: Ycon.mat_Ycon.pat


title: Ycs.mat_Ycon.mat


title: PBLs of healthy control 4


title: PBLs of healthy control 6


title: PBLs of healthy control 7


title: PBLs of healthy control 3


title: PBLs of healthy control 2


title: PBLs of patient 1 pre therapy


title: ASBatch2_LPS_A_Nr.12

value: LPS for 30mins


title: ASBatch2_LPS_B_Nr.13

value: LPS for 6hrs


title: PBLs of healthy control 1


title: PBLs of healthy control 5


title: ASBatch2_rhCD40L_B_Nr.11

value: rhCD40L for 6hrs


title: Bmal1fxSf-1Cre vs Control 3

city: Madison

first: Brian

middle: P

last: Johnson

state: WI

address: 1400 University Ave

department: Oncology

institute: UW-Madison

description: Sample 3

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

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

data_processing: Agilent Feature extraction versions 9.1 and 9..5 for background subtraction - Local background subtraction and normalization Linear LOWESS.

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

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark. ZT0=time lights turn on the room ~6:00 AM.

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

treatment_protocol: Sacrificed and dissected at given time and placed in RNAlater

tag: strain

value: female

tag: genotype/variation

value: Bmal1fxfx (wild type)

value: 10 weeks

value: Ovary

tag: time of cacrifice

value: ZT12 on 3.5 days post copulation


title: R_AJC_906_Muscle

city: King Salmon

first: Scott

middle: A

last: Pavey

state: Alaska

address: PO Box 7

department: Natural Resources

institute: Katmai National Park

description: SAMPLE 49

hyb_protocol: We used the cGRASP 16 k cDNA microarray to compare the transcriptomes of these populations with divergent life histories. This microarray consists of 16,006 elements chosen from 300,000 Atlantic salmon and rainbow trout cDNA libraries. The libraries were derived from a variety of tissue types at different development stages, and conditions. Element sequences were chosen for minimum overlap, sequence quality, andother criteria. We followed an established hybridization protocol for the 16 k cDNA array [50]. In brief, both 250 ng of reference aRNA and 500 ng of sample cDNA were collectedin a single tube and kept dark. The mixture was concentrated with a speed vacuum and brought up to 23 ul with RNase free water (Gibco). Hybridization buffer #3 (Ambion) was heated to 65°C while occasionally mixing for one hour. The heated buffer and LNAdt blocker (Genesphere) was then added to the collected sample, as per manufacturer's instructions. We used the Tecan HS 4800 Pro, an automated hybridization machine to hybridize sample cDNA to the arrays (Tecan). Before the sample injection, the programmed Tecan washed with several solutions containing first 1 × SSC, then 0.1 × SSC 0.014% SDS, then 5 × SSC, 0.01% SDS, and 0.2% BSA. Samples were heated to 80°C for 5 minutes, and then kept at 65°C until injected onto the pre-washed arrays in a Tecan HS 4800 Pro, as per manufacturer's instructions. Microarrays were hybridized for 16 hours. Post-hybridization, arrays were rinsed in the Tecanmodules with increasingly stringent SSC and SDS solutions, starting with 2 × SSC, 0.014%SDS for four washes incrementally decreasing temperature, then one final wash of 0.2 × SSC at 23 °C. Finally, slides were dried with 37 psi nitrogen gas and kept dark until scanned.

scan_protocol: All microarrays were scanned immediately after hybridization was complete using a ScanArray Express (Perkin-Elmer). The microarray images were quantified manually with ImaGene 5.6.1 (BioDiscovery). Spots with unusual morphology, offset, or other poor quality parameters   were flagged as marginal and excluded these from downstream analyses.

data_processing: Only the signal Cy5 channel was considered for this experiment. The reference Cy3 channel was ignored. Normalization was performed using the Limma R package BetweenArrayNormalization function with the Quantile method

organism: Oncorhynchus nerka

label_protocol: Indirect cDNA labeling system kits per manufacturer's instructions. In brief, 10 ug of total RNA from a single individual was combined with a master mix includingreverse-transcriptase and oligo (dT) 20 primers. This reaction was incubated for three hours at 46°C tosynthesize single-stranded cDNA. The samples were  cleaned with the S.N.A.P TM column purification procedure (Invitrogen). A reference pool was prepared with representative total RNA samples of juvenile sockeye muscle and liver, and adult sockeye brain, muscle and liver. Though this reference pool was hybridized to the arrays, this chanel (Cy3) was ignored  fro this experiment and the signal (Cy5)  channel was treated as a single color experiment.    Individual samples and were coupledwith mono-reactive CyDyeTM packs (GE Healthcare). In short, the common reference pool of aRNA was coupled with Cy3 and the individual sockeye muscle tissue cDNA with Cy5 dyes for one hour at 4°C. The samples were then purified to remove all uncoupled dye using S.N.A.P.TM columns as per manufacturer's instructions (Invitrogen). The dye coupled sample and reference were stored at 4°C in the dark until hybridization.

extract_protocol: The samples were thawed and blotted with a Kimwipe®. All of the primary locomotion muscle tissue including red and white muscle tissue was removed from each fish. Total RNA was extracted with a modified protocol of the Invitrogen TRIzol ® Plus RNA purification kit using PureLinkTM Micro-to-MidiTM columns. Disruption and homogenization were achieved with a MixerMill MM301 (Retsch). The manufacturer's protocol was followed for each extraction with the exception of using 150 ul of chloroform and 150 ul of low pH phenol to ensure dissociation of proteins and isolation of RNA. The quality of all RNA samples was verified on a 1% agarose gel. All samples were quantified with a Spectrophotometer ND-1000 (NanoDrop).

tag: development stage

value: spawning

value: muscle

tag: tissue source

value: river


title: Bmal1fxSf-1Cre vs Control 2

description: Sample 2


title: ASBatch2_rhIL21_Nr.16

tag: cell line

tag: treated with

value: rhIL21 for 2hrs


title: R_AJC_606_Muscle

description: SAMPLE 47


title: R_AJC_706_Muscle

description: SAMPLE 48


title: ASBatch2_rhCD40L_A_Nr.10

tag: cell type

value: rhCD40L for 30min

tag: biological replicate


title: R_AJC_406_Muscle

description: SAMPLE 45


title: ASBatch2_Kontrolle_Nr.9

value: none (control)


title: ASBatch2_antiIgM F(ab) fragments_Nr.15

value: antiIgM F(ab) fragments for 3hrs


title: Bmal1fxSf-1Cre vs Control 1

description: Sample 1


title: O_O_507_Muscle

description: SAMPLE 39

value: outlet


title: O_O_707_Muscle

description: SAMPLE 41


title: R_AJC_506_Muscle

description: SAMPLE 46


title: O_O_907_Muscle

description: SAMPLE 42


title: R_AJC_1006_Muscle

description: SAMPLE 43


title: R_AJC_306_Muscle

description: SAMPLE 44


title: ASBatch1_Kontrolle_Nr.1

value: Burkitt Lymphoma cells


title: O_O_407_Muscle

description: SAMPLE 38


title: O_O_307_Muscle

description: SAMPLE 37


title: ASBatch1_LPS_A_Nr.4

value: LPS for 30mins


title: ASBatch1_LPS_B_Nr.5

value: LPS for 6hrs


title: O_O_2006_Muscle

description: SAMPLE 35


title: O_O_607_Muscle

description: SAMPLE 40


title: O_O_207_Muscle

description: SAMPLE 36


title: O_O_1806_Muscle

description: SAMPLE 34


title: ASBatch1_rhIL21_Nr.8


title: Glioma-EORTC26951 A1487_21.CEL

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FFPE

tag: idhmut

value: wt

tag: 1p19q loh

value: no loss

tag: egfr

tag: mgmt

value: meth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: deceased

tag: Sex

value: F

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment

value: pt 1


title: O_O_1506_Muscle

description: SAMPLE 33

tag: gender

value: female

tag: development stage

value: spawning

tag: tissue

value: muscle

tag: tissue source


title: Glioma-EORTC26951 A1487_20.CEL

tag: sample

tag: igs

tag: tcga classification

value: mut

value: LOH

value: alive

tag: age


title: O_O_1406_Muscle

description: SAMPLE 32

value: outlet


title: O_O_107_Muscle

description: SAMPLE 28


title: O_O_1106_Muscle

description: SAMPLE 29


title: ASBatch1_rhCD40L_A_Nr.2

tag: cell line

tag: cell type

value: Burkitt Lymphoma cells

tag: treated with

value: rhCD40L for 30min

tag: biological replicate


title: ASBatch1_antiIgM F(ab) fragments_Nr.7

value: antiIgM F(ab) fragments for 3hrs


title: O_O_1306_Muscle

description: SAMPLE 31


title: ASBatch1_rhCD40L_B_Nr.3

value: rhCD40L for 6hrs


title: O_O_1206_Muscle

description: SAMPLE 30


title: HIV-1 inoculated 2

city: Lincoln

first: Andrew

last: Block

state: Nebraska

address: 4240 Fair Street

department: Department of Biology

institute: University of Nebraska - Lincoln

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: Raw microarray data were processed and analyzed using Affy and Limma packages of Bioconductor, an R package (http://www.bioconductor.org/, http://www.r-project.org/).  The backgrounds were corrected with Robust Multiple-array Average (RMA).  Significance of differentially expressed genes in controls and HIV-1 exposed group were compared with a moderated t-statistic. Significantly altered genes in expression were defined as a log 2 fold change of > 1 or < 1,  P <0.05, and False Discovery Rate of 1.

source_name: Human endocervical epithelial cell line, 4hrs after HIV-1 exposure

label_protocol: standard affymetrix protocol

growth_protocol: Human endocervical epithelial cell line, CRL-2615, was cultured in DMEM supplemented with 10% FBS.

extract_protocol: RNA was extracted using the QIAGEN MicroRNeasy mini kit in accordance with the prescribed protocol provided with the kit.  The mRNA was amplified and labeled with biotin using Ovation WGA System and Ovation Pico WTA System from NuGEN. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: Human endocervical epithelial cell line was inoculated with HIV-1 ME1 and collected 4hrs post exposure

value: endocervical epithelial


title: ASBatch1_rhBAFF_Nr.6

value: rhBAFF for 9hrs


title: Glioma-EORTC26951 A1487_17.CEL

value: glioma

value: C

tag: tissue type

value: FFPE

tag: idhmut

value: wt

tag: 1p19q loh

value: no loss

tag: egfr

tag: mgmt

value: meth

tag: trt

value: RT

tag: ss (y)

tag: event

value: deceased

value: M

value: GBM/AA


title: L_I3_806_Muscle

description: SAMPLE 26

tag: gender

value: female

tag: development stage

value: spawning

tag: tissue

value: muscle

tag: tissue source

value: beach


title: Glioma-EORTC26951 A1487_19.CEL

tag: sample

tag: igs

tag: tcga classification

value: mut

value: RT/PCV

value: alive

tag: age

tag: Sex

value: F

tag: original diagnosis

value: AOA

tag: review diagnosis

value: AOD

tag: experiment

value: pt 1


title: L_I3_706_Muscle

description: SAMPLE 25


title: L_I3_906_Muscle

description: SAMPLE 27


title: HIV-1 inoculated 1

tag: cell line

tag: cell type

value: endocervical epithelial


title: L_I3_407_Muscle

description: SAMPLE 21


title: L_I3_606_Muscle

description: SAMPLE 24


title: L_I3_507_Muscle

description: SAMPLE 23


title: L_I3_307_Muscle

description: SAMPLE 20


title: Glioma-EORTC26951 A1487_14.CEL

value: glioma

value: C

tag: tissue type

value: FFPE

tag: idhmut

value: wt

tag: 1p19q loh

value: no loss

tag: egfr

value: amp

tag: mgmt

value: unmeth

tag: trt


title: L_I3_506_Muscle

description: SAMPLE 22

tag: gender

value: female

tag: development stage

value: spawning

tag: tissue

value: muscle

tag: tissue source


title: Glioma-EORTC26951 A1487_18.CEL

tag: sample

tag: igs

tag: tcga classification

value: mut

value: LOH

value: meth

value: RT

tag: ss (y)

tag: event

value: deceased

tag: age

value: M


title: Negative control 2

source_name: Human endocervical epithelial cell line, control

tag: cell line

tag: cell type

value: endocervical epithelial


title: L_I3_206_Muscle

description: SAMPLE 18

value: beach


title: Negative control 1


title: L_I3_107_Muscle

description: SAMPLE 17


title: Glioma-EORTC26951 A1487_10.CEL

value: glioma

value: C

tag: tissue type

value: RT/PCV

value: alive

tag: Sex

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment

value: pt 1


title: Glioma-EORTC26951 A1487_11.CEL

value: FFPE

tag: idhmut

tag: 1p19q loh

tag: egfr

value: wt

tag: mgmt

tag: trt

value: F


title: L_I3_207_Muscle

description: SAMPLE 19

tag: gender

value: female

tag: development stage

value: spawning

tag: tissue

value: muscle

tag: tissue source


title: L_I3_1006_Muscle

description: SAMPLE 15


title: L_I3_106_Muscle

description: SAMPLE 16


title: Glioma-EORTC26951 A1487_13.CEL

tag: sample

tag: igs

tag: tcga classification

value: RT

tag: ss (y)

tag: event

tag: age

value: AOA


title: ASBatch2_rhBAFF_Nr.14

tag: cell line

tag: cell type

value: Burkitt Lymphoma cells

tag: treated with

value: rhBAFF for 9hrs

tag: biological replicate


title: Glioma-EORTC26951 A1487_07.CEL

tag: tissue type

tag: idhmut

value: mut

tag: 1p19q loh

value: no loss

value: deceased

tag: Sex

value: M

tag: original diagnosis

tag: review diagnosis

tag: experiment


title: L_I2AM_407_Muscle

description: SAMPLE 13

tag: gender

tag: development stage

tag: tissue

tag: tissue source

value: beach


title: L_I2AM_307_Muscle

description: SAMPLE 12


title: L_I2AM_507_Muscle

description: SAMPLE 14


title: Glioma-EORTC26951 A1487_12.CEL

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

tag: egfr

tag: mgmt

value: meth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: AOD


title: Glioma-EORTC26951 A1487_05.CEL

tag: tissue type

value: FFPE

tag: cimp

value: CIMP+

tag: idhmut

value: wt

tag: 1p19q loh

value: LOH

tag: age

value: F

value: pt 1


title: Glioma-EORTC26951 A1487_04.CEL

value: CIMP-

value: amp

value: RT

tag: Sex

tag: original diagnosis

tag: review diagnosis

tag: experiment


title: L_I2_307_Muscle

description: SAMPLE 8

tag: gender

value: female

tag: development stage

value: spawning

tag: tissue

value: muscle

tag: tissue source


title: L_I2_407_Muscle

description: SAMPLE 9

value: beach


title: L_CS8_507_Muscle

description: SAMPLE 5


title: L_I2_507_Muscle

description: SAMPLE 10


title: L_I2_107_Muscle

description: SAMPLE 6


title: Glioma-EORTC26951 A1487_02.CEL

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

value: mut

tag: egfr

tag: mgmt

value: deceased

value: M


title: L_I2_207_Muscle

description: SAMPLE 7


title: Glioma-EORTC26951 A1372_85.CEL

tag: tissue type

value: FFPE

value: no loss

value: meth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: AOA


title: Glioma-EORTC26951 A1487_03.CEL

tag: 1p19q loh

tag: age

tag: Sex

value: AOD

value: pt 1


title: L_CS8_207_Muscle

description: SAMPLE 2


title: L_I2AM_207_Muscle

description: SAMPLE 11


title: L_CS8_407_Muscle

description: SAMPLE 4


title: L_CS8_307_Muscle

description: SAMPLE 3


title: L_CS8_107_Muscle

description: SAMPLE 1


title: ADMEC_2

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

institute: Centro di Riferimento Oncologico

description: Gene expression after isolation and maintenance in culture

hyb_protocol: 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v107_Sep09 and Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Endothelial cells from human skin

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

growth_protocol: DECs were isolated, characterized, and seeded on 12,5 cm2 flask precoated with 2µg/cm2 fibronectin and maintained in endothelial serum free basal medium supplemented with 20ng/ml bFGF, 10ng/ml EGF, 10% human serum. ADMECs were isolated and seeded on 12,5 cm2 flask precoated with 2µg/cm2 fibronectin in Medium 199 supplemented with 10% New Born Calf Serum, 10% human serum, cAMP 25ug/ml, hydrocortisone 1ug/ml, heparin 50ug/ml and EGF 10ng/ml.

extract_protocol: Total RNAs were purified with euroGOLDtrifast reagents

value: Skin


title: ADMEC_3

value: female


title: Ler wild-type flower buds, biological replicate 1

city: University Park

first: Dihong

last: Lu

state: PA

address: 416 Life Sciences Building

institute: Penn state university

description: Ler unopened flower buds

hyb_protocol: Prepare hybridization cocktail using the GeneChip Hybridization Wash and Stain Kit (#702232) and hybridize arrays according to the manufacturer’s instructions in the Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Microarray datasets (.CEL files) were normalized by R package RMA and exported as Excel files

organism: Arabidopsis thaliana

source_name: Ler wild-type, unopened flower buds

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Plants were grown in soil for about 5-6 weeks until unopened flower buds were collected.

extract_protocol: Ler and ask1 flower bud total RNA was extracted using the NucleoSpin® RNA Plant kit (MACHEREY-NAGEL).

treatment_protocol: not applicable

tag: genotype/variation

value: Ler

value: unopened flower buds


title: Ler wild-type flower buds, biological replicate 2

description: Ler unopened flower buds


title: Glioma-EORTC26951 A1372_82.CEL

tag: cimp

value: CIMP-

value: wt

value: alive

value: F

tag: original diagnosis

tag: review diagnosis

tag: experiment


title: Glioma-EORTC26951 A1372_83.CEL

tag: tissue

value: glioma

tag: sample

value: P

tag: idhmut

value: mut

value: RT

value: deceased


title: ask1 mutant flower buds, biological replicate 3

description: ask1-/- mutant unopened flower buds

source_name: ask1-/-, unopened flower buds


title: DEC_3

source_name: Endothelial cells from decidual

value: Decidua

tag: gender


title: ADMEC_1


title: Glioma-EORTC26951 A1372_81.CEL

tag: igs

tag: tcga classification

value: C

value: FF

value: RT/PCV

value: M


title: Glioma-EORTC26951 A1372_80.CEL

tag: tissue type

value: no loss

tag: egfr

value: amp

tag: mgmt

value: meth

tag: trt

value: AOD

value: pt 1


title: Glioma-EORTC26951 A1372_84.CEL

value: FFPE

value: wt

tag: 1p19q loh

tag: ss (y)

tag: event

tag: age


title: Glioma-EORTC26951 A1372_79.CEL

value: glioma

tag: Sex

tag: original diagnosis

value: LGG


title: DEC_2

value: female


title: DEC_1


title: Glioma-EORTC26951 A1372_78.CEL

value: unmeth

tag: review diagnosis

tag: experiment


title: ask1 mutant flower buds, biological replicate 1

description: ask1-/- mutant unopened flower buds

tag: genotype/variation

tag: tissue

value: unopened flower buds


title: Glioma-EORTC26951 A1372_76.CEL

tag: sample

value: P

tag: idhmut

value: mut

value: RT

value: deceased

value: F


title: ask1 mutant flower buds, biological replicate 2

description: ask1-/- mutant unopened flower buds


title: normal colon 21

type: genomic

city: Moscow

first: Vladimir

last: Naumov

address: Malaya Pirogovskaya 1a

department: Molecular Biology

country: Russia

institute: Research Institute of Physico-Chemical Medicine

description: Genomic DNA extracted from normal colon and colon adenocarcinoma samples was genotyped using Illumina HumanOmni1-Quad BeadChip (Illumina).

hyb_protocol: standard Illumina protocol

data_processing: GenomeStudio software was used for data processing

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: normal colon

label_protocol: standard Illumina protocol

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using Promega DNA purification kit (cat #A1120)

value: normal colon

tag: subject


title: WT, R. solani AG2-1 treated, biological rep 2

city: Floreat

first: Rhonda

last: Foley

address: Underwood Ave

department: Plant Industry

country: Australia

institute: CSIRO

description:
WT_AG2-1 -2
af1c1759-1-C2-170908

Gene expression data from one-week-old WT seedlings + 7 days of R. solani AG2-1.

hyb_protocol: cRNA was hybridized to the GeneChip® Arabidopsis ATH1 Genome Array using a GeneChip instrument system with scanner 3000 7G and autoloader for expression array processing and analysis, following the manufacturer's protocol. Hybridization was performed at the Australian Genome Research Facility Ltd. (Melbourne, Victoria, Australia).

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: The raw data files underwent background correction, normalization, probe specific correction, and summary value computation using the Robust Multichip Average (RMA) method in the Bioconductor package.

source_name: one-week-old seedlings + 7 days of R.solani AG2-1 infection

label_protocol: Whole plant RNA (15ug for each sample) was sent to the Australian Genome Research Facility Ltd. (Melbourne, Victoria, Australia) for labelling. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Col-0 seedlings were grown on vertical MS plates.

extract_protocol: Three biological repeats of 100mg seedling tissue from the non-infected control, AG8- and AG2-1-treated plants were obtained. RNA was extracted using the Qiagen RNA easy kit following the manufacturer’s protocol.

treatment_protocol: One-week-old seedlings grown on vertical MS plates were treated by touching the root/crown region by a toothpick containing mycelia from R. solani grown on PDA. At the same time, GSTF8::luciferase transgenic plants were grown on MS plates with luciferin, and luciferase activity was measured at day 0, 3, 4, 5, 6, 7 and 10 days. Based on a measurement of maximum GSTF8::luciferase activity, whole seedlings were collected seven days after treatment. Three biological replicates were used for each treatment.

tag: ecotype

tag: genotype

value: wild-type

value: 2 weeks

value: whole seedling

tag: treatment

value: Rhizoctonia solani AG2-1


title: Glioma-EORTC26951 A1372_77.CEL

source_name: Glioma, clinical trial RT v RT+PCV

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FFPE

tag: cimp

value: CIMP+

value: no loss

tag: egfr

tag: trt

value: M

value: AOA

value: pt 1


title: normal colon 22

scan_protocol: standard Illumina protocol


title: colon adenocarcinoma 21

source_name: colon adenocarcinoma

value: colon adenocarcinoma


title: Glioma-EORTC26951 A1372_75.CEL

value: glioma

tag: 1p19q loh

tag: ss (y)

tag: event

tag: age

tag: Sex

tag: original diagnosis

value: AOD

value: GBM/AA


title: WT, R. solani AG2-1 treated, biological rep 1

description:
WT_AG2-1 -1
af1c1759-1-C1-170908

Gene expression data from one-week-old WT seedlings + 7 days of R. solani AG2-1.

tag: tissue


title: colon adenocarcinoma 19

tag: subject


title: Glioma-EORTC26951 A1372_73.CEL

tag: sample

value: RT/PCV

value: deceased

tag: review diagnosis

value: LGG

tag: experiment


title: WT, R. solani AG2-1 treated, biological rep 3

description:
WT_AG2-1 -3
af1c1759-1-C3-170908

Gene expression data from one-week-old WT seedlings + 7 days of R. solani AG2-1.

tag: ecotype

tag: genotype

value: wild-type

value: 2 weeks

tag: treatment


title: Glioma-EORTC26951 A1372_71.CEL

tag: igs

tag: tcga classification

tag: tissue type

value: amp

tag: mgmt

value: unmeth

value: RT


title: colon adenocarcinoma 18


title: Glioma-EORTC26951 A1372_72.CEL

value: C

value: FFPE

tag: 1p19q loh

tag: egfr

value: wt

tag: trt

tag: ss (y)


title: Glioma-EORTC26951 A1372_74.CEL

value: LOH

tag: event

tag: age

tag: Sex

value: M

tag: original diagnosis

value: AOA


title: Reh cells_valproic acid and bortezomib_12h

city: Berlin

first: Shabnam

last: Shalapour

address: Augustenburger Platz 1

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent)

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent). Further data analysis was performed using the Partek® Genomics Suits software, version 6.5 beta © 2009 (Partek Inc., USA).

source_name: Reh cells, treatment with valproic acid and bortezomib

label_protocol: Labeling was performed according to the protocol using the Agilent Low Input Quick Amp Labeling Kit (Agilent)

growth_protocol: RPMI 1640 Medium, 10%FCS, 1%Pen/Strep, 37°C, 5%CO2

extract_protocol: mRNA was extracted by using the RNeasy Kit (Quiagen).

treatment_protocol: Reh cells were seeded at a denstity of 1x10E06 cells/ml in 12 well plates with corresponding drugs added from 100x stock solutions to achieve final concentrations.

tag: cell line

value: Reh

tag: tissue

value: leukoblasts


title: normal colon 18

value: normal colon

tag: subject


title: colon adenocarcinoma 20

value: colon adenocarcinoma


title: normal colon 20


title: normal colon 19


title: colon adenocarcinoma 17


title: Glioma-EORTC26951 A1372_70.CEL

value: glioma

tag: sample

tag: idhmut

value: no loss

value: RT/PCV

value: deceased

value: F

value: AOD

tag: review diagnosis

tag: experiment

value: pt 1


title: WT, R. solani AG8 treated, biological rep 3

description:
WT_AG8-3
af1c1682-4-b3-210808

Gene expression data from one-week-old WT seedlings + 7 days of R. solani AG8.

source_name: one-week-old seedlings + 7 days of R.solani AG8 infection

tag: ecotype

tag: genotype

value: wild-type

value: 2 weeks

value: whole seedling

tag: treatment

value: Rhizoctonia solani AG8


title: Reh cells_valproic acid_12h

source_name: Reh cells, treatment with valproic acid, 12h


title: WT, control treated, biological rep 3

description:
WT_control-3
af1c1682-1-a3-210808

Gene expression data from one-week-old WT seedlings + 7 days of non-infected control.

source_name: one-week-old seedlings + 7 days of non-infected control

value: mock


title: colon adenocarcinoma 22


title: normal colon 17


title: WT, R. solani AG8 treated, biological rep 2

description:
WT_AG8-2
af1c1682-4-b2-210808

Gene expression data from one-week-old WT seedlings + 7 days of R. solani AG8.


title: Glioma-EORTC26951 A1372_68.CEL

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FFPE

value: wt

tag: 1p19q loh

value: LOH

tag: egfr

value: alive

value: M


title: Reh cells_control_12h

source_name: Reh cells, treatment control, 12h

value: Reh

value: leukoblasts


title: WT, R. solani AG8 treated, biological rep 1

description:
WT_AG8-1
af1c1682-4-b1-210808

Gene expression data from one-week-old WT seedlings + 7 days of R. solani AG8.

tag: age


title: WT, control treated, biological rep 2

description:
WT_control-2
af1c1682-1-a2-210808

Gene expression data from one-week-old WT seedlings + 7 days of non-infected control.


title: colon adenocarcinoma 16

value: colon adenocarcinoma


title: MG1655, heat shock, biological rep 3

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

description: 5 min at 45˚C

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009).
The log10 mRNA concentration (pM) data are provided as a supplementary file on the SERIES record.

organism: Escherichia coli

source_name: heat shock response in the minimal medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 108 cells/mL within the exponential growth phase.

extract_protocol: Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions.

treatment_protocol: The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use.

tag: strain

value: MG1655 (parent)

tag: growth protocol

value: heat shock


title: MG1655, heat shock, biological rep 2

description: 5 min at 45˚C


title: MG1655, heat shock, biological rep 1

description: 5 min at 45˚C


title: Glioma-EORTC26951 A1372_66.CEL

tag: tissue

value: glioma

tag: cimp

value: CIMP-

value: no loss

value: amp

tag: trt

value: RT

tag: ss (y)

tag: event

value: deceased

tag: Sex

value: F

tag: original diagnosis

value: AOD

value: pt 1


title: Glioma-EORTC26951 A1372_67.CEL

tag: sample

value: FF

value: CIMP+

tag: idhmut

value: mut

value: LOH

value: wt

value: RT/PCV

tag: review diagnosis

value: LGG

tag: experiment


title: 252800411749-2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: miR-199a-5p (2)

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing (version 10.7.3.1)

label_protocol:
Agilent - Low RNA input QuickAmp
Amplification protocol: cRNA Agilent

extract_protocol: Trizol+RNeasy+Minelute

tag: cell type

value: HFL1 fibroblast

tag: amount in (µg)

tag: rin number


title: 252800411760-5

description: Control (1)

source_name: Control (1)


title: colon adenocarcinoma 15

value: colon adenocarcinoma

tag: subject


title: 252800411760-6

description: Control (2)

source_name: Control (2)


title: normal colon 15

value: normal colon


title: MG1655, biological rep 7

description: final cell concentration ~ 10^8 cells/mL

source_name: MG1655 exponentially grown in the minimal medium

tag: strain

value: MG1655 (parent)

value: steady growth


title: 252800411760-7

description: TGFbeta (1)

source_name: TGFbeta (1)


title: Reh cells_bortezomib_12h

source_name: Reh cells, treatment with bortezomib, 12h

tag: cell line

value: Reh

value: leukoblasts


title: MG1655, biological rep 6

tag: growth protocol


title: Glioma-EORTC26951 A1372_63.CEL

tag: tissue

value: glioma

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FFPE

tag: cimp

value: CIMP-

tag: 1p19q loh

value: no loss

tag: egfr

value: RT

value: deceased

tag: age

value: F


title: 252800411749-1

description: miR-Neg (2)

source_name: miR-Neg (2)


title: normal colon 16


title: Glioma-EORTC26951 A1372_65.CEL

tag: sample

tag: idhmut

value: wt

tag: trt

tag: ss (y)

tag: event

tag: Sex

value: M

tag: original diagnosis

value: AOA

tag: review diagnosis

value: AOD

value: pt 1


title: colon adenocarcinoma 14

value: colon adenocarcinoma

tag: subject


title: MG1655, biological rep 5

tag: strain

value: MG1655 (parent)

tag: growth protocol

value: steady growth


title: 252800411760-8

description: TGFbeta (2)

source_name: TGFbeta (2)

tag: cell type

value: HFL1 fibroblast

tag: amount in (µg)

tag: rin number


title: Glioma-EORTC26951 A1372_64.CEL

tag: tissue

value: glioma

tag: igs

tag: tcga classification

tag: tissue type

value: mut

tag: 1p19q loh

tag: mgmt

value: meth

value: RT/PCV

tag: experiment


title: Glioma-EORTC26951 A1372_62.CEL

tag: sample

value: C

value: FFPE

tag: cimp

value: CIMP+

tag: idhmut

value: no loss

tag: egfr

value: amp

tag: trt

tag: ss (y)

tag: event

tag: age

value: GBM/AA


title: Glioma-EORTC26951 A1372_60.CEL

value: CIMP-

value: wt

value: RT

value: deceased

tag: Sex

value: M

tag: original diagnosis

tag: review diagnosis

value: AOA


title: MG1655, biological rep 4

tag: strain

value: MG1655 (parent)

tag: growth protocol

value: steady growth


title: MG1655, biological rep 3


title: normal colon 14

source_name: normal colon

tag: tissue

value: normal colon

tag: subject


title: WT, control treated, biological rep 1

description:
WT_control-1
af1c1682-1-a1-210808

Gene expression data from one-week-old WT seedlings + 7 days of non-infected control.

tag: ecotype

tag: genotype

value: wild-type

value: 2 weeks

value: whole seedling

tag: treatment

value: mock


title: 252800411749-7

tag: cell type

value: HFL1 fibroblast

tag: amount in (µg)

tag: rin number


title: 252800411749-6

description: Si-Neg (2)

source_name: Si-Neg (2)


title: Glioma-EORTC26951 A1372_61.CEL

source_name: Glioma, clinical trial RT v RT+PCV

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FFPE

tag: cimp

tag: idhmut

tag: 1p19q loh

value: no loss

tag: egfr

tag: trt

value: F

value: AOD

tag: experiment

value: pt 1


title: 252800411749-5


title: MG1655, biological rep 2

tag: strain

tag: growth protocol


title: 252800411748-1


title: colon adenocarcinoma 13

source_name: colon adenocarcinoma

tag: tissue

value: colon adenocarcinoma

tag: subject


title: MG1655, biological rep 1


title: Glioma-EORTC26951 A1372_57.CEL

value: wt

value: RT

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

tag: original diagnosis

tag: review diagnosis

value: GBM/AA


title: Glioma-EORTC26951 A1372_58.CEL

tag: sample

tag: igs

tag: tcga classification

tag: tissue type

value: CIMP-

value: RT/PCV


title: MDS42, heat shock, biological rep 3

description: 5 min at 45˚C

value: MDS42 (genome reduced)

value: heat shock


title: 252800411748-2

description: miR-199a-5p (1)

tag: cell type

value: HFL1 fibroblast

tag: amount in (µg)

tag: rin number


title: Glioma-EORTC26951 A1372_56.CEL

value: glioma

tag: cimp

tag: idhmut

tag: 1p19q loh

tag: egfr

value: amp

tag: trt

value: M

value: AOA

tag: experiment


title: MDS42, heat shock, biological rep 2

description: 5 min at 45˚C

tag: strain

tag: growth protocol


title: 252800411748-5

description: miR-21 (1)


title: normal colon 11

tag: tissue

value: normal colon

tag: subject


title: 252800411748-6

description: Si-Neg (1)

source_name: Si-Neg (1)


title: Glioma-EORTC26951 A1372_55.CEL

tag: sample

value: C

value: FFPE

value: mut

value: no loss

tag: mgmt

value: meth

tag: ss (y)

tag: event

tag: age

tag: Sex

tag: original diagnosis

value: AOD

tag: review diagnosis


title: colon adenocarcinoma 12

value: colon adenocarcinoma


title: Glioma-EORTC26951 A1372_53.CEL

tag: igs

tag: tcga classification

tag: tissue type

value: wt

value: deceased

value: pt 1


title: normal colon 13


title: Glioma-EORTC26951 A1372_52.CEL

tag: cimp

value: CIMP-

tag: idhmut

tag: 1p19q loh

tag: egfr

tag: trt

value: RT

value: F


title: 252800411748-7

description: Si-CAV1 (1)

source_name: Si-CAV1 (1)

tag: cell type

value: HFL1 fibroblast

tag: amount in (µg)

tag: rin number


title: non-Cancer stem like cell 2

city: Seoul

first: Young Dong

last: Yoo

address: 28 Yeon-gun dong Jongnogu

country: South Korea

institute: Seoul National University

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human HT-12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing:
Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)).
Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using LPE test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: MDA-MB453 (breast cancer cell line)

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: Cells were cultured in Dulbecco’s Modified MEM (DMEM) supplemented with 10% FBS

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

tag: marker

value: GFP-negative

value: non-Cancer stem like cell


title: colon adenocarcinoma 11

tag: tissue

tag: subject


title: Glioma-EORTC26951 A1372_50.CEL

value: glioma

tag: sample

value: LOH

value: RT/PCV

tag: ss (y)

tag: event

tag: age

tag: Sex

value: AOA

tag: experiment


title: non-Cancer stem like cell 1


title: colon adenocarcinoma 9


title: Glioma-EORTC26951 A1372_49.CEL

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FFPE

value: mut

value: no loss

tag: mgmt

value: M

tag: original diagnosis

tag: review diagnosis

value: GBM/AA


title: Glioma-EORTC26951 A1372_51.CEL

tag: idhmut

value: wt

tag: 1p19q loh

value: meth

tag: trt

value: alive

value: AOD

value: pt 1


title: normal colon 12

tag: tissue

value: normal colon


title: MDS42, biological rep 6

source_name: MDS42 exponentially grown in the minimal medium

tag: strain

value: MDS42 (genome reduced)

tag: growth protocol

value: steady growth


title: MDS42, biological rep 7


title: MDS42, biological rep 5


title: normal colon 10

tag: subject


title: Glioma-EORTC26951 A1372_47.CEL

value: glioma

tag: sample

tag: egfr

value: RT

tag: ss (y)

tag: event

value: deceased


title: normal colon 9


title: Glioma-EORTC26951 A1372_48.CEL

tag: igs

value: C

value: RT/PCV

tag: age

tag: Sex

value: AOA

tag: experiment


title: MDS42, heat shock, biological rep 1

description: 5 min at 45˚C

value: heat shock


title: MDS42, biological rep 4


title: MDS42, biological rep 3


title: colon adenocarcinoma 8

value: colon adenocarcinoma


title: colon adenocarcinoma 10


title: Cancer stem like cell 2

tag: marker

value: GFP-positive

tag: cell type

value: Cancer stem like cell


title: Cancer stem like cell 1


title: MDS42, biological rep 2


title: SW1736_t48h_rep2

city: New York

first: Cristina

last: Montero-Conde

state: NY

department: HOPP

institute: MSKCC

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Partek GS Software

source_name: thyroid cancer cell line

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

growth_protocol: Cells were growth in RPMI growth media supplemented with 10% of fetal bovine serum, 2 mM glutamine, 50 U/ml penicillin and 50 ug/ml streptomycin.

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

treatment_protocol: Cell were untreated or treated with 2 uM vemurafenib for 1, 6 or 48 h.

tag: cell line

tag: time point

tag: mutation

tag: treatment

value: treated with 2 uM vemurafenib for 48 h


title: SW1736_t48h_rep3

description: replicate 3


title: MDS42, biological rep 1

tag: strain


title: colon adenocarcinoma 6

tag: tissue


title: normal colon 6

tag: subject


title: normal colon 8


title: 353238-1

description:
balb pbs 14j-3
Date:2009/05/15

hyb_protocol: Agilent : 20000.0 ng at 53 degree_C during 24 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : none, Background norm. : none, Software used : onechannelgui --> VALUE data obtained from average signal.

source_name: balb pbs 14j-3

label_protocol: Invitrogen - Ulysis

extract_protocol: Chomzynski

tag: agent

value: PBS

value: lung

value: BALB/c


title: SW1736_t48h_rep1

description: replicate 1


title: 353238-2

description:
balb bleo 14j-3
Date:2009/05/15

source_name: balb bleo 14j-3

value: bleomycin


title: SW1736_t6h_rep3

description: replicate 3

value: treated with 2 uM vemurafenib for 6 h


title: SW1736_t6h_rep2

description: replicate 2


title: colon adenocarcinoma 7


title: Glioma-EORTC26951 A1372_43.CEL

data_processing: RMA

tag: sample

tag: tcga classification

tag: tissue type

value: FFPE

tag: idhmut

value: wt

tag: 1p19q loh

value: LOH

tag: mgmt

value: meth

tag: trt

value: M

tag: original diagnosis

value: AOD

tag: review diagnosis

value: pt 1


title: SW1736_t6h_rep1

description: replicate 1

tag: cell line


title: colon adenocarcinoma 5


title: 352959-1

description:
balb pbs 7j-2
Date:2009/05/15

source_name: balb pbs 7j-2

tag: time point


title: normal colon 5

value: normal colon


title: Glioma-EORTC26951 A1372_46.CEL

value: glioma

tag: igs

value: C

value: mut

value: no loss

tag: egfr

value: RT/PCV

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

value: AOA

tag: experiment


title: Glioma-EORTC26951 A1372_45.CEL

tag: tissue

tag: sample

tag: tcga classification

value: RT

value: F

value: GBM/AA


title: 352959-2

description:
balb bleo 7j-2
Date:2009/05/15

source_name: balb bleo 7j-2

tag: agent

value: bleomycin

value: lung

tag: strain

value: BALB/c


title: normal colon 7

tag: subject


title: 353244-1

description:
balb pbs 14j-2
Date:2009/05/15

source_name: balb pbs 14j-2

value: PBS


title: 352979-1

description:
c57 pbs 7j-1
Date:2009/05/15

source_name: c57 pbs 7j-1


title: normal colon 4


title: Glioma-EORTC26951 A1372_40.CEL

tag: tissue type

value: FFPE

tag: idhmut

tag: 1p19q loh

value: LOH

value: wt

tag: trt

tag: original diagnosis

value: AOD

value: LGG


title: Glioma, clinical trial RT v RT+PCV 246

hyb_protocol: Hybridization was performed according to the manufacturers instructions

data_processing: unnormalized data was used to classify samples into one of the intrinsic glioma subtypes. Quantile normalization performed in R

label_protocol: labelling was performed according to the manufacturers instructions

extract_protocol: Qiagen Rneasy

value: glioma

tag: igs

value: mut

tag: egfr

value: amp

tag: mgmt

value: meth

tag: review diagnosis

value: pt 6


title: Glioma-EORTC26951 A1372_42.CEL

label_protocol: cDNA synthesis and cRNA labeling was done using the alternative protocol for one-cycle cDNA synthesis.Biotin-labeled cRNA was generated using the ENZO Highyield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). Affymetrix (Santa Clara, CA)

extract_protocol: Trizol

value: C

value: RT/PCV

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

value: AOA

value: pt 1


title: Glioma-EORTC26951 A1372_44.CEL

tag: tissue

tag: sample

tag: tcga classification

value: RT

value: M

tag: experiment


title: SW1736_t1h_rep2

description: replicate 2

tag: cell line

tag: time point

tag: mutation

tag: treatment

value: treated with 2 uM vemurafenib for 1 h


title: SW1736_t1h_rep3

description: replicate 3


title: SW1736_t1h_rep1

description: replicate 1


title: Glioma-EORTC26951 A1372_39.CEL

tag: tissue type

value: FFPE

tag: 1p19q loh

value: no loss

tag: trt

tag: original diagnosis


title: 353244-2

description:
balb bleo 14j-2
Date:2009/05/15

source_name: balb bleo 14j-2

tag: agent

value: bleomycin

value: lung

tag: strain

value: BALB/c


title: Glioma, clinical trial RT v RT+PCV 291

value: glioma

tag: igs

tag: idhmut

value: mut

value: LOH

tag: egfr

value: wt

tag: mgmt

tag: ss (y)

tag: event

value: alive

value: AOD

tag: review diagnosis


title: Glioma-EORTC26951 A1372_41.CEL

tag: tissue

tag: sample

tag: tcga classification

value: C

value: deceased

tag: age

tag: Sex

value: F

value: LGG

tag: experiment


title: 7th time point of the Time-course Replicate 3

city: Paris

first: AGIER

last: nicolas

address: 15 rue de l'école de médecine

department: microorganism genomic

institute: CNRS-UPMC

description: Biological replicate 3 of 3, seventh sample of the time-course. G1 is the reference where there is no replication. Sample is the seventh time for which replication is happening.

hyb_protocol: 500ng of G1 and sample labeled DNA were competitively hybridized on 2x105K Agilent custom microarrays, Hybridization (40 hours) and washing were performed using Agilent Oligonucleotide ArrayBased CGH protocol

scan_protocol: Microarrays were scanned using Axon 4000B scanner (5µm resolution, PMT 700-550) Data were extracted with Genepix 6,0,1,00 software

data_processing: For each time point, the fluorescent signals for eahc probe (F635 and F532) were normalised using the median fluorescent signals of the corresponding microarray and scaled using the mean DNA content for the corresponding time point (Calculated by flow cytometry analysis). Then, for eahc probe, processed ratios were calculated from the scaled ratios by adjusting the lowest and the highest ratio value between 1 and 2, respectively.

organism: Lachancea kluyveri

label_protocol: 2µg of DNA from G1 arrested cells and samples were labeled with respectively Cy3 or Cy5 fluorescent dye (GE Healthcare), using the Bioprime DNA labeling kit (Invitrogen) and following the manufacturer' protocol

growth_protocol: Cells were grown in YPD medium (1% peptone, 1% Yeast extract, 2% glucose)

extract_protocol: genomic DNA was extracted using the genomic-tip 20/G isolation kit (Qiagen)

tag: time point

value: 60 min

tag: origin

value: Cell culture


title: Glioma-EORTC26951 A1372_38.CEL

city: Rotterdam

first: Pim

last: French

institute: Erasmus MC

tag: tissue type

value: FFPE

tag: 1p19q loh

tag: trt

value: RT

value: M

tag: original diagnosis

value: pt 1


title: SW1736_t0h_rep3

description: replicate 3

tag: cell line

tag: mutation

tag: treatment

value: untreated


title: 352979-2

description:
c57 bleo 7j-1
Date:2009/05/15

source_name: c57 bleo 7j-1

tag: agent

value: bleomycin

value: lung

tag: strain


title: 352981-1

description:
c57 pbs 7j-3
Date:2009/05/15

source_name: c57 pbs 7j-3

value: PBS

tag: tissue


title: Glioma-EORTC26951 A1372_37.CEL

value: glioma

tag: sample

tag: igs

tag: idhmut

value: mut

value: LOH

tag: egfr

value: wt

value: RT/PCV

tag: ss (y)

tag: event

tag: review diagnosis


title: 352981-2

description:
c57 bleo 7j-3
Date:2009/05/15

source_name: c57 bleo 7j-3

tag: time point


title: Glioma-EORTC26951 A1372_36.CEL

source_name: Glioma, clinical trial RT v RT+PCV

tag: tcga classification

value: C

tag: tissue type

tag: 1p19q loh

value: no loss

value: deceased

tag: age

tag: Sex

value: F

value: AOD

tag: experiment


title: 5th time point of the Time-course Replicate 3

description: Biological replicate 3 of 3, fifth sample of the time-course. G1 is the reference where there is no replication. Sample is the fifth time for which replication is happening.

value: 50 min

tag: origin

value: Cell culture


title: Glioma-EORTC26951 A1372_34.CEL

value: FFPE

value: amp

tag: trt

value: M

tag: original diagnosis

value: pt 1


title: SW1736_t0h_rep1

description: replicate 1

tag: cell line

tag: mutation

tag: treatment

value: untreated


title: 352993-2

description:
balb bleo 7j-1
Date:2009/05/15

source_name: balb bleo 7j-1

tag: agent

value: bleomycin

tag: tissue

value: lung

tag: strain

value: BALB/c


title: 3rd time point of the Time-course Replicate 3

description: Biological replicate 3 of 3, third sample of the time-course. G1 is the reference where there is no replication. Sample is the third time for which replication is happening.

value: 35 min


title: colon adenocarcinoma 3

source_name: colon adenocarcinoma

value: colon adenocarcinoma

tag: subject


title: SKMEL28_t48h_rep3

description: replicate 3

source_name: melanoma cell line

tag: time point

value: treated with 2 uM vemurafenib for 48 h


title: 4th time point of the Time-course Replicate 3

description: Biological replicate 3 of 3, fourth sample of the time-course. G1 is the reference where there is no replication. Sample is the fourth time for which replication is happening.

value: 40 min


title: SKMEL28_t48h_rep1

description: replicate 1


title: Glioma-EORTC26951 A1372_35.CEL

description: Abbreviations: IGS: intrinsic glioma subtype; Trt: treatment; SS: survival in years; C: classical; P: proneural; M: mesenchymal; N:neural

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

tag: idhmut

value: mut

value: no loss

tag: egfr

value: wt

tag: mgmt

value: meth

value: RT

tag: ss (y)

tag: event

value: deceased

tag: review diagnosis

value: AOA


title: 8th time point of the Time-course Replicate 3

description: Biological replicate 3 of 3, eigth sample of the time-course. G1 is the reference where there is no replication. Sample is the eigth time for which replication is happening.

value: 71 min

tag: origin

value: Cell culture


title: SKMEL28_t48h_rep2

description: replicate 2

tag: cell line

tag: mutation


title: SKMEL28_t6h_rep3

description: replicate 3

tag: treatment

value: treated with 2 uM vemurafenib for 6 h


title: 352993-1

description:
balb pbs 7j-1
Date:2009/05/15

source_name: balb pbs 7j-1

tag: agent

value: PBS

tag: tissue

value: lung

value: BALB/c


title: SW1736_t0h_rep2

description: replicate 2

value: untreated


title: normal colon 1

description: Genomic DNA extracted from normal colon and colon adenocarcinoma samples was genotyped using Illumina HumanOmni1-Quad BeadChip (Illumina).

source_name: normal colon

value: normal colon

tag: subject


title: 352995-1

description:
c57 pbs 14j-4
Date:2009/05/15

tag: time point

tag: strain


title: Glioma-EORTC26951 A1372_31.CEL

value: glioma

tag: sample

tag: igs

tag: tissue type

value: FFPE

tag: 1p19q loh

value: LOH

tag: trt

tag: age

tag: Sex

value: M

tag: original diagnosis

value: AOD

tag: experiment

value: pt 1


title: colon adenocarcinoma 2

value: colon adenocarcinoma


title: normal colon 3


title: colon adenocarcinoma 1


title: 353228-1

description:
c57 pbs 14j-1
Date:2009/05/15


title: Glioma-EORTC26951 A1372_33.CEL

tag: tcga classification

value: C

tag: idhmut

value: wt

tag: egfr

tag: mgmt

value: meth

value: RT

tag: ss (y)

tag: event

value: deceased

tag: review diagnosis


title: 353228-2

description:
c57 bleo 14j-1
Date:2009/05/15

source_name: c57 bleo 14j-1

tag: agent

value: bleomycin

tag: time point

tag: tissue

tag: strain


title: 1st time point of the Time-course Replicate 3

description: Biological replicate 3 of 3, first sample of the time-course. G1 is the reference where there is no replication. Sample is the first time for which replication is happening.

value: 25 min

tag: origin

value: Cell culture


title: colon adenocarcinoma 4

tag: subject


title: SKMEL28_t6h_rep2

description: replicate 2

tag: cell line

tag: mutation

tag: treatment

value: treated with 2 uM vemurafenib for 6 h


title: 353230-1

description:
c57 pbs 14j-3
Date:2009/05/15

value: PBS

value: lung


title: normal colon 2

value: normal colon


title: SKMEL28_t6h_rep1

description: replicate 1


title: Glioma-EORTC26951 A1372_32.CEL

value: glioma

tag: sample

tag: igs

tag: tissue type

value: FFPE

value: mut

tag: 1p19q loh

value: no loss

tag: trt

value: RT/PCV

tag: age

tag: Sex

value: F

tag: original diagnosis

tag: experiment


title: SKMEL28_t1h_rep3

description: replicate 3

tag: time point

value: treated with 2 uM vemurafenib for 1 h


title: Glioma-EORTC26951 A1372_30.CEL

tag: tissue

tag: tcga classification

value: C

tag: idhmut

value: wt

tag: mgmt

value: meth

tag: ss (y)

tag: event

value: AOD

tag: review diagnosis

value: pt 1


title: 6th time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, sixth sample of the time-course. G1 is the reference where there is no replication. Sample is the sixth time for which replication is happening.

tag: strain

value: 50 min

tag: origin

value: Cell culture


title: 353230-2

description:
c57 bleo 14j-3
Date:2009/05/15

source_name: c57 bleo 14j-3

tag: agent

value: bleomycin


title: SKMEL28_t1h_rep2

description: replicate 2

tag: cell line

tag: mutation

tag: treatment


title: SKMEL28_t1h_rep1

description: replicate 1


title: Glioma-EORTC26951 A1372_28.CEL

tag: sample

tag: igs

tag: tissue type

tag: 1p19q loh

tag: egfr

tag: trt

value: RT

value: deceased

tag: age

tag: Sex

value: M

value: GBM/AA


title: 6th time point of the Time-course Replicate 3

description: Biological replicate 3 of 3, sixth sample of the time-course. G1 is the reference where there is no replication. Sample is the sixth time for which replication is happening.

tag: time point

value: 56 min


title: 7th time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, seventh sample of the time-course. G1 is the reference where there is no replication. Sample is the seventh time for which replication is happening.

value: 55 min


title: 8th time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, eigth sample of the time-course. G1 is the reference where there is no replication. Sample is the eigth time for which replication is happening.

value: 70 min


title: 352955-1

description:
c57 pbs 7j-2
Date:2009/05/15

source_name: c57 pbs 7j-2

value: PBS

tag: tissue

value: lung


title: 5th time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, fifth sample of the time-course. G1 is the reference where there is no replication. Sample is the fifth time for which replication is happening.

value: 45 min


title: Glioma-EORTC26951 A1372_27.CEL

value: glioma

tag: tcga classification

value: C

value: FFPE

value: no loss

value: wt

value: RT/PCV

tag: ss (y)

tag: event

tag: original diagnosis

value: AOA

tag: review diagnosis

tag: experiment


title: 353232-1

description:
balb pbs 14j-1
Date:2009/05/15

source_name: balb pbs 14j-1

tag: agent

tag: strain

value: BALB/c


title: SKMEL28_t0h_rep3

description: replicate 3

tag: cell line

tag: mutation

tag: treatment

value: untreated


title: 4th time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, fourth sample of the time-course. G1 is the reference where there is no replication. Sample is the fourth time for which replication is happening.

value: 40 min

tag: origin

value: Cell culture


title: 352955-2

description:
c57 bleo 7j-2
Date:2009/05/15

source_name: c57 bleo 7j-2

value: bleomycin


title: Glioma-EORTC26951 A1372_26.CEL

tag: sample

tag: igs

tag: tissue type

tag: 1p19q loh

value: LOH

tag: trt

value: deceased

value: F

value: AOD

value: pt 1


title: 3rd time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, third sample of the time-course. G1 is the reference where there is no replication. Sample is the third time for which replication is happening.

tag: time point

value: 35 min


title: SKMEL28_t0h_rep2

description: replicate 2


title: SKMEL28_t0h_rep1

description: replicate 1


title: 1st time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, first sample of the time-course. G1 is the reference where there is no replication. Sample is the first time for which replication is happening.

value: 25 min


title: 2nd time point of the Time-course Replicate 2

description: Biological replicate 2 of 3, second sample of the time-course. G1 is the reference where there is no replication. Sample is the second time for which replication is happening.

value: 30 min


title: 352995-2

description:
c57 bleo 14j-4
Date:2009/05/15

source_name: c57 bleo 14j-4

tag: tissue

value: lung


title: Glioma-EORTC26951 A1372_25.CEL

value: glioma

tag: tcga classification

value: C

value: FFPE

tag: idhmut

value: wt

value: no loss

tag: egfr

tag: mgmt

value: meth

tag: ss (y)

tag: event

tag: age

tag: Sex


title: delta_gap1_dikaryon_F15_x_F28_biological_replicate_1

city: Jena

first: Erika

last: Kothe

address: Neugasse 25

department: Microbial Communication, Institute of Microbiology

institute: Friedrich-Schiller-University

description: whole genome array with single T nucleotide as background control

hyb_protocol: Hybridization was done automatically over night (16 hours) at 45°C using RT-Analyzer from febit. The biotin labeling was detected with streptavidinphycoerythrin (SAPE), in combination with Consecutive Signal Enhancement (CSE) procedure from febit.

scan_protocol: The feature recognition, using Cy3 filter set, and signal calculation were done automatically within milliseconds using the Geniom RT Analyzer.

data_processing: Background correction was performed using the intensities of blank probes which consist only of one single ”T” nucleotide. The median background intensity was subtracted from spot intensity. After converting any negative values to a low positive value (7), signal intensities were log2-transformed. The obtained data were processed using quantile normalization, and duplicate spots were averaged.

organism: Schizophyllum commune

source_name: mated mycelium, interaction of ∆gap1 strains

label_protocol: For each array 1 µg of total RNA was labeled using the MassageAmpTM-Biotin Enhanced RNA Kit from Ambion.

growth_protocol: The S. commune strains were grown on solid medium (CYM) on a cellophane membrane at 28°C for 3 days in the dark.

extract_protocol: Total RNA was isolated from < 100 mg tissue powder using “Qiagen RNeasy plant mini kit” (Qiagen, Hilden, Germany), quality controlled with Agilent 2100 Bioanalyzer, using RNA 6000 Nano Kit, and a NanoDropTM 1000 Spectrophotometer (Thermo Scientific).

treatment_protocol: Mycelium was harvested, frozen in liquid nitrogen and ground with mortar and pestle to a powder.

tag: developmental stage

value: dikaryon

tag: strain(s)

tag: mating type loci

tag: genotype

tag: stage of clamp formation

value: elongated clamps


title: 2nd time point of the Time-course Replicate 3

description: Biological replicate 3 of 3, second sample of the time-course. G1 is the reference where there is no replication. Sample is the second time for which replication is happening.

tag: strain

tag: origin

value: Cell culture


title: delta_gap1_dikaryon_F15_x_F28_biological_replicate_2


title: cdc42_G12V_mutant_biological_replicate_2

source_name: monokaryotic mycelium of strain cdc42G12V

value: monokaryon

value: no clamps


title: Glioma-EORTC26951 A1372_23.CEL

address: Dr Molewaterplein 50

tag: sample

tag: igs

tag: tissue type

tag: 1p19q loh

value: unmeth

tag: trt

value: RT/PCV

value: deceased

value: M

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment


title: 353051-2

description:
balb bleo 7j-3
Date:2009/05/15

source_name: balb bleo 7j-3

tag: agent

value: bleomycin

tag: time point

tag: tissue

value: lung


title: 353232-2

description:
balb bleo 14j-1
Date:2009/05/15

source_name: balb bleo 14j-1

value: BALB/c


title: Glioma-EORTC26951 A1372_24.CEL

value: glioma

tag: tcga classification

value: C

value: FFPE

tag: idhmut

tag: egfr

tag: mgmt

value: RT

tag: ss (y)

tag: event

value: alive

tag: age

tag: Sex

value: GBM/AA

value: pt 1


title: Glioma-EORTC26951 A1372_22.CEL

tag: sample

tag: igs

tag: tissue type

value: mut

value: LOH

value: wt

value: meth


title: 7th time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, seventh sample of the time-course. G1 is the reference where there is no replication. Sample is the seventh time for which replication is happening.

tag: strain

value: 55 min

tag: origin

value: Cell culture


title: 8th time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, eigth sample of the time-course. G1 is the reference where there is no replication. Sample is the eigth time for which replication is happening.

value: 60 min


title: T2G12V_constitutive-active-Ras1_biological_replicate_2

source_name: monokaryotic mycelium of strain T2G12V

tag: developmental stage

value: monokaryon

tag: strain(s)

tag: mating type loci

tag: genotype

value: ura-; ras1G12V

tag: stage of clamp formation

value: no clamps


title: T2G12V_constitutive-active-Ras1_biological_replicate_1


title: Glioma-EORTC26951 A1372_20.CEL

description: Abbreviations: IGS: intrinsic glioma subtype; Trt: treatment; SS: survival in years; C: classical; P: proneural; M: mesenchymal; N:neural

source_name: Glioma, clinical trial RT v RT+PCV

tag: tissue

value: glioma

tag: tcga classification

tag: idhmut

tag: 1p19q loh

value: no loss

tag: trt

value: RT/PCV

value: deceased

value: M

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment


title: cdc42_G12V_mutant_biological_replicate_1


title: 6th time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, sixth sample of the time-course. G1 is the reference where there is no replication. Sample is the sixth time for which replication is happening.

tag: time point

value: 50 min


title: Glioma-EORTC26951 A1372_21.CEL

tag: sample

tag: igs

value: C

tag: tissue type

value: FFPE

tag: ss (y)

tag: event

tag: age

tag: Sex

value: F

value: AOA

value: pt 1


title: 5th time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, fifth sample of the time-course. G1 is the reference where there is no replication. Sample is the fifth time for which replication is happening.

tag: strain

value: 45 min

tag: origin

value: Cell culture


title: Glioma-EORTC26951 A1372_19.CEL

tag: tissue

tag: tcga classification

value: mut

value: LOH

tag: egfr

value: wt

tag: mgmt

value: meth

value: RT

value: alive


title: 4th time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, fourth sample of the time-course. G1 is the reference where there is no replication. Sample is the fourth time for which replication is happening.

value: 40 min


title: 1st time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, first sample of the time-course. G1 is the reference where there is no replication. Sample is the first time for which replication is happening.

value: 0 min


title: Glioma-EORTC26951 A1372_16.CEL

value: glioma

tag: idhmut

tag: 1p19q loh

value: no loss

tag: trt

value: deceased

value: M

tag: original diagnosis

value: AOD


title: 2nd time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, second sample of the time-course. G1 is the reference where there is no replication. Sample is the second time for which replication is happening.

tag: time point

value: 30 min


title: Glioma-EORTC26951 A1372_18.CEL

tag: sample

tag: igs

value: C

value: FFPE

value: RT/PCV

tag: review diagnosis

tag: experiment

value: pt 1


title: 3rd time point of the Time-course Replicate 1

description: Biological replicate 1 of 3, third sample of the time-course. G1 is the reference where there is no replication. Sample is the third time for which replication is happening.

value: 35 min

value: Cell culture


title: Glioma-EORTC26951 A1372_15.CEL

tag: tissue type

value: wt

value: meth

tag: ss (y)

tag: event

tag: age

value: AOA