title: P52_B_T0_O

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.0).

source_name: PBMC, subject 52, MUFA-shake, baseline measurement (T=0hr), obese subject

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Lean (predefined BMI 18-25 kg/m2) and obese (predefined BMI >30 kg/m2) male subjects between 50-70 years old were included from a subpopulation of a previously reported study (van Dijk et al, 2012; PubMed ID: 22844471). All subjects were non-smoking, normoglycemic (WHO criteria) and were not diagnosed with any long-term medical condition. All subjects gave written informed consent, and the study was approved by the local Medical Ethics Committee. The study was registered at clinicaltrials.gov as NCT00977262.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using BD Vacutainer Cell Preparation Tubes according to the manufacturer's instructions. Total RNA was extracted using the Qiagen RNeasy Micro Kit (Qiagen, Venlo, Netherlands). RNA quantity was measured with the ND-100 spectrophotometer (Isogen Life Science, Ijsselstein, the Netherlands), and RNA integrity was analysed on an Agilent 2100 BioAnalyzer (Agilent Technologies, Amsterdam, The Netherlands) using nanochips according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: The study had a double-blind randomized cross-over intervention study design in which each participant visited the university two times. On each study day, the subjects consumed milkshake with 95g of fat, which was high in either saturated (SFA) or monounsaturated (MUFA) fatty acids. Blood samples were collected before and 4 hours after shake consumption. Subjects were randomly assigned to a treatment order and a one-week washout period was the minimum between consecutive study days. On the day prior to each study day, subjects consumed a standardized low fat evening meal, were refrained from alcohol or strenuous exercise and were not allowed to eat or drink anything except water after 08.00 pm. This study was conducted according to the principles of the Declaration of Helsinki and in accordance with the Dutch Medical Research Involving Human Subjects Act (WMO).

tag: subject id

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: phenotype

value: obese

tag: intervention shake

value: MUFA

tag: time post consumption (hours)


title: ID162_120_0_F09

status: Public on May 13 2015

type: RNA

city: Kuopio

first: Jussi

last: Paananen

address: Yliopistonranta 1

country: Finland

institute: University of Eastern Finland

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix Expression Console version 1.1. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probeset scaling-to-target signal of 100.. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: RNA was extracted using the miRNeasy mini kit (cat.no 217004, Qiagen). RNA samples were treated with RNase-free DNase (cat.no 79254, Qiagen).

treatment_protocol: Patients had been fasting over night. PBMCs were extracted from a blood sample.

tag: time point

tag: diet

value: CONTROL

tag: age

tag: bmi


title: P52_G_T0_O

source_name: PBMC, subject 52, SFA-shake, baseline measurement (T=0hr), obese subject

tag: gender

value: male

value: SFA


title: ID031_238_0_C05


title: P01_B_T0_L

source_name: PBMC, subject 01, MUFA-shake, baseline measurement (T=0hr), lean subject

value: lean


title: P07_G_T0_L

source_name: PBMC, subject 07, SFA-shake, baseline measurement (T=0hr), lean subject


title: P57_B_T4_O

source_name: PBMC, subject 57, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P01_G_T4_L

source_name: PBMC, subject 01, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P52_B_T4_O

source_name: PBMC, subject 52, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P07_G_T4_L

source_name: PBMC, subject 07, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P07_B_T0_L

source_name: PBMC, subject 07, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P07_B_T4_L

source_name: PBMC, subject 07, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P57_G_T0_O

source_name: PBMC, subject 57, SFA-shake, baseline measurement (T=0hr), obese subject


title: P01_G_T0_L

source_name: PBMC, subject 01, SFA-shake, baseline measurement (T=0hr), lean subject


title: P28_G_T0_O

source_name: PBMC, subject 28, SFA-shake, baseline measurement (T=0hr), obese subject


title: P52_G_T4_O

source_name: PBMC, subject 52, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P28_G_T4_O

source_name: PBMC, subject 28, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P01_B_T4_L

source_name: PBMC, subject 01, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P57_B_T0_O

source_name: PBMC, subject 57, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P57_G_T4_O

source_name: PBMC, subject 57, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P28_B_T4_O

source_name: PBMC, subject 28, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P56_B_T4_O

source_name: PBMC, subject 56, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P28_B_T0_O

source_name: PBMC, subject 28, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P09_G_T4_L

source_name: PBMC, subject 09, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P09_B_T4_L

source_name: PBMC, subject 09, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P09_G_T0_L

source_name: PBMC, subject 09, SFA-shake, baseline measurement (T=0hr), lean subject


title: P09_B_T0_L

source_name: PBMC, subject 09, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P56_B_T0_O

source_name: PBMC, subject 56, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P56_G_T4_O

source_name: PBMC, subject 56, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P56_G_T0_O

source_name: PBMC, subject 56, SFA-shake, baseline measurement (T=0hr), obese subject


title: P53_B_T4_L

source_name: PBMC, subject 53, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P53_G_T4_L

source_name: PBMC, subject 53, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P51_G_T0_L

source_name: PBMC, subject 51, SFA-shake, baseline measurement (T=0hr), lean subject


title: P53_G_T0_L

source_name: PBMC, subject 53, SFA-shake, baseline measurement (T=0hr), lean subject


title: P50_G_T0_O

source_name: PBMC, subject 50, SFA-shake, baseline measurement (T=0hr), obese subject


title: P48_B_T4_O

source_name: PBMC, subject 48, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P50_G_T4_O

source_name: PBMC, subject 50, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P51_G_T4_L

source_name: PBMC, subject 51, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P47_B_T4_L

source_name: PBMC, subject 47, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P51_B_T0_L

source_name: PBMC, subject 51, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P39_G_T4_L

source_name: PBMC, subject 39, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P48_G_T0_O

source_name: PBMC, subject 48, SFA-shake, baseline measurement (T=0hr), obese subject


title: ID68b_402_12_H07

source_name: Peripheral blood mononuclear cells


title: P34_B_T0_O

source_name: PBMC, subject 34, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P47_G_T0_L

source_name: PBMC, subject 47, SFA-shake, baseline measurement (T=0hr), lean subject


title: P48_G_T4_O

source_name: PBMC, subject 48, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P48_B_T0_O

source_name: PBMC, subject 48, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P39_B_T4_L

source_name: PBMC, subject 39, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P39_B_T0_L

source_name: PBMC, subject 39, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P39_G_T0_L

source_name: PBMC, subject 39, SFA-shake, baseline measurement (T=0hr), lean subject


title: P47_B_T0_L

source_name: PBMC, subject 47, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P50_B_T0_O

source_name: PBMC, subject 50, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P47_G_T4_L

source_name: PBMC, subject 47, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P50_B_T4_O

source_name: PBMC, subject 50, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P53_B_T0_L

source_name: PBMC, subject 53, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P34_B_T4_O

source_name: PBMC, subject 34, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P34_G_T4_O

source_name: PBMC, subject 34, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P26_B_T0_O

source_name: PBMC, subject 26, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P26_B_T4_O

source_name: PBMC, subject 26, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P34_G_T0_O

source_name: PBMC, subject 34, SFA-shake, baseline measurement (T=0hr), obese subject


title: P51_B_T4_L

source_name: PBMC, subject 51, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P26_G_T4_O

source_name: PBMC, subject 26, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P23_B_T0_L

source_name: PBMC, subject 23, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P21_B_T0_L

source_name: PBMC, subject 21, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P22_B_T4_O

source_name: PBMC, subject 22, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P22_G_T0_O

source_name: PBMC, subject 22, SFA-shake, baseline measurement (T=0hr), obese subject


title: P19_B_T4_O

source_name: PBMC, subject 19, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P21_B_T4_L

source_name: PBMC, subject 21, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P20_B_T0_L

source_name: PBMC, subject 20, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P18_B_T0_O

source_name: PBMC, subject 18, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P20_G_T0_L

source_name: PBMC, subject 20, SFA-shake, baseline measurement (T=0hr), lean subject


title: P23_G_T0_L

source_name: PBMC, subject 23, SFA-shake, baseline measurement (T=0hr), lean subject


title: P21_G_T0_L

source_name: PBMC, subject 21, SFA-shake, baseline measurement (T=0hr), lean subject


title: P17_B_T4_L

source_name: PBMC, subject 17, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P19_G_T4_O

source_name: PBMC, subject 19, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P23_B_T4_L

source_name: PBMC, subject 23, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P23_G_T4_L

source_name: PBMC, subject 23, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P18_B_T4_O

source_name: PBMC, subject 18, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P20_B_T4_L

source_name: PBMC, subject 20, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P26_G_T0_O

source_name: PBMC, subject 26, SFA-shake, baseline measurement (T=0hr), obese subject


title: P18_G_T0_O

source_name: PBMC, subject 18, SFA-shake, baseline measurement (T=0hr), obese subject


title: P21_G_T4_L

source_name: PBMC, subject 21, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P20_G_T4_L

source_name: PBMC, subject 20, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P17_G_T4_L

source_name: PBMC, subject 17, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P18_G_T4_O

source_name: PBMC, subject 18, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P22_G_T4_O

source_name: PBMC, subject 22, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P19_G_T0_O

source_name: PBMC, subject 19, SFA-shake, baseline measurement (T=0hr), obese subject


title: P19_B_T0_O

source_name: PBMC, subject 19, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P22_B_T0_O

source_name: PBMC, subject 22, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P17_G_T0_L

source_name: PBMC, subject 17, SFA-shake, baseline measurement (T=0hr), lean subject


title: P17_B_T0_L

source_name: PBMC, subject 17, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P16_B_T0_O

source_name: PBMC, subject 16, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P16_B_T4_O

source_name: PBMC, subject 16, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P15_G_T4_L

source_name: PBMC, subject 15, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P16_G_T0_O

source_name: PBMC, subject 16, SFA-shake, baseline measurement (T=0hr), obese subject


title: P14_G_T4_L

source_name: PBMC, subject 14, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P15_B_T4_L

source_name: PBMC, subject 15, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P14_B_T0_L

source_name: PBMC, subject 14, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P10_B_T4_L

source_name: PBMC, subject 10, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P10_B_T0_L

source_name: PBMC, subject 10, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P03_B_T4_L

source_name: PBMC, subject 03, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P10_G_T0_L

source_name: PBMC, subject 10, SFA-shake, baseline measurement (T=0hr), lean subject


title: P46_G_T4_L

source_name: PBMC, subject 46, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P14_G_T0_L

source_name: PBMC, subject 14, SFA-shake, baseline measurement (T=0hr), lean subject


title: P04_B_T4_L

source_name: PBMC, subject 04, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P14_B_T4_L

source_name: PBMC, subject 14, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P46_B_T4_L

source_name: PBMC, subject 46, MUFA-shake, 4hr after consumption (T=4hr), lean subject


title: P03_G_T4_L

source_name: PBMC, subject 03, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P10_G_T4_L

source_name: PBMC, subject 10, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P15_B_T0_L

source_name: PBMC, subject 15, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P04_G_T4_L

source_name: PBMC, subject 04, SFA-shake, 4hr after consumption (T=4hr), lean subject


title: P02_B_T4_O

source_name: PBMC, subject 02, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P04_B_T0_L

source_name: PBMC, subject 04, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P46_B_T0_L

source_name: PBMC, subject 46, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P03_G_T0_L

source_name: PBMC, subject 03, SFA-shake, baseline measurement (T=0hr), lean subject


title: P03_B_T0_L

source_name: PBMC, subject 03, MUFA-shake, baseline measurement (T=0hr), lean subject


title: P02_B_T0_O

source_name: PBMC, subject 02, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P02_G_T4_O

source_name: PBMC, subject 02, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P15_G_T0_L

source_name: PBMC, subject 15, SFA-shake, baseline measurement (T=0hr), lean subject


title: P02_G_T0_O

source_name: PBMC, subject 02, SFA-shake, baseline measurement (T=0hr), obese subject


title: P16_G_T4_O

source_name: PBMC, subject 16, SFA-shake, 4hr after consumption (T=4hr), obese subject


title: P46_G_T0_L

source_name: PBMC, subject 46, SFA-shake, baseline measurement (T=0hr), lean subject


title: P13_B_T4_O

source_name: PBMC, subject 13, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P13_B_T0_O

source_name: PBMC, subject 13, MUFA-shake, baseline measurement (T=0hr), obese subject


title: P08_B_T4_O

source_name: PBMC, subject 08, MUFA-shake, 4hr after consumption (T=4hr), obese subject


title: P04_G_T0_L

source_name: PBMC, subject 04, SFA-shake, baseline measurement (T=0hr), lean subject


title: P13_G_T0_O

source_name: PBMC, subject 13, SFA-shake, baseline measurement (T=0hr), obese subject


title: P08_G_T0_O

source_name: PBMC, subject 08, SFA-shake, baseline measurement (T=0hr), obese subject


title: P08_B_T0_O

source_name: PBMC, subject 08, MUFA-shake, baseline measurement (T=0hr), obese subject


title: JMC_193

city: Bordeaux

first: céline

last: brulard

address: 229 cours de l'argonne

country: France

institute: Institut Bergonié

data_processing: Bioconductor package, GCRMA algorithm

source_name: desmoid tumor

extract_protocol: Total RNAs were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures

treatment_protocol: Frozen tissue

tag: tissue

value: desmoid tumor

tag: Sex

value: M


title: JMC_191

hyb_protocol: according to the manufacturer’s procedures

value: F

tag: tumor location

value: extra abdominal

tag: age at diagnosis

tag: recurrence

value: N


title: JMC_201

scan_protocol: according to the manufacturer’s procedures

value: intra abdominal

tag: tumor size (mm)

value: Y

tag: follow up (month)


title: JMC_184

label_protocol: according to the manufacturer’s procedures


title: P08_G_T4_O

source_name: PBMC, subject 08, SFA-shake, 4hr after consumption (T=4hr), obese subject

tag: subject id


title: JMC_168


title: JMC_171


title: JMC_175


title: JMC_204


title: JMC_203


title: JMC_206


title: JMC_202


title: JMC_197


title: JMC_186


title: JMC_185


title: JMC_194


title: JMC_173

value: abdominal wall


title: JMC_180


title: JMC_177


title: JMC_189


title: JMC_164


title: JMC_170


title: JMC_163


title: JMC_162


title: JMC_146


title: JMC_144


title: JMC_143


title: JMC_141


title: JMC_161


title: JMC_130


title: JMC_118


title: JMC_137


title: JMC_131


title: JMC_139


title: JMC_133


title: JMC_115


title: P13_G_T4_O

source_name: PBMC, subject 13, SFA-shake, 4hr after consumption (T=4hr), obese subject

tag: cell type


title: JMC_122


title: JMC_138


title: JMC_110


title: JMC_119


title: JMC_116


title: JMC_109


title: JMC_102


title: JMC_125


title: JMC_111


title: JMC_103


title: JMC_114


title: JMC_123


title: JMC_113


title: JMC_165


title: JMC_097


title: JMC_106


title: JMC_094


title: JMC_095


title: JMC_100


title: JMC_090


title: JMC_083


title: JMC_091


title: JMC_081


title: JMC_148


title: JMC_085


title: JMC_082


title: JMC_073


title: JMC_065


title: JMC_069


title: JMC_074


title: JMC_067


title: JMC_092


title: JMC_080


title: JMC_076


title: JMC_077


title: JMC_075


title: JMC_084


title: JMC_078


title: JMC_063


title: JMC_061


title: JMC_062


title: JMC_058


title: JMC_053


title: JMC_051


title: JMC_055


title: JMC_050


title: JMC_060


title: JMC_064


title: JMC_046


title: JMC_049


title: JMC_039


title: JMC_048


title: JMC_045


title: JMC_029


title: JMC_041


title: JMC_028


title: JMC_043


title: JMC_044


title: JMC_025


title: JMC_030


title: JMC_036


title: JMC_040


title: JMC_035


title: JMC_026


title: JMC_042


title: JMC_024


title: JMC_027


title: JMC_038


title: JMC_034


title: JMC_056


title: JMC_047


title: JMC_031


title: JMC_021


title: JMC_032


title: JMC_017


title: EXP-576: TCGA-05-4249-01A-01R-1107-07

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

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

source_name: Primary solid tumor

tag: histologic type

value: Lung Adenocarcinoma- Not Otherwise Specified (NOS)

tag: disease state

value: Lung Adenocarcinoma

tag: clinical m staging

tag: pathologic t staging

tag: pathologic n staging

value: MALE

tag: organism part

value: Lung

tag: number pack years smoked

tag: smoking history

value: Current reformed smoker for > 15 years

tag: disease staging

value: Stage IB

value: LUNG

source_name: Stratagene Univeral Reference

tag: tissue type

value: Stratagene Univeral Reference


title: JMC_016

tag: tissue

tag: Sex

tag: tumor location


title: JMC_022

tag: tumor size (mm)

tag: age at diagnosis

tag: recurrence


title: JMC_023

tag: follow up (month)


title: JMC_020


title: EXP-576: TCGA-44-2661-01A-01R-1107-07

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

tag: histologic type

tag: age

value: FEMALE

value: [Not Available]

value: Lifelong Non-smoker

value: Stage IA


title: EXP-576: TCGA-05-4244-01A-01R-1107-07

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

tag: disease state

tag: clinical m staging

value: Current reformed smoker for < or = 15 years

value: Stage IV


title: EXP-576: TCGA-07-0249-20A-01R-1107-07

source_name: Control Analyte

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

value: NOT SPECIFIED

tag: pathologic t staging

tag: pathologic n staging


title: EXP-576: TCGA-44-3918-01A-01R-1107-07

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

tag: organism part

tag: number pack years smoked


title: EXP-576: TCGA-44-2657-01A-01R-1107-07

value: NX

tag: smoking history

tag: disease staging


title: JMC_011

tag: tissue

value: desmoid tumor

value: F

value: extra abdominal

value: N


title: EXP-576: TCGA-44-3919-01A-02R-1107-07

value: Lung Adenocarcinoma- Not Otherwise Specified (NOS)

value: Lung Adenocarcinoma

tag: Sex

value: Lung

tag: tissue type


title: JMC_012

tag: tumor location

tag: tumor size (mm)


title: JMC_008

value: M

value: abdominal wall

tag: age at diagnosis

tag: recurrence


title: JMC_006

tag: follow up (month)


title: EXP-576: TCGA-44-4112-01A-01R-1107-07

tag: histologic type

tag: age

value: FEMALE

value: Current reformed smoker for > 15 years

value: Stage IB

value: LUNG

value: Stratagene Univeral Reference


title: JMC_009


title: EXP-576: TCGA-05-4250-01A-01R-1107-07

tag: disease state

tag: clinical m staging

value: Current reformed smoker for < or = 15 years

value: Stage IIIA


title: EXP-576: TCGA-44-3398-01A-01R-1107-07

tag: pathologic t staging

tag: pathologic n staging

value: Stage IA


title: JMC_010

value: desmoid tumor


title: JMC_014

value: F


title: EXP-576: TCGA-35-3621-01A-01R-1107-07

value: NOT SPECIFIED

tag: organism part

tag: number pack years smoked


title: EXP-576: TCGA-35-4123-01A-01R-1107-07

value: MALE

tag: smoking history

tag: disease staging


title: EXP-576: TCGA-35-3615-01A-01R-0946-07

value: Lung Adenocarcinoma- Not Otherwise Specified (NOS)

tag: Sex

value: [Not Available]

value: Lifelong Non-smoker


title: JMC_005

tag: tissue

value: extra abdominal

value: N


title: EXP-576: TCGA-35-4122-01A-01R-1107-07

value: Lung Adenocarcinoma

value: Lung

tag: tissue type


title: JMC_003

tag: tumor location

tag: tumor size (mm)


title: JMC_004

tag: age at diagnosis

tag: recurrence


title: JMC_002

value: abdominal wall

tag: follow up (month)


title: JMC_001

value: M


title: EXP-576: TCGA-55-1595-01A-01R-0946-07

tag: histologic type

value: Lung Clear Cell Adenocarcinoma

tag: age

value: FEMALE

value: LUNG

value: Stratagene Univeral Reference


title: EXP-592: TCGA-33-4532-01A-01R-1199-01

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: Current smoker

value: Stage IB

tag: sample

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-66-2783-01A-01R-1199-01

value: Current reformed smoker for < or = 15 years

tag: pathologic t staging

value: Stage IIIB

tag: pathologic n staging

value: MALE

tag: organism part


title: JMC_013

value: desmoid tumor

value: F

value: extra abdominal


title: EXP-576: TCGA-07-0249-20A-01R-0946-07

value: NOT SPECIFIED

tag: number pack years smoked

tag: smoking history

tag: disease staging


title: EXP-576: TCGA-44-2665-01A-01R-0946-07

value: Lung Adenocarcinoma- Not Otherwise Specified (NOS)

value: Lung Adenocarcinoma

tag: Sex

value: Lung

value: [Not Available]

value: Lifelong Non-smoker

value: Stage IIB

tag: tissue type


title: EXP-576: TCGA-64-1676-01A-01R-0946-07

value: Stage IA

value: LUNG

value: Stratagene Univeral Reference


title: EXP-576: TCGA-64-1680-01A-02R-0946-07

value: Lung Adenocarcinoma Mixed Subtype

value: Stage IV


title: EXP-576: TCGA-44-2656-01A-02R-0946-07

value: Current reformed smoker for < or = 15 years

value: Stage IB


title: EXP-576: TCGA-55-1596-01A-01R-0946-07

value: MALE

value: Current smoker


title: EXP-592: TCGA-22-4604-01A-01R-1199-01

value: Lung Squamous Cell Carcinoma

value: Stage IIA

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-66-2773-01A-01R-1199-01

value: Current reformed smoker for > 15 years


title: EXP-592: TCGA-22-4607-01A-01R-1199-01

value: Lung


title: EXP-592: TCGA-37-3783-01A-01R-1199-01

value: [Not Available]

value: Stage IIIA


title: EXP-576: TCGA-64-1678-01A-01R-0946-07

value: Lung Adenocarcinoma- Not Otherwise Specified (NOS)

value: Lung Adenocarcinoma

value: FEMALE


title: EXP-576: TCGA-67-3774-01A-01R-0946-07

value: LUNG

value: Stratagene Univeral Reference


title: EXP-592: TCGA-66-2800-01A-01R-1199-01

value: Stage IIIB


title: EXP-576: TCGA-67-3770-01A-01R-0946-07

value: Stage IA


title: EXP-592: TCGA-22-4596-01A-01R-1199-01

value: Current reformed smoker for < or = 15 years

value: Stage IB


title: EXP-576: TCGA-67-3773-01A-01R-0946-07


title: EXP-592: TCGA-66-2777-01A-01R-1199-01

value: MALE


title: EXP-592: TCGA-66-2794-01A-01R-1199-01

value: Lung Squamous Cell Carcinoma


title: EXP-576: TCGA-55-1592-01A-01R-0946-07


title: EXP-592: TCGA-60-2725-01A-01R-1199-01


title: EXP-592: TCGA-33-4547-01A-01R-1199-01


title: EXP-576: TCGA-67-3771-01A-01R-0946-07


title: EXP-592: TCGA-22-4594-01A-01R-1199-01


title: EXP-576: TCGA-44-2659-01A-01R-0946-07

value: Stage IIB


title: EXP-592: TCGA-22-4595-01A-01R-1199-01

value: Current smoker

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-576: TCGA-44-2668-01A-01R-0946-07

value: Lung


title: EXP-576: TCGA-44-2655-01A-01R-0946-07

value: Current reformed smoker for > 15 years


title: EXP-592: TCGA-22-4591-01A-01R-1199-01

value: [Not Available]

value: Stage IIIA


title: EXP-592: TCGA-33-4538-01A-01R-1199-01


title: EXP-576: TCGA-44-2666-01A-01R-0946-07

value: Lung Adenocarcinoma- Not Otherwise Specified (NOS)

value: Lung Adenocarcinoma


title: EXP-592: TCGA-66-2793-01A-01R-1199-01


title: EXP-576: TCGA-44-2662-01A-01R-0946-07

value: LUNG


title: EXP-592: TCGA-33-4533-01A-01R-1199-01

value: FEMALE


title: EXP-576: TCGA-64-1677-01A-01R-0946-07

value: Stratagene Univeral Reference


title: EXP-592: TCGA-60-2716-01A-01R-0849-01

value: Lifelong Non-smoker

value: Lung Papillary Squamous Cell Caricnoma


title: EXP-576: TCGA-55-1594-01A-01R-0946-07


title: EXP-576: TCGA-67-3772-01A-01R-0946-07

value: Stage IB


title: EXP-592: TCGA-34-2596-01A-01R-0849-01

value: MALE


title: EXP-592: TCGA-66-2756-01A-01R-0849-01

value: Lung Squamous Cell Carcinoma

value: Current reformed smoker for < or = 15 years

value: Stage IIIB


title: EXP-592: TCGA-66-2768-01A-01R-0849-01

value: Stage IIB

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-66-2757-01A-01R-0849-01

value: Stage IA

value: Lung


title: EXP-592: TCGA-66-2769-01A-02R-0849-01

value: Current reformed smoker for > 15 years


title: EXP-574: TCGA-CJ-4638-01A-01R-1188-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

value: Stage IV

tag: laterality

value: Left

value: KIDNEY

tag: tissue


title: EXP-574: TCGA-B2-4102-01A-01R-1188-07

value: Stage I

value: Right

value: Stratagene Univeral Reference


title: EXP-592: TCGA-60-2726-01A-01R-0849-01

value: Stage IIA

tag: histologic type


title: EXP-592: TCGA-66-2785-01A-01R-0849-01

tag: age

value: Stage IB

value: MALE


title: EXP-574: TCGA-CJ-4636-01A-01R-1188-07

value: Stage III


title: EXP-574: TCGA-B8-4154-01A-01R-1188-07

value: [Not Available]

value: FEMALE


title: EXP-592: TCGA-60-2707-01A-01R-0849-01

tag: disease state

value: Lung Squamous Cell Carcinoma

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-60-2715-01A-01R-0849-01

tag: clinical m staging

value: Current reformed smoker for < or = 15 years

value: Stage IA

value: Lung


title: EXP-574: TCGA-CJ-4639-01A-01R-1188-07

value: Kidney Clear Cell Renal Carcinoma

value: Stage II


title: EXP-592: TCGA-66-2786-01A-01R-0849-01

tag: sample


title: EXP-574: TCGA-B8-4151-01A-01R-1188-07

value: KIDNEY


title: EXP-574: TCGA-07-0249-20A-01R-1188-07

value: NOT SPECIFIED


title: EXP-592: TCGA-66-2755-01A-01R-0849-01

value: Current reformed smoker for > 15 years

tag: pathologic t staging


title: EXP-592: TCGA-66-2767-01A-01R-0849-01

value: Stage IIIB

tag: pathologic n staging


title: EXP-574: TCGA-CJ-4634-01A-01R-1188-07

value: Stage I

value: Right

tag: organism part

value: Stratagene Univeral Reference


title: HCC2302

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Lung cancer cell line

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: RPMI 5% BFS

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

tag: histology

value: Adenocarcinoma


title: HCC122

tag: race

value: Black

tag: gender

value: M


title: EXP-592: TCGA-60-2706-01A-01R-0849-01

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

tag: smoking history

value: Current smoker

tag: disease staging

tag: Sex

value: MALE


title: H2444

tag: atcc alias

value: NSCLC


title: EXP-592: TCGA-60-2714-01A-01R-0849-01

value: Current reformed smoker for < or = 15 years

value: Stage IIB

value: FEMALE

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-574: TCGA-B2-3924-01A-01R-1188-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

tag: laterality

value: Left

value: KIDNEY

tag: tissue


title: EXP-592: TCGA-60-2724-01A-01R-0849-01

tag: age

tag: disease state

tag: clinical m staging

value: Stage IIIA

tag: histologic type


title: EXP-592: TCGA-60-2698-01A-01R-0849-01

value: [Not Available]

tag: pathologic t staging

tag: pathologic n staging

tag: organism part

tag: sample


title: EXP-592: TCGA-66-2766-01A-01R-0849-01

tag: number pack years smoked


title: EXP-574: TCGA-A3-3349-01A-01R-1188-07

value: Stage I

value: Stratagene Univeral Reference


title: EXP-574: TCGA-B2-4098-01A-01R-1188-07


title: EXP-574: TCGA-AK-3456-01A-01R-1188-07

value: Stage II

value: Right


title: EXP-592: TCGA-66-2781-01A-01R-0849-01

value: Lung Squamous Cell Carcinoma

tag: smoking history

value: Stage IB


title: EXP-574: TCGA-B2-4099-01A-02R-1188-07

tag: disease staging

value: MALE


title: EXP-592: TCGA-66-2782-01A-01R-0849-01

value: Current reformed smoker for < or = 15 years

tag: Sex


title: H1870

tag: atcc alias

tag: histology

value: SCLC

tag: gender

value: F


title: EXP-592: TCGA-60-2712-01A-01R-0849-01

value: Current reformed smoker for > 15 years

value: Stage IIB

value: FEMALE

value: Lung


title: H1694

tag: race

value: Caucasian

value: M


title: EXP-574: TCGA-BP-4167-01A-01R-1188-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

value: Stage III

tag: laterality

value: KIDNEY

tag: tissue


title: EXP-592: TCGA-34-2609-01A-01R-0849-01

tag: age

tag: disease state

tag: clinical m staging

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-60-2713-01A-01R-0849-01

value: Current smoker

tag: pathologic t staging

tag: pathologic n staging

tag: organism part

tag: sample


title: EXP-592: TCGA-60-2696-01A-01R-0849-01

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

tag: smoking history

tag: disease staging

value: Stage IIA

tag: Sex


title: H1876

tag: atcc alias

tag: histology

tag: race

tag: gender


title: EXP-592: TCGA-60-2722-01A-01R-0849-01

value: MALE


title: H1963

value: Black


title: EXP-574: TCGA-BP-4163-01A-01R-1188-07

tag: diseasestate

tag: tumor grading

tag: laterality

value: Right

tag: tissue

value: Stratagene Univeral Reference


title: EXP-592: TCGA-60-2723-01A-01R-0849-01

tag: age

tag: disease state

tag: clinical m staging

value: Current reformed smoker for < or = 15 years

value: Stage IB

tag: histologic type


title: EXP-592: TCGA-34-2608-01A-02R-0849-01

value: [Not Available]

tag: pathologic t staging

tag: pathologic n staging

tag: organism part

tag: sample


title: EXP-592: TCGA-66-2765-01A-01R-0849-01

tag: number pack years smoked

tag: smoking history

tag: disease staging

tag: Sex

value: Lung


title: H1341

tag: atcc alias

tag: histology

value: SCLC

tag: race

value: Caucasian

tag: gender

value: F


title: EXP-592: TCGA-60-2695-01A-01R-0849-01

value: Current reformed smoker for > 15 years

value: FEMALE

value: Lung Basaloid Squamous Cell Carcinoma


title: H1435

value: Adenocarcinoma


title: H1436

value: M


title: EXP-592: TCGA-66-2780-01A-01R-0849-01

value: Lung Squamous Cell Carcinoma

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-574: TCGA-AK-3426-01A-01R-1188-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

value: Stage III

value: MALE

tag: laterality

value: KIDNEY

tag: tissue


title: EXP-574: TCGA-B8-4619-01A-01R-1188-07

tag: age

value: Left

value: Stratagene Univeral Reference


title: EXP-574: TCGA-BP-4162-01A-01R-1188-07

value: Stage I

value: Right


title: H1092

value: SCLC

value: Caucasian


title: JMC_015

value: desmoid tumor

value: F

tag: tumor location

value: abdominal wall

tag: tumor size (mm)

tag: age at diagnosis

tag: recurrence

value: N

tag: follow up (month)


title: EXP-592: TCGA-66-2763-01A-01R-0849-01

tag: number pack years smoked

tag: disease state

tag: clinical m staging

tag: smoking history

value: Current reformed smoker for < or = 15 years

tag: pathologic t staging

value: Stage IB

tag: pathologic n staging

value: FEMALE

tag: organism part

value: Lung

tag: sample

tag: histologic type


title: EXP-592: TCGA-60-2721-01A-01R-0849-01

value: Lung Squamous Cell Carcinoma

tag: disease staging

tag: Sex

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: H835

tag: atcc alias

tag: histology

value: Carcinoid

tag: age

tag: race

value: Black

tag: gender


title: EXP-592: TCGA-66-2759-01A-01R-0849-01

value: Current reformed smoker for > 15 years

value: Stage IIIA

value: MALE


title: EXP-592: TCGA-34-2605-01A-01R-0849-01

value: Stage IIIB


title: EXP-592: TCGA-60-2710-01A-01R-0849-01

value: Stage IIA


title: EXP-592: TCGA-60-2720-01A-01R-0849-01


title: EXP-592: TCGA-60-2711-01A-01R-0849-01


title: H1045

value: SCLC

value: Caucasian

value: M


title: EXP-592: TCGA-43-2578-01A-01R-0849-01

value: Stage IA


title: EXP-592: TCGA-34-2604-01A-01R-0849-01

value: Current smoker


title: EXP-592: TCGA-66-2778-01A-02R-0849-01


title: EXP-574: TCGA-A3-3351-01A-01R-1188-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

value: Stage II

tag: laterality

value: Right

value: KIDNEY

tag: tissue

value: Stratagene Univeral Reference


title: EXP-592: TCGA-66-2770-01A-01R-0849-01

tag: number pack years smoked

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

tag: smoking history

value: Stage IB

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-574: TCGA-CJ-4637-01A-01R-1188-07

value: Stage IV

value: FEMALE

value: Left

tag: organism part


title: EXP-592: TCGA-66-2758-01A-02R-0849-01

value: Current reformed smoker for < or = 15 years

tag: pathologic t staging

tag: pathologic n staging

value: MALE

tag: sample

tag: histologic type


title: EXP-574: TCGA-B8-4148-01A-01R-1188-07

tag: disease staging

value: [Not Available]

tag: Sex


title: H810

tag: atcc alias

tag: histology

value: Large Cell

tag: age

tag: race

value: Black

value: M


title: EML1 infected with the TEL-AML1 ccs cloned into thepWPI lentiviral vector treated with IL7 and FLT3L for 7 days- rep 2

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: EML1 cell line: Bone marrow cells of male BDF1 mice infected with the retroviral vector LRARalpha403SN. They can be induced with IL-7 and bone marrow stromal cells to express characteristics of pre-pro-B lymphocytes.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

data_processing: standard Affymetrix protocol

organism: Mus musculus

source_name: EML1 hematopoietic progenitor cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA  The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.

growth_protocol: EML1 cells were grown in IMDM (Iscove Modified Dulbecco’s Medium) supplemented with 20% heat-inactivated horse serum and 15% BHK/MKL cell-conditioned medium. For B-cell differentiation, OP9 stromal cells were plated in 6-well plates in Alpha Minimum Essential Medium (α-MEM) with 20% of fetal bovine serum. When they reached confluency, 50 000 EML1 cells were plated on top of the stromal cells in their specific culture medium plus supplements (IL7 10 ng/ml; FLT3L 80 ng/ml; β-mercaptoethanol, 50 μM).

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen).

tag: cell line

tag: treatment


title: H60

value: SCLC

value: Caucasian

tag: gender

value: F


title: EXP-574: TCGA-B8-4143-01A-01R-1188-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

tag: laterality

value: KIDNEY

tag: tissue

value: Stratagene Univeral Reference


title: EML1 infected with the TEL-AML1 ccs cloned into thepWPI lentiviral vector treated with IL7 and FLT3L for 5 days- rep 2


title: EXP-574: TCGA-A3-3362-01A-01R-1188-07

value: Stage I

tag: organism part


title: EXP-592: TCGA-60-2708-01A-01R-0849-01

tag: number pack years smoked

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

tag: smoking history

tag: pathologic t staging

value: Stage IIB

tag: pathologic n staging

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-60-2719-01A-01R-0849-01

value: Current reformed smoker for > 15 years

tag: disease staging

value: Stage IB

tag: Sex

value: FEMALE

tag: sample

tag: histologic type


title: EXP-574: TCGA-BP-4164-01A-01R-1188-07

tag: age

value: Stage III

value: Left


title: EML1 infected with the TEL-AML1 ccs cloned into thepWPI lentiviral vector treated with IL7 and FLT3L for 5 days- rep 1

tag: cell line

tag: treatment


title: EXP-592: TCGA-56-1622-01A-01R-0690-01

value: Current reformed smoker for < or = 15 years

value: MALE


title: EXP-592: TCGA-43-2576-01A-01R-0849-01

value: Stage IIIA


title: EML1 infected with the TEL-AML1 ccs cloned into thepWPI lentiviral vector - rep 2


title: EXP-592: TCGA-22-1000-01A-01R-0690-01


title: EXP-574: TCGA-B8-4620-01A-01R-1188-07

tag: diseasestate

tag: tumor grading

value: [Not Available]


title: EXP-592: TCGA-22-1017-01A-01R-0690-01

value: NOT SPECIFIED


title: EXP-592: TCGA-21-1076-01A-02R-0690-01


title: EXP-574: TCGA-CJ-4643-01A-01R-1188-07

value: Kidney Clear Cell Renal Carcinoma

value: Stage II

tag: laterality

value: Right

value: KIDNEY

tag: tissue


title: EXP-574: TCGA-BP-4161-01A-01R-1188-07

value: Stage I

tag: organism part

value: Stratagene Univeral Reference


title: EXP-592: TCGA-21-1083-01A-01R-0690-01

tag: number pack years smoked

tag: disease state

value: Lung Squamous Cell Carcinoma

value: Current smoker

value: Stage IA

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-21-1077-01A-01R-0690-01

tag: clinical m staging

tag: smoking history

value: Current reformed smoker for > 15 years

value: Stage IIB


title: EXP-592: TCGA-22-1016-01A-01R-0690-01

tag: pathologic t staging

value: Stage IB

tag: pathologic n staging

value: MALE


title: EXP-574: TCGA-CJ-4644-01A-01R-1188-07

tag: disease staging

value: Stage IV

tag: Sex

value: FEMALE

value: Left


title: EXP-592: TCGA-22-0944-01A-01R-0690-01

tag: sample

tag: histologic type


title: EXP-592: TCGA-22-0940-01A-01R-0690-01

tag: age

value: Stage IIA


title: EML1 infected with the empty pWPI lentiviral vector treated with IL7 and FLT3L for 7 days- rep 2

tag: cell line

tag: treatment


title: EML1 infected with the TEL-AML1 ccs cloned into thepWPI lentiviral vector treated with IL7 and FLT3L for 7 days- rep 1


title: EML1 infected with the TEL-AML1 ccs cloned into thepWPI lentiviral vector - rep 1


title: EXP-592: TCGA-21-1076-01A-01R-0690-01


title: EXP-574: TCGA-A3-3347-01A-01R-1188-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

value: Stage III

value: Right


title: EXP-592: TCGA-21-1078-01A-01R-0690-01

value: Current reformed smoker for < or = 15 years


title: Control

type: SRA

city: Boulder

first: Eric

middle: Michael

last: Davis

state: Colorado

address: MCDB 347 UCB, Gold A345C

department: MCDB

institute: University of Colorado, Boulder

library_source: genomic

data_processing:
Library strategy: PhiT-Seq
FASTQ files were preprocessed to filter duplicate reads.
FASTQ files containing unique sequences were aligned to the human genome (hg19) using Bowtie software v0.12.08
Aligned sequences were intersected with gene tables obtained from the UCSC genome browser containing either exons or introns using BEDTools software v2.17.0
Unique insertions per gene were counted for exons and for introns. The total numbers of sense and antisense insertions within introns were counted for each gene. The total number of insertions were counted for exons for each gene, regardless of strand.
Genome_build: hg19
Supplementary_files_format_and_content: Uniqe insertion counts per intron (sense and antisense) and exon, per gene.

molecule: genomic DNA

source_name: HAP1 cells

growth_protocol: HAP1 cells were cultured in Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum (FBS, Sigma) and penicillin/streptomycin (Sigma).

extract_protocol:
Genomic DNA was extracted from HAP1 cells using a QIAamp DNA Mini Kit (Qiagen).
Linear PCR was performed using 2 mg of genomic DNA as template and the following primer: 5¢-Biotin-GGTCTCCAAATCTCGGTGGAAC-3¢. After 125 cycles of amplification, the linear PCR products were purified using Dynabeads (M280 Biotin Binder, Life Technologies). On-bead ligation of a 5¢ phosphorylated, 3¢ ddC linker was performed using Circligase II (Epicentre). The product was purified and used as a template for PCR to add Illumina adapter sequences.

treatment_protocol: Live HAP1 cells were labeled on ice with anti PrP or anti CD59 antibodies, and sorted for cells with reduced cell surface levels of the coresponding protein levels.

tag: genotype

value: Haploid

tag: mutagenesis

value: Gene trap mutated


title: EXP-592: TCGA-21-1072-01A-01R-0690-01

tag: number pack years smoked

value: [Not Available]

value: Lung Squamous Cell Carcinoma

tag: organism part


title: EXP-592: TCGA-21-1082-01A-01R-0690-01

tag: disease state

tag: clinical m staging

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EML1 infected with the empty pWPI lentiviral vector treated with IL7 and FLT3L for 5 days- rep 1


title: EML1 infected with the empty pWPI lentiviral vector - rep 2

value: empty pWPI lentiviral vector


title: Escell_Dax1KO_rep1-rep3

city: Kobe

first: Hitoshi

last: Niwa

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
ES cell, Dax1 KO, replicate1
ES cell, Dax1 KO, replicate2
ES cell, Dax1 KO, replicate3

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating 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 air dried.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) at the resolution of 3um.

data_processing: The scanned images were quantified with Feature Extraction Software 10.7.3.1 (Agilent).

source_name: ES cell, Dax1 KO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini column purification (QIAGEN, Valencia, CA).

extract_protocol: RNA was prepared using the QuickGene RNA cultured cell HC kit (KURABO) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Dax1 KO/Y


title: EML1 infected with the empty pWPI lentiviral vector treated with IL7 and FLT3L for 5 days- rep 2


title: EScell_Dax1del_4d_rep1-rep3

description:
ES cell, Dax1 induced KO, 4days, replicate1
ES cell, Dax1 induced KO, 4days, replicate2
ES cell, Dax1 induced KO, 4days, replicate3

source_name: ES cell, Dax1 induced KO, 4days

value: Dax1 flox/Y + Cre 4days


title: EXP-592: TCGA-22-1012-01A-01R-0690-01

tag: smoking history

value: Current reformed smoker for > 15 years

tag: pathologic t staging

value: Stage IB


title: EXP-574: TCGA-A3-3311-01A-01R-0864-07

tag: disease staging

value: Stage I

value: MALE

tag: laterality

value: KIDNEY

tag: tissue

value: Stratagene Univeral Reference


title: EXP-592: TCGA-21-1081-01A-01R-0690-01

value: Stage IIB

tag: pathologic n staging

tag: Sex

tag: sample

tag: histologic type


title: EXP-574: TCGA-AK-3444-01A-01R-0864-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: age

value: FEMALE

value: Left


title: EXP-574: TCGA-A3-3323-01A-01R-0864-07

tag: tumor grading

value: Right


title: EXP-574: TCGA-B2-3923-01A-01R-1188-07

value: Stage II


title: EXP-574: TCGA-CJ-4641-01A-01R-1188-07

value: Stage IV


title: EML1 infected with the empty pWPI lentiviral vector - rep 1

tag: cell line

tag: treatment


title: EXP-592: TCGA-21-1075-01A-01R-0690-01

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

value: Current smoker

tag: organism part

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-22-1011-01A-01R-0690-01

tag: disease state

tag: clinical m staging


title: H446

tag: atcc alias

tag: histology

value: SCLC

tag: race

value: Caucasian

tag: gender

value: M


title: EXP-574: TCGA-A3-3329-01A-01R-0864-07

tag: disease staging

value: Stage I

value: MALE

tag: laterality

tag: tissue


title: Enterospheres_Diff_rep2

city: Tuebingen

first: Roland

middle: Alexander

last: Mohr

address: Oesterbergstrasse 3

department: Experimental Embryology

country: Germany

institute: Institute of Anatomy

description: Diff. enterospheres untreated

hyb_protocol: Standard Affymetrix hybridisation protocol

scan_protocol: Using Affymetrix GeneArray Scanner 3000 7G

data_processing: RMA normalisation

source_name: enterospheres crafted from 3 neonatal C57BL/6 mice

label_protocol: Standard Affymetrix biotin labeling protocol

growth_protocol: For each sample, gut from 3 neonatal C57BL/6 mice (age up to 12 hours) were prepared. Circular muscle was removed, chopped and incubated in Collagenase Type XI (750 U/mL; Sigma-Aldrich, Taufkirchen, Germany) and Dispase II (250 µg/mL; Roche Diagnostics, Mannheim, Germany) dissolved in Hanks’ balanced salt solution with Ca2+/Mg2+ (HBSS; PAA, Pasching, Austria) for 30 min at 37 °C. Tissue was carefully trituated every 10 min with a flame polished blue pipette tip. Prior to the trituation, 0.05% DNAse I (Sigma-Aldrich) was added. After tissue dissociation, 10% fetal calf serum (FCS; PAA) was added. Remaining bigger cell constructs were removed by a 40 µm cell strainer. Two washing steps in HBSS were performed at 200 g, 23 °C. The pellet was resuspended in proliferation medium consistent of Dulbecco’s modified Eagle’s Medium with Ham’s F12 Medium (DMEM/F12; PAA) containing N2 supplement (1:100; Invitrogen GmbH, Darmstadt, Germany), a Penicillin/Streptomycin mix (1:100; PAA), L-Glutamine (1:100; PAA) and B27 serum free supplement (1:50; Invitrogen). Cells were seeded into 6-well plates (Becton-Dickinson, Franklin Lakes, NJ, USA) in a concentration of 2.5 x 10^4 cells / cm2. Epidermal growth factor (10 ng/mL; Sigma-Aldrich) and fibroblast growth factor (20 ng/mL; Sigma-Aldrich) were added every day. Cultures were incubated for 4 days at 37°C and 5 % CO2.

extract_protocol: Qiagen RNA protocol

treatment_protocol: After 4 days of proliferation, only free floating enterospheres were picked and transferred into petri dishes (Ø 60 mm, Greiner Bio One, Frickenhausen, Germany) in 5 ml fresh proliferation medium. Cell cultures were then incubated another 5 days with adding growth factors EGF / FGF daily. Then again, only free floating enterospheres (about 50 enterospheres / dish) were picked, washed 3 times in tris buffer and transferred into fresh petri dishes with either proliferation medium (50% of enterospheres) or differentiation medium (DMEM/F12 containing N2 supplement (1:100), Penicillin/Streptomycin (1:100), L-Glutamine (1:100) and ascorbic acid-2-phosphate (200 µmol/mL)). After 2 days of incubation, enterospheres were picked, transferred into 1.5 ml Eppendorf cups and washed in tris buffer at 13k rpm for 10 min. Then, enterospheres were frozen in 300 µl RLT buffer / cup at -80 °C until RNA isolation.

tag: strain

value: ENS, P0

tag: Stage

value: proliferating for 9 days and differentiating for 2 days


title: EXP-574: TCGA-A3-3313-01A-01R-0864-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: age

tag: Sex

value: KIDNEY

value: Stratagene Univeral Reference


title: EScell_Dax1floxed_rep1-rep3

description:
ES cell, Dax1-floxed, replicate1
ES cell, Dax1-floxed, replicate2
ES cell, Dax1-floxed, replicate3

source_name: ES cell, Dax1-floxed

tag: genotype

value: Dax1 flox/Y


title: Enterospheres_Diff_rep3

description: Diff. enterospheres untreated


title: EXP-592: TCGA-21-1079-01A-01R-0690-01

tag: number pack years smoked

tag: smoking history

value: Current reformed smoker for > 15 years

tag: pathologic t staging

value: Stage IIIA

tag: pathologic n staging

tag: sample

tag: histologic type


title: EML1 infected with the empty pWPI lentiviral vector treated with IL7 and FLT3L for 7 days- rep 1

tag: cell line

tag: treatment


title: Enterospheres_Prol_rep3

description: Prol. enterospheres untreated

value: proliferating for 11 days


title: EXP-574: TCGA-A3-3372-01A-01R-0864-07

tag: tumor grading

tag: disease staging

value: Stage III

value: Left

tag: organism part


title: EXP-574: TCGA-A3-3363-01A-01R-0864-07

value: Stage II

tag: laterality

tag: tissue


title: EXP-592: TCGA-22-1002-01A-01R-0690-01

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: Current reformed smoker for < or = 15 years

value: Stage IA

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: Enterospheres_Prol_rep2

description: Prol. enterospheres untreated

tag: strain

value: ENS, P0

tag: Stage


title: EXP-592: TCGA-21-1071-01A-01R-0690-01

tag: age

tag: number pack years smoked

value: Current smoker

value: Stage IB

tag: Sex

value: MALE


title: EXP-574: TCGA-A3-3331-01A-01R-0864-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

value: Stage I

value: FEMALE

value: Right

value: KIDNEY

value: Stratagene Univeral Reference


title: EXP-574: TCGA-AS-3778-01A-01R-0864-07


title: EXP-574: TCGA-A3-3328-01A-01R-0864-07

value: Left


title: Enterospheres_Diff_rep1

description: Diff. enterospheres untreated

value: proliferating for 9 days and differentiating for 2 days


title: Enterospheres_Prol_rep1

description: Prol. enterospheres untreated

value: proliferating for 11 days


title: EXP-592: TCGA-43-2581-01A-01R-0849-01

value: Lung Squamous Cell Carcinoma

tag: smoking history

tag: pathologic t staging

value: Stage IIIA

tag: pathologic n staging

tag: sample


title: EXP-592: TCGA-21-1080-01A-01R-0690-01

value: Current reformed smoker for < or = 15 years

value: Lung

tag: histologic type


title: EXP-574: TCGA-A3-3382-01A-01R-0864-07

tag: tumor grading

tag: disease staging


title: EXP-574: TCGA-A3-3335-01A-01R-0864-07

value: Stage II

tag: laterality

tag: organism part


title: EXP-574: TCGA-A3-3378-01A-01R-0864-07

tag: tissue


title: EXP-592: TCGA-22-1005-01A-01R-0690-01

tag: disease state

tag: clinical m staging

value: Stage IA

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-66-2753-01A-01R-1031-01

value: Stage IB

value: MALE


title: EXP-592: TCGA-43-3920-01A-01R-1031-01


title: GICs-TM-GN1

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with R (v. 2.10)/Bioconductor software (v. 2.5) using RMA algorithm.

source_name: GICs from the tumor mass

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Tissues were subjected to enzymatic digestion, and then  tumor cells were resuspended in serum-free DMEM/F12 medium (Invitrogen, Carlsbad, CA) containing human recombinant EGF (20 ng/ml; Sigma, St. Louis, MO), bFGF (20 ng/ml; Sigma), and B-27 (20 ul per ml of medium; Invitrogen) as previously described [PMID: 21423202]. Primary neurospheres were dissociated every 3-4 days to facilitate cell growth.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: tissue source

value: glioblastoma

tag: tissue type

value: TM (tumor mass)

tag: cell type

value: glioblastoma initiating cells (GICs)


title: GICs-TM-G97


title: GICs-PT-GN1

source_name: GICs from the peritumoral tissue

value: PT (peritumoral tissue surrounding the tumor mass)


title: GICs-PT-G104


title: EXP-574: TCGA-A3-3326-01A-01R-0864-07

value: Kidney Clear Cell Renal Carcinoma

tag: age

value: Stage I

tag: Sex

value: Right

value: KIDNEY

value: Stratagene Univeral Reference


title: EXP-574: TCGA-CJ-4640-01A-01R-1188-07

tag: diseasestate

value: Stage III

value: Left


title: EXP-592: TCGA-18-3414-01A-01R-1031-01

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

tag: smoking history

value: Current reformed smoker for < or = 15 years

tag: pathologic t staging

value: Stage IV

value: Lung


title: GICs-TM-G104


title: EXP-592: TCGA-34-2600-01A-01R-0849-01

value: Stage IA

tag: pathologic n staging

value: FEMALE

tag: sample

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: control to Sample 23

city: Porto Alegre

first: Marcelo

middle: Dutra

last: Arbo

address: Avenida Paulo Gama, 110

department: Departamento de Análises

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: Sample 24

hyb_protocol: 12.5 μg of labeled and fragmented cRNA were hybridized to Rat Genome 430 2.0 AffymetrixGeneChips

scan_protocol: Microarrays were scanned with an Affymetrix Gene-Chip Scanner-3000-7G controlled by GCOS software.

data_processing: Data were processed using the statistical programming language ‘R-version 2.15.1’. For the normalisation of the entire set of Affymetrix gene expression arrays was used the Robust Multi-array Average (RMA) algorithm

organism: Rattus norvegicus

source_name: hepatocytes treated with 0.1% DMSO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: Cells were incubated 24 h after seeding.

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

treatment_protocol: Cells were incubated with the piperazine designer drugs at EC20 for 24 h.

value: hepatocytes


title: EXP-592: TCGA-66-2737-01A-01R-1031-01

value: Current reformed smoker for > 15 years

tag: disease staging

value: Stage IIB

value: MALE


title: EXP-574: TCGA-07-0249-20A-01R-0864-07

value: NOT SPECIFIED

tag: tumor grading

tag: laterality

tag: organism part


title: EXP-574: TCGA-AS-3777-01A-01R-0864-07

value: Kidney Clear Cell Renal Carcinoma

value: [Not Available]

value: Stage I

tag: tissue


title: GICs-PT-G97

tag: tissue source

value: glioblastoma

value: PT (peritumoral tissue surrounding the tumor mass)

value: glioblastoma initiating cells (GICs)


title: treatment with MDBP, replicate 2

description: Sample 21

source_name: hepatocytes treated with 467 μM MDBP


title: EXP-592: TCGA-43-3394-01A-01R-1031-01

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: Current smoker

value: Stage IB


title: treatment with MDBP, replicate 3

description: Sample 23

tag: cell type


title: EXP-574: TCGA-A3-3374-01A-01R-0864-07

tag: age

tag: Sex

value: Right

value: KIDNEY

value: Stratagene Univeral Reference


title: EXP-592: TCGA-66-2791-01A-01R-1031-01

tag: number pack years smoked

value: Current reformed smoker for < or = 15 years

value: Stage IIIB

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-18-3412-01A-01R-1031-01

tag: smoking history

value: Current reformed smoker for > 15 years

value: MALE


title: EXP-592: TCGA-66-2734-01A-01R-1031-01

tag: pathologic t staging

value: FEMALE


title: EXP-574: TCGA-A3-3316-01A-01R-0864-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

value: Stage II

value: Left


title: control to Sample 19

description: Sample 20

value: hepatocytes


title: EXP-574: TCGA-AK-3443-01A-01R-0864-07

value: [Not Available]


title: EXP-592: TCGA-18-3411-01A-01R-1031-01

value: Lung Squamous Cell Carcinoma

value: Current smoker

value: Stage IIIA

tag: pathologic n staging

tag: sample


title: treatment with MDBP, replicate 1

description: Sample 19


title: control to Sample 21

description: Sample 22


title: EXP-592: TCGA-66-2790-01A-01R-1031-01

tag: disease staging

value: Stage IIB

tag: histologic type


title: EXP-592: TCGA-66-2727-01A-01R-1031-01

value: Stage IB


title: treatment with MeOPP, replicate 3

description: Sample 17

source_name: hepatocytes treated with 522 μM MeOPP


title: control to Sample 17

description: Sample 18


title: EXP-592: TCGA-37-3792-01A-01R-1031-01

value: Lifelong Non-smoker


title: control to Sample 15

description: Sample 16


title: EXP-574: TCGA-A3-3308-01A-01R-0864-07

tag: tumor grading

tag: laterality

value: Right

value: KIDNEY

value: Stratagene Univeral Reference


title: EXP-574: TCGA-A3-3325-01A-01R-0864-07

value: Stage I

tag: organism part

tag: tissue


title: treatment with MeOPP, replicate 2

description: Sample 15


title: EXP-592: TCGA-66-2789-01A-01R-1031-01

tag: disease state

value: Current reformed smoker for > 15 years

value: Stage IIIB

value: MALE

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-37-3789-01A-01R-1031-01

tag: clinical m staging


title: EXP-574: TCGA-AK-3465-01A-01R-0864-07

value: Kidney Clear Cell Renal Carcinoma

value: FEMALE

value: Left


title: treatment with MeOPP, replicate 1

description: Sample 13

tag: cell type

value: hepatocytes


title: EXP-574: TCGA-AK-3427-01A-01R-0864-07

tag: age

value: GX


title: control to Sample 13

description: Sample 14


title: control to Sample 11

description: Sample 12


title: EXP-592: TCGA-66-2788-01A-01R-1031-01

value: Lung Squamous Cell Carcinoma

value: Current reformed smoker for < or = 15 years

tag: Sex


title: treatment with TFMPP, replicate 3

description: Sample 11

source_name: hepatocytes treated with 35 μM TFMPP


title: EXP-592: TCGA-46-3768-01A-01R-1031-01

tag: number pack years smoked

value: [Not Available]

value: Stage IIIA


title: control to Sample 9

description: Sample 10


title: EXP-574: TCGA-A3-3352-01A-01R-0864-07

value: Stage III

value: KIDNEY


title: EXP-592: TCGA-46-3769-01A-01R-1031-01

tag: smoking history

value: Stage IIB


title: EXP-574: TCGA-AK-3455-01A-01R-0864-07

value: Right

value: Stratagene Univeral Reference


title: treatment with TFMPP, replicate 2

description: Sample 9


title: EXP-574: TCGA-A3-3365-01A-01R-0864-07

value: Stage I

value: MALE


title: EXP-592: TCGA-66-2787-01A-01R-1031-01

tag: pathologic t staging

value: Stage IA

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: control to Sample 7

description: Sample 8


title: treatment with TFMPP, replicate 1

description: Sample 7


title: EXP-574: TCGA-AK-3453-01A-01R-0864-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

value: FEMALE


title: EXP-574: TCGA-AK-3440-01A-01R-0864-07

value: GX

value: Left


title: EXP-574: TCGA-A3-3383-01A-01R-0864-07


title: EXP-574: TCGA-A3-3317-01A-01R-0864-07

value: Stage II


title: EXP-574: TCGA-AK-3447-01A-01R-0864-07

value: [Not Available]


title: EXP-592: TCGA-18-3421-01A-01R-1031-01

value: Lung Squamous Cell Carcinoma

value: Current reformed smoker for < or = 15 years

value: Stage IB

tag: pathologic n staging


title: EXP-592: TCGA-18-3419-01A-01R-1031-01

value: Stage IIB

tag: sample


title: EXP-592: TCGA-46-3767-01A-01R-1031-01

value: Current reformed smoker for > 15 years

tag: disease staging


title: EXP-574: TCGA-A3-3322-01A-01R-0864-07

value: KIDNEY

value: Stratagene Univeral Reference


title: control to Sample 5

description: Sample 6

value: hepatocytes


title: EXP-592: TCGA-18-3409-01A-01R-1031-01

value: MALE

tag: histologic type

value: Lung Basaloid Squamous Cell Carcinoma


title: EXP-574: TCGA-A3-3319-01A-01R-0864-07

tag: tumor grading

value: Stage I


title: EXP-592: TCGA-21-1070-01A-01R-0690-01

value: Stage IIIA

value: Lung

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: treatment with BZP, replicate 3

description: Sample 5

source_name: hepatocytes treated with 625 μM BZP


title: EXP-592: TCGA-18-3408-01A-01R-1031-01

source_name: Primary solid tumor

value: FEMALE


title: treatment with BZP, replicate 2

description: Sample 3


title: EXP-574: TCGA-A3-3380-01A-01R-0864-07

value: Kidney Clear Cell Renal Carcinoma

tag: laterality

value: Left

source_name: Stratagene Univeral Reference


title: EXP-574: TCGA-A3-3324-01A-01R-0864-07

value: Right

tag: organism part


title: EXP-574: TCGA-A3-3343-01A-01R-0864-07

value: Stage II

tag: tissue


title: EXP-592: TCGA-66-2771-01A-01R-1031-01

tag: disease state

value: Lung Squamous Cell Carcinoma

value: Current reformed smoker for < or = 15 years


title: EXP-574: TCGA-A3-3306-01A-01R-0864-07


title: EXP-592: TCGA-46-3766-01A-01R-1031-01

value: [Not Available]

tag: clinical m staging

value: Stage IA


title: EXP-574: TCGA-A3-3307-01A-01R-0864-07

value: KIDNEY

value: Stratagene Univeral Reference


title: EXP-592: TCGA-66-2792-01A-01R-1031-01

value: Stage IIB

value: MALE


title: treatment with BZP, replicate 1

description: Sample 1

tag: cell type

value: hepatocytes


title: control to Sample 3

description: Sample 4


title: EXP-574: TCGA-A3-3320-01A-01R-0864-07

tag: age

value: Stage I


title: EXP-592: TCGA-18-3410-01A-01R-1031-01

value: Current reformed smoker for > 15 years

value: Stage IIIA

tag: Sex

value: Lung


title: EXP-592: TCGA-66-2744-01A-01R-1031-01

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-66-2795-01A-02R-1031-01

tag: smoking history

value: Stage IIIB


title: EXP-592: TCGA-18-3416-01A-01R-1031-01

tag: pathologic t staging


title: EXP-592: TCGA-66-2754-01A-01R-1031-01


title: EXP-592: TCGA-46-3765-01A-01R-1031-01

value: Current smoker

value: FEMALE


title: control to Sample 1

description: Sample 2


title: EXP-592: TCGA-66-2742-01A-01R-1031-01

value: Lung Squamous Cell Carcinoma

value: Stage IV


title: EXP-592: TCGA-18-3415-01A-01R-1031-01

value: Stage IB


title: EXP-592: TCGA-18-3407-01A-01R-1031-01


title: EXP-592: TCGA-18-3406-01A-01R-1031-01

value: Current reformed smoker for < or = 15 years

value: Stage IA


title: EXP-574: TCGA-A3-3346-01A-01R-0864-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

value: Left

value: KIDNEY

value: Stratagene Univeral Reference


title: SC DRa1-Mmog

city: portland

first: Arthur

last: Vandenbark

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Neurology

institute: Oregon Health and Science University

description: SAMPLE 2

hyb_protocol: Amplified and labeled cDNA target samples were each hybridized to a Mouse Gene 2.0 ST array.

scan_protocol: Image processing was performed using Affymetrix Command Console (AGCC) v.3.1.1 software

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: Spinal cord of DRa1-mMOG-35-55 treated DR*1501-Tg mice with EAE

label_protocol: Labeled target cDNA was prepared from mouse spinal cord total RNA samples. Samples were amplified and labeled using the Affymetrix GeneChip WT Plus protocol

growth_protocol: Mice between 8 and 12 weeks of age were immunized s.c. at four sites on the flanks with 0.2 ml of an emulsion of 200 ug immunogenic peptide and complete Freund’s adjuvant containing 400 ug of heat-killed Mycobacterium tuberculosis H37RA.  In addition, mice were given Pertussis toxin (Ptx) f) on days 0 and 2 post-immunization (75 ng and 200 ng per mouse respectively).

extract_protocol: total RNA was isolated using Qiagen total RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: mice were treated with DRα1-mMOG-35-55 (100ug daily x 3) or Vehicle after disease onset at a clinical score of 2.  Twenty four hr after the last treatment, total RNA was isolated from spinal cords

tag: strain background

tag: genotype/variation

value: DR*1501-Tg mice

value: 8-10 weeks

tag: treated with

value: Spinal cord


title: SC Vehicle

description: SAMPLE 1

source_name: Spinal cord of Vehicle treated DR*1501-Tg mice with EAE

value: Vehicle


title: EXP-574: TCGA-A3-3359-01A-01R-0864-07

tag: disease staging

value: Stage I


title: EXP-592: TCGA-37-4133-01A-01R-1101-01

value: Current reformed smoker for > 15 years

value: Stage IIIB

tag: pathologic n staging

value: MALE

value: Lung

tag: sample

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-592: TCGA-37-4135-01A-01R-1101-01

value: Lung Squamous Cell Carcinoma

tag: organism part


title: Daphnia pulex MFP strain, kairomone, 5 hr, rep3

city: Utsunomiya

last: Miyakawa

state: Tochigi

address: 350 Mine-machi

institute: Utsunomiya University

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: The slide was scanned by a microarray scanner G2565CA (Agilent Technologies, Santa Clara, CA, USA). To increase the accuracy of signal measurements by the scanner, we used two different photo-multiplier tube laser power settings (10% and 100%) for the target signal.

data_processing: Raw data were extracted as pair files using NimbleScan software version 2.6 (Roche NimbleGen) and combined to obtain a raw expression value for each probe (Dudley et al., 2002, Proc Natl Acad Sci U S A; Sato et al., 2007, Plant J).

organism: Daphnia pulex

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The clone of D. pulex used in the experiments was collected from a pool at Maeda Forest Park in Sapporo in 2009. The clone was reared in the laboratory at 20°C in aged tap water and fed unicellular green algae (Chlorella Industry Co. Ltd, Fukuoka, Japan) over generations in a temperature- and photocycle-controlled incubator (20°C, 16-h light/8-h dark)

extract_protocol: RNAqueous®-Micro Kit (Life Technologies, Gaithersburg, MD, USA)

treatment_protocol: Six hundred two pink-eye stage embryos, i.e., the late stage of the kairomone-sensitive period, were removed from maternal brood chambers and treated with either fed or starved Chaoborus-conditioned media. After incubation at 20°C for 1 hr, about half the animals in each treatment culture (150 embryos each) were collected and total RNA was extracted. After 4 hr additional incubation, the remaining animals were collected and total RNA was extracted. This procedure was repeated three times independently, resulting in 12 samples (4 conditions x 3 replicates)

tag: strain

value: MFP

tag: kairomone

value: Kairomone

tag: time

value: 5 hr

tag: replicate


title: EXP-592: TCGA-51-4081-01A-01R-1101-01

tag: age

tag: disease state

tag: clinical m staging

value: Current smoker

value: Stage IIB

tag: Sex


title: EXP-592: TCGA-37-4130-01A-01R-1101-01

tag: number pack years smoked

tag: smoking history

tag: pathologic t staging

value: Stage IB


title: EXP-592: TCGA-37-4132-01A-01R-1101-01

value: [Not Available]

value: Lifelong Non-smoker

value: Stage IV

value: FEMALE


title: EXP-592: TCGA-18-4086-01A-01R-1101-01

value: Current reformed smoker for < or = 15 years


title: EXP-592: TCGA-37-4129-01A-01R-1101-01

value: Current reformed smoker for > 15 years


title: EXP-592: TCGA-51-4079-01A-01R-1101-01


title: EXP-592: TCGA-51-4080-01A-01R-1101-01

value: Stage IIIB

value: Lung Basaloid Squamous Cell Carcinoma


title: EXP-592: TCGA-18-4083-01A-01R-1101-01

value: MALE

value: Lung


title: EXP-592: TCGA-37-4141-01A-02R-1101-01

value: Lung Squamous Cell Carcinoma

value: Stage IA

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: Daphnia pulex MFP strain, control, 5 hr, rep3

source_name: Daphnia pulex MFP strain, control, 5 hr

value: MFP

value: Control

value: 5 hr


title: Daphnia pulex MFP strain, kairomone, 1 hr, rep3

value: Kairomone

value: 1 hr


title: K14CreER:SmoM2 9WPI Replicate 2

city: Brussels

first: Jean-Christophe

last: Larsimont

state: Brussels

address: 808, route de Lennik

department: Faculté de médecine

country: Belgium

institute: Université Libre de Bruxelles (ULB)

description: Gene expression of SmoM2+ cells 9W following tamoxifen administration in presence of Sox9, replicate 2

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MOE 430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

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

data_processing: The data were analyzed with R (version 2.14.0) Bioconductor fRMA (version 1.6) package with default analysis settings.

source_name: K14CreER:SmoM2 9WPI N2

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).were stained with anti-integrin alpha 6 antibody and anti-CD34

growth_protocol: Mice were maintained in a certified animal house according to European guidelines

extract_protocol: Qiagen Rneasy Micro

treatment_protocol: Mice were injected with 2,5mg of tamoxifen for 10 consecutive days and sacrifice 9 weeks after the first injection. Tail epidermis was digested in trypsin and single cells were stained with the appropriate antibodies and FACS sorted before RNA extraction.

tag: cell type

value: FACS purified cells:basal interfolicular cells

tag: genotype

value: K14CreER:SmoM2 9WPI N2

value: Alpha6+ CD34-


title: K14CreER:SmoM2:Sox9cKO 9WPI Replicate 2

description: Gene expression of SmoM2+ cells 9W following tamoxifen administration in absence of Sox9, replicate 2

source_name: K14CreER:SmoM2:Sox9cKO 9WPI N2

value: K14CreER:SmoM2:Sox9cKO 9WPI N2


title: K14CreER:SmoM2:Sox9cKO 9WPI Replicate 1

description: Gene expression of SmoM2+ cells 9W following tamoxifen administration in absence of Sox9, replicate 1

source_name: K14CreER:SmoM2:Sox9cKO 9WPI N1

value: K14CreER:SmoM2:Sox9cKO 9WPI N1


title: Daphnia pulex MFP strain, control, 5 hr, rep2


title: K14CreER:SmoM2 9WPI Replicate 1

description: Gene expression of SmoM2+ cells 9W following tamoxifen administration in presence of Sox9, replicate 1

source_name: K14CreER:SmoM2 9WPI N1

value: K14CreER:SmoM2 9WPI N1


title: Daphnia pulex MFP strain, control, 1 hr, rep3

source_name: Daphnia pulex MFP strain, control, 1 hr


title: EXP-574: TCGA-A3-3336-01A-01R-0864-07

tag: diseasestate

value: Kidney Clear Cell Renal Carcinoma

tag: tumor grading

tag: disease staging

value: Stage I

value: FEMALE

tag: laterality

value: Right

value: KIDNEY

tag: tissue

value: Stratagene Univeral Reference


title: Daphnia pulex MFP strain, kairomone, 5 hr, rep2

tag: strain

value: MFP

tag: kairomone


title: Daphnia pulex MFP strain, kairomone, 1 hr, rep2

tag: time

tag: replicate


title: epithelium_tumor_sample_508_rep2

status: Public on May 12 2015

city: Montreal

first: Morag

last: Park

state: Quebec

address: 1160 Ave. des Pins O.

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

description:
part of dyeswap pair
508E_rep1

hyb_protocol: Whole Human Genome 44K arrays (Agilent Technologies, product G4112A) were used for all experiments. RNA samples (500 ng) were subjected to fragmentation followed by 18 h hybridization, washing, and scanning (Agilent Technologies, model G2505B) according to the manufacturer’s protocol (manual ID #G4140-90030). Samples were hybridized against Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA). Duplicate hybridizations were performed for all samples using reverse-dye labeling

scan_protocol: Microarray data were feature extracted using Feature Extraction Software (v. 9.5.3) from Agilent with the default parameters

data_processing: Outlier features on arrays were flagged by the software. Arrays were required to have an average raw signal intensity of 800 in each channel, and a signal to noise ratio above 16 per channel. MvA plots were examined for signs of hybridization or labeling problems. Replicate arrays were required to have a concordance above 0.90. This level was established empirically using sets of known good replicate arrays in our database.  Data preprocessing and normalization were automated using the BIAS system. Raw feature intensities were background corrected using the RMA background correction algorithm. Resulting expression estimates were converted to log2-ratios. Within array normalization was performed using spatial and intensity-dependent loess. Median absolute deviation scale normalization was used to normalize between arrays.

source_name: microdissected breast tumor epithelium

label_protocol: Sample RNA was subjected to two rounds of T7 linear amplification using Ambion Amino Allyl MessageAmp kit (Ambion, Austin, Texas, USA) and labeled with Cy3 and Cy5 dyes according to the manufacturer’s procedure. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA). Reference RNA  RNA was subjected to one round of T7 linear amplification using Ambion Amino Allyl MessageAmp kit (Ambion, Austin, Texas, USA) and then processed as per the procedure described above.

growth_protocol: Breast tumor tissue samples were obtained at primary surgery from patients providing written informed consent.

extract_protocol: Total RNA was extracted from each population of microdissected cells using a GITC (guanidinium isothiocyanate) extraction protocol. Briefly, LCM caps were incubated for 5 minutes (room temperature) in 200 μl GITC extraction buffer (4 M GITC, 25 mM sodium citrate pH 7.0, 0.1 M β-mercaptoethanol, 0.5% N-lauroylsarcosine) supplemented with 1.6 μl β-mercaptoethanol. Subsequently, 20 μl of 2 M NaOAc, pH 4.0, 220 μl of water-saturated phenol and 60 μl of chloroform-isoamyl alcohol (23:1) were added to the extraction buffer. Following 15 minutes incubation on ice and centrifugation (12,000 rpm, 15 minutes) the aqueous phase was removed and RNA was precipitated with 2 μl glycogen (GenHunter, Nashville, Tennessee, USA) and 200 μl isopropanol. Samples were placed at -80°C for 30 minutes and centrifuged at 4°C (12,000 rpm) for 30 minutes to pellet RNA. Pellets were washed with 70% ethanol, air dried and subjected to DNAseI treatment (Roche, Basel, Switzerland). DNAseI treatment was performed in the presence of an RNase inhibitor (Invitrogen, Carlsbad, California, USA). Subsequently, samples were re-extracted as described above and re-suspended in 10 μl of diethylpyrocarbonate-treated water. RNA was quantified using a RiboGreen assay (Molecular Probes, Carlsbad, California, USA).

treatment_protocol: Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within three hours following tissue staining.

tag: tissue type

value: epithelium

tag: sample id

source_name: Reference

tag: sample type


title: Daphnia pulex MFP strain, control, 1 hr, rep1

value: Control


title: stroma_tumor_sample_409_rep1

description:
part of dyeswap pair
409S_rep1

source_name: microdissected breast tumor-associated stroma

value: stroma

value: Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)


title: stroma_tumor_sample_351_rep1

description:
part of dyeswap pair
351S_rep1


title: Daphnia pulex MFP strain, control, 1 hr, rep2

value: 1 hr


title: epithelium_tumor_sample_351_rep1

description:
part of dyeswap pair
351E_rep1


title: stroma_tumor_sample_508_rep2

description:
part of dyeswap pair
508S_rep1


title: Daphnia pulex MFP strain, kairomone, 1 hr, rep1

value: Kairomone


title: epithelium_tumor_sample_409_rep2

description:
part of dyeswap pair
409E_rep2


title: epithelium_tumor_sample_508_rep1

description:
part of dyeswap pair
508E_rep2


title: Daphnia pulex MFP strain, kairomone, 5 hr, rep1

value: 5 hr


title: epithelium_tumor_sample_328_rep1

description:
part of dyeswap pair
328E_rep1


title: stroma_tumor_sample_328_rep2

description:
part of dyeswap pair
328S_rep2


title: stroma_tumor_sample_328_rep1

description:
part of dyeswap pair
328S_rep1


title: stroma_tumor_sample_301_rep2

description:
part of dyeswap pair
301S_rep2


title: stroma_tumor_sample_301_rep1

description:
part of dyeswap pair
301S_rep1


title: stroma_tumor_sample_409_rep2

description:
part of dyeswap pair
409S_rep2


title: epithelium_tumor_sample_328_rep2

description:
part of dyeswap pair
328E_rep2


title: Daphnia pulex MFP strain, control, 5 hr, rep1


title: epithelium_tumor_sample_351_rep2

description:
part of dyeswap pair
351E_rep2


title: epithelium_tumor_sample_301_rep1

description:
part of dyeswap pair
301E_rep1


title: epithelium_tumor_sample_409_rep1

description:
part of dyeswap pair
409E_rep1


title: epithelium_tumor_sample_301_rep2

description:
part of dyeswap pair
301E_rep2


title: stroma_tumor_sample_278_rep2

description:
part of dyeswap pair
278S_rep2


title: Tumor DNA

type: genomic

city: Rotterdam

first: Esther

last: Korpershoek

address: Wytemaweg 80

department: Pathology

institute: Erasmus MC University Medical Center Rotterdam

description: snap frozen pheochromocytoma tissue

hyb_protocol: According standard Illumina procedures

scan_protocol: As described by S. Hopman et al, Eur J Cancer 2013

data_processing:
Data for each bead chip were self-normalized in Genomestudio GT (Illumina) using information contained within the array. Copy number estimates for each individual sample were determined by comparison with a common reference set of 200 samples from the HapMAP project (www.hapmap.org/downloads/raw_data) supplied by Illumina (Manifest files) and visualized in the Nexus software program (version five, Biodiscovery, El Segundo, CA, USA) as log2 ratios.
Nexus normalized log R intensities and B-allele frequencies

label: Cy3 and Cy5

source_name: Pheochromocytoma

label_protocol: According standard Illumina procedures

growth_protocol: not applicable

extract_protocol: DNA was isolated using a Gentrakit according manufacturers procedures

treatment_protocol: not applicable

value: male pheochromocytoma tissue

value: pheochromocytoma tissue


title: epithelium_tumor_sample_259_rep2

description:
part of dyeswap pair
259E_rep1


title: stroma_tumor_sample_281_rep1

description:
part of dyeswap pair
281S_rep2


title: stroma_tumor_sample_508_rep1

description:
part of dyeswap pair
508S_rep2


title: stroma_tumor_sample_259_rep1

description:
part of dyeswap pair
259S_rep1


title: stroma_tumor_sample_246_rep2

description:
part of dyeswap pair
246S_rep1


title: epithelium_tumor_sample_295_rep1

description:
part of dyeswap pair
295E_rep1


title: epithelium_tumor_sample_295_rep2

description:
part of dyeswap pair
295E_rep2


title: epithelium_tumor_sample_281_rep2

description:
part of dyeswap pair
281E_rep1


title: epithelium_tumor_sample_278_rep2

description:
part of dyeswap pair
278E_rep1


title: epithelium_tumor_sample_281_rep1

description:
part of dyeswap pair
281E_rep2


title: epithelium_tumor_sample_246_rep1

description:
part of dyeswap pair
246E_rep1


title: stroma_tumor_sample_238_rep2

description:
part of dyeswap pair
238S_rep1


title: stroma_tumor_sample_281_rep2

description:
part of dyeswap pair
281S_rep1


title: Germline DNA

description: blood DNA from sample 1

source_name: Blood

value: Corresponding germline DNA isolated from blood


title: epithelium_tumor_sample_246_rep2

description:
part of dyeswap pair
246E_rep2


title: epithelium_tumor_sample_278_rep1

description:
part of dyeswap pair
278E_rep2


title: stroma_tumor_sample_259_rep2

description:
part of dyeswap pair
259S_rep2


title: epithelium_tumor_sample_259_rep1

description:
part of dyeswap pair
259E_rep2


title: stroma_tumor_sample_238_rep1

description:
part of dyeswap pair
238S_rep2


title: stroma_tumor_sample_223_rep1

description:
part of dyeswap pair
223S_rep1


title: stroma_tumor_sample_246_rep1

description:
part of dyeswap pair
246S_rep2


title: stroma_tumor_sample_278_rep1

description:
part of dyeswap pair
278S_rep1


title: epithelium_tumor_sample_238_rep2

description:
part of dyeswap pair
238E_rep2


title: stroma_tumor_sample_295_rep1

description:
part of dyeswap pair
295S_rep1


title: epithelium_tumor_sample_238_rep1

description:
part of dyeswap pair
238E_rep1


title: stroma_tumor_sample_295_rep2

description:
part of dyeswap pair
295S_rep2


title: stroma_tumor_sample_223_rep2

description:
part of dyeswap pair
223S_rep2


title: epithelium_tumor_sample_223_rep1

description:
part of dyeswap pair
223E_rep2


title: epithelium_tumor_sample_223_rep2

description:
part of dyeswap pair
223E_rep1


title: stroma_tumor_sample_215_rep3

description:
technical replicate 2_part of dyeswap pair
215S_rep3


title: stroma_tumor_sample_215_rep2

description:
technical replicate 1_part of dyeswap pair
215S_rep2


title: stroma_tumor_sample_215_rep4

description:
technical replicate 2_part of dyeswap pair
215S_rep4


title: stroma_tumor_sample_215_rep1

description:
technical replicate 1_part of dyeswap pair
215S_rep1


title: epithelium_tumor_sample_215_rep1

description:
part of dyeswap pair
215E_rep1


title: epithelium_tumor_sample_167_rep1

description:
part of dyeswap pair
167E_rep1


title: stroma_tumor_sample_161_rep2

description:
part of dyeswap pair
161S_rep1


title: stroma_tumor_sample_190_rep3

description:
technical replicate 2_part of dyeswap pair
190S_rep3


title: epithelium_tumor_sample_167_rep2

description:
part of dyeswap pair
167E_rep2


title: stroma_tumor_sample_167_rep1

description:
part of dyeswap pair
167S_rep2


title: epithelium_tumor_sample_161_rep2

description:
part of dyeswap pair
161E_rep2


title: epithelium_tumor_sample_190_rep2

description:
part of dyeswap pair
190E_rep2


title: stroma_tumor_sample_167_rep2

description:
part of dyeswap pair
167S_rep1


title: stroma_tumor_sample_176_rep1

description:
part of dyeswap pair
176S_rep1


title: stroma_tumor_sample_190_rep4

description:
technical replicate 2_part of dyeswap pair
190S_rep4


title: epithelium_tumor_sample_215_rep2

description:
part of dyeswap pair
215E_rep2


title: epithelium_tumor_sample_176_rep2

description:
part of dyeswap pair
176E_rep2


title: epithelium_tumor_sample_176_rep1

description:
part of dyeswap pair
176E_rep1


title: stroma_tumor_sample_176_rep2

description:
part of dyeswap pair
176S_rep2


title: stroma_tumor_sample_190_rep1

description:
technical replicate 1_part of dyeswap pair
190S_rep1


title: stroma_tumor_sample_190_rep2

description:
technical replicate 1_part of dyeswap pair
190S_rep2


title: stroma_tumor_sample_351_rep2

description:
part of dyeswap pair
351S_rep2


title: stroma_tumor_sample_146_rep2

description:
part of dyeswap pair
146S_rep1


title: epithelium_tumor_sample_146_rep1

description:
part of dyeswap pair
146E_rep2


title: stroma_tumor_sample_161_rep1

description:
part of dyeswap pair
161S_rep2


title: stroma_tumor_sample_144_rep1

description:
part of dyeswap pair
144S_rep1


title: epithelium_tumor_sample_161_rep1

description:
part of dyeswap pair
161E_rep1


title: epithelium_tumor_sample_190_rep1

description:
part of dyeswap pair
190E_rep1


title: epithelium_tumor_sample_144_rep1

description:
part of dyeswap pair
144E_rep1


title: stroma_tumor_sample_144_rep2

description:
part of dyeswap pair
144S_rep2


title: stroma_tumor_sample_146_rep1

description:
part of dyeswap pair
146S_rep2


title: epithelium_tumor_sample_144_rep2

description:
part of dyeswap pair
144E_rep2


title: stroma_tumor_sample_136_rep2

description:
part of dyeswap pair
136S_rep1


title: epithelium_tumor_sample_136_rep2

description:
part of dyeswap pair
136E_rep2


title: stroma_tumor_sample_122_rep1

description:
part of dyeswap pair
122S_rep1


title: epithelium_tumor_sample_122_rep1

description:
part of dyeswap pair
122E_rep2


title: epithelium_tumor_sample_113_rep1

description:
part of dyeswap pair
113E_rep1


title: stroma_tumor_sample_083_rep1

description:
part of dyeswap pair
083S_rep1


title: epithelium_tumor_sample_083_rep2

description:
part of dyeswap pair
083E_rep2


title: epithelium_tumor_sample_076_rep1

description:
part of dyeswap pair
076E_rep2


title: stroma_tumor_sample_076_rep1

description:
part of dyeswap pair
076S_rep1


title: epithelium_tumor_sample_083_rep1

description:
part of dyeswap pair
083E_rep1


title: stroma_tumor_sample_113_rep2

description:
part of dyeswap pair
113S_rep2


title: stroma_tumor_sample_113_rep1

description:
part of dyeswap pair
113S_rep1


title: stroma_tumor_sample_122_rep2

description:
part of dyeswap pair
122S_rep2


title: stroma_tumor_sample_076_rep2

description:
part of dyeswap pair
076S_rep2


title: stroma_tumor_sample_136_rep1

description:
part of dyeswap pair
136S_rep2


title: epithelium_tumor_sample_122_rep2

description:
part of dyeswap pair
122E_rep1


title: epithelium_tumor_sample_076_rep2

description:
part of dyeswap pair
076E_rep1


title: stroma_tumor_sample_070_rep1

description:
part of dyeswap pair
070S_rep1


title: epithelium_tumor_sample_070_rep1

description:
part of dyeswap pair
070E_rep2


title: epithelium_tumor_sample_146_rep2

description:
part of dyeswap pair
146E_rep1


title: stroma_tumor_sample_070_rep2

description:
part of dyeswap pair
070S_rep2


title: epithelium_tumor_sample_070_rep2

description:
part of dyeswap pair
070E_rep1


title: stroma_tumor_sample_083_rep2

description:
part of dyeswap pair
083S_rep2


title: epithelium_tumor_sample_113_rep2

description:
part of dyeswap pair
113E_rep2


title: epithelium_tumor_sample_065_rep2

description:
part of dyeswap pair
065E_rep2


title: stroma_tumor_sample_065_rep1

description:
part of dyeswap pair
065S_rep1


title: stroma_tumor_sample_063_rep2

description:
part of dyeswap pair
063S_rep2


title: epithelium_tumor_sample_065_rep1

description:
part of dyeswap pair
065E_rep1


title: epithelium_tumor_sample_063_rep1

description:
part of dyeswap pair
063E_rep2


title: stroma_tumor_sample_060_rep2

description:
part of dyeswap pair
060S_rep2


title: stroma_tumor_sample_065_rep2

description:
part of dyeswap pair
065S_rep2


title: epithelium_tumor_sample_063_rep2

description:
part of dyeswap pair
063E_rep1


title: stroma_tumor_sample_063_rep1

description:
part of dyeswap pair
063S_rep1


title: stroma_tumor_sample_057_rep2

description:
part of dyeswap pair
057S_rep1


title: epithelium_tumor_sample_057_rep1

description:
part of dyeswap pair
057E_rep2


title: stroma_tumor_sample_060_rep1

description:
part of dyeswap pair
060S_rep1


title: epithelium_tumor_sample_057_rep2

description:
part of dyeswap pair
057E_rep1


title: stroma_tumor_sample_057_rep1

description:
part of dyeswap pair
057S_rep2


title: epithelium_tumor_sample_047_rep1

description:
part of dyeswap pair
047E_rep1


title: stroma_tumor_sample_047_rep2

description:
part of dyeswap pair
047S_rep2


title: epithelium_tumor_sample_027_rep1

description:
part of dyeswap pair
027E_rep2


title: epithelium_tumor_sample_047_rep2

description:
part of dyeswap pair
047E_rep2


title: stroma_tumor_sample_047_rep1

description:
part of dyeswap pair
047S_rep1


title: epithelium_tumor_sample_060_rep1

description:
part of dyeswap pair
060E_rep1


title: stroma_tumor_sample_027_rep2

description:
part of dyeswap pair
027S_rep1


title: epithelium_tumor_sample_031_rep1

description:
part of dyeswap pair
031E_rep2


title: stroma_tumor_sample_027_rep1

description:
part of dyeswap pair
027S_rep2


title: epithelium_tumor_sample_031_rep2

description:
part of dyeswap pair
031E_rep1


title: stroma_tumor_sample_031_rep1

description:
part of dyeswap pair
031S_rep2


title: epithelium_tumor_sample_136_rep1

description:
part of dyeswap pair
136E_rep1


title: stroma_tumor_sample_025_rep2

description:
part of dyeswap pair
025S_rep1


title: epithelium_tumor_sample_025_rep1

description:
part of dyeswap pair
025E_rep1


title: epithelium_tumor_sample_024_rep2

description:
part of dyeswap pair
024E_rep2


title: epithelium_tumor_sample_024_rep1

description:
part of dyeswap pair
024E_rep1


title: stroma_tumor_sample_024_rep1

description:
part of dyeswap pair
024S_rep1


title: epithelium_tumor_sample_025_rep2

description:
part of dyeswap pair
025E_rep2


title: stroma_tumor_sample_022_rep1

description:
part of dyeswap pair
022S_rep1


title: stroma_tumor_sample_031_rep2

description:
part of dyeswap pair
031S_rep1


title: stroma_tumor_sample_025_rep1

description:
part of dyeswap pair
025S_rep2


title: stroma_tumor_sample_024_rep2

description:
part of dyeswap pair
024S_rep2


title: stroma_tumor_sample_022_rep2

description:
part of dyeswap pair
022S_rep2


title: Thyroid B

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

hyb_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions

scan_protocol: scanning of HuEx1.0 microarrays was carried out following the manufacturer’s instructions

data_processing:
Signal intensities from core probesets were quantile normalized by robust multichip averaging and transcript expression levels median summarized using Partek Genomics Suite software (Partek, St. Louis, MO).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Affymetrix tissue data

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara)

extract_protocol: Qiagen miRNA easy

value: normal tissue


title: Testes A


title: Thyroid C


title: stroma_tumor_sample_012_rep2

description:
part of dyeswap pair
012S_rep2


title: Spleen C


title: stroma_tumor_sample_012_rep1

description:
part of dyeswap pair
012S_rep1


title: Spleen B


title: epithelium_tumor_sample_027_rep2

description:
part of dyeswap pair
027E_rep1


title: Testes B


title: epithelium_tumor_sample_012_rep2

description:
part of dyeswap pair
012E_rep2


title: Thyroid A


title: epithelium_tumor_sample_012_rep1

description:
part of dyeswap pair
012E_rep1


title: Testes C


title: epithelium_tumor_sample_022_rep2

description:
part of dyeswap pair
022E_rep1


title: Prostate B


title: Muscle A


title: Pancreas C


title: Prostate A


title: Spleen A


title: Pancreas A


title: Muscle C


title: Pancreas B


title: Muscle B


title: Liver C


title: Liver B


title: Liver A


title: Prostate C


title: Cerebellum B


title: Cerebellum C


title: Kidney B


title: Heart B


title: Breast C


title: Kidney A


title: Heart C


title: Kidney C


title: Breast B


title: Cerebellum A


title: BM-MSC rep3 reanalysis

description: adult bone-marrow MSC

source_name: BM-MSC

value: Bone marrow-MSC


title: BM-MSC rep2 reanalysis

description: adult bone-marrow MSC


title: Breast A


title: BM-MSC rep1 reanalysis

description: adult bone-marrow MSC


title: NCSC rep3 reanalysis

description: hESC-derived NCSC

source_name: hNCSC

value: NCSC


title: EWS#29

source_name: tumor biopsy

value: local tumor, pre-chemo


title: EWS#30


title: EWS#32


title: NC-MSC control rep2 reanalysis

description: hESC-derived neural crest-MSC isolated after 5 days in culture

source_name: hNC-MSC

value: NC-MSC


title: NC-MSC control rep1 reanalysis


title: EWS#28


title: NCSC rep2 reanalysis

description: hESC-derived NCSC


title: EWS#31


title: EWS#26


title: NCSC rep1 reanalysis

description: hESC-derived NCSC


title: EWS#27


title: EWS#24


title: EWS#25


title: EWS#23


title: NC-MSC control rep3 reanalysis


title: EWS#15


title: EWS#18


title: EWS#17


title: EWS#12


title: EWS#16


title: EWS#13


title: EWS#19


title: EWS#22


title: EWS#14


title: EWS#10


title: EWS#7


title: EWS#8


title: EWS#5


title: EWS#11


title: EWS#9


title: EWS#2


title: EWS#21


title: EWS#6


title: EWS#3