title: hLung_Laval_297


title: hLung_Laval_291

status: Public on Jun 11 2012

type: RNA

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

description: Lung specimen was obtained from a patient undergoing lung cancer surgery.

hyb_protocol: The amplified cDNAs were hybridized to Affymetrix gene expression chips (Human Rosetta Custom Affymetrix 2.0, Affymetrix, Santa Clara, CA) using standard Affymetrix protocols.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 7G. The images were analyzed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Expression values were extracted using the Robust Multichip Average method (Irizarry RA et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003;4:249-64) as implemented in the Affymetrix Power Tools software (available at: http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lung

label_protocol: Samples were amplified and labeled using the Ovation WB protocol (NuGEN Technologies, San Carlos, CA), according to the manufacturer’s instructions. In brief, 50 ng of total RNA was amplified using the Ribo-SPIA technology (NuGEN Technologies). After quantification, 4.4 ug cDNA was fragmented and labeled with biotin using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).

extract_protocol: Total RNA was extracted and purified from the clinical lung specimens using the SV96 Total RNA Isolation System (Promega) according to a custom automated protocol. The extracted RNA was quantified using RiboGreen RNA Quantitation Reagent (Invitrogen) and its quality was assessed using Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA) in an Agilent 2100 Bioanalyzer (Agilent).

tag: tissue

value: lung

tag: tumor status

value: non-tumorous


title: hLung_Laval_290


title: hLung_Laval_337


title: hLung_Laval_292


title: hLung_Laval_302


title: hLung_Laval_287


title: hLung_Laval_284


title: hLung_Laval_282


title: hLung_Laval_275


title: hLung_Laval_281


title: hLung_Laval_277


title: hLung_Laval_280


title: hLung_Laval_279


title: hLung_Laval_273


title: hLung_Laval_276


title: hLung_Laval_274


title: hLung_Laval_285


title: hLung_Laval_272


title: hLung_Laval_270


title: hLung_Laval_283


title: hLung_Laval_268


title: hLung_Laval_265


title: hLung_Laval_264


title: hLung_Laval_258


title: hLung_Laval_263


title: hLung_Laval_267


title: hLung_Laval_269


title: hLung_Laval_261


title: hLung_Laval_262


title: hLung_Laval_278


title: hLung_Laval_266


title: hLung_Laval_271


title: hLung_Laval_259


title: hLung_Laval_260


title: hLung_Laval_255


title: hLung_Laval_256


title: hLung_Laval_251


title: hLung_Laval_253


title: hLung_Laval_248


title: hLung_Laval_246


title: hLung_Laval_252


title: hLung_Laval_244


title: hLung_Laval_254


title: hLung_Laval_249


title: hLung_Laval_242


title: hLung_Laval_303


title: hLung_Laval_238


title: hLung_Laval_239


title: hLung_Laval_237


title: hLung_Laval_241


title: hLung_Laval_300


title: hLung_Laval_243


title: hLung_Laval_232


title: hLung_Laval_247


title: hLung_Laval_236


title: hLung_Laval_235


title: hLung_Laval_234


title: hLung_Laval_257


title: hLung_Laval_229


title: hLung_Laval_250


title: hLung_Laval_226


title: hLung_Laval_223


title: hLung_Laval_220


title: hLung_Laval_218


title: hLung_Laval_231


title: hLung_Laval_219


title: hLung_Laval_216


title: hLung_Laval_221


title: hLung_Laval_233


title: hLung_Laval_228


title: hLung_Laval_224


title: hLung_Laval_213


title: hLung_Laval_211


title: hLung_Laval_214


title: hLung_Laval_207


title: hLung_Laval_205


title: hLung_Laval_225


title: hLung_Laval_209


title: hLung_Laval_203


title: hLung_Laval_202


title: hLung_Laval_212


title: hLung_Laval_206


title: hLung_Laval_215


title: hLung_Laval_199


title: hLung_Laval_240


title: hLung_Laval_196


title: hLung_Laval_198


title: hLung_Laval_192


title: hLung_Laval_194


title: hLung_Laval_195


title: hLung_Laval_222


title: hLung_Laval_201


title: hLung_Laval_204


title: hLung_Laval_245


title: hLung_Laval_210


title: hLung_Laval_191


title: hLung_Laval_189


title: hLung_Laval_190


title: hLung_Laval_187


title: hLung_Laval_182


title: hLung_Laval_185


title: hLung_Laval_197


title: hLung_Laval_183


title: hLung_Laval_177


title: hLung_Laval_180


title: hLung_Laval_178


title: hLung_Laval_173


title: hLung_Laval_170


title: hLung_Laval_179


title: hLung_Laval_176


title: hLung_Laval_181


title: hLung_Laval_172


title: hLung_Laval_171


title: hLung_Laval_193


title: hLung_Laval_188


title: hLung_Laval_186


title: hLung_Laval_174


title: hLung_Laval_168


title: hLung_Laval_169


title: hLung_Laval_167


title: hLung_Laval_175


title: hLung_Laval_200


title: hLung_Laval_230


title: hLung_Laval_159


title: hLung_Laval_162


title: hLung_Laval_155


title: hLung_Laval_166


title: hLung_Laval_158


title: hLung_Laval_160


title: hLung_Laval_184


title: hLung_Laval_152


title: hLung_Laval_161


title: hLung_Laval_148


title: hLung_Laval_151


title: hLung_Laval_165


title: hLung_Laval_154


title: hLung_Laval_153


title: hLung_Laval_157


title: hLung_Laval_164


title: hLung_Laval_150


title: hLung_Laval_156


title: hLung_Laval_163


title: hLung_Laval_143


title: hLung_Laval_145


title: hLung_Laval_144


title: hLung_Laval_149


title: hLung_Laval_147


title: hLung_Laval_142


title: hLung_Laval_208


title: hLung_Laval_132


title: hLung_Laval_135


title: hLung_Laval_126


title: hLung_Laval_134


title: hLung_Laval_125


title: hLung_Laval_137


title: hLung_Laval_130


title: hLung_Laval_217


title: hLung_Laval_127


title: hLung_Laval_139


title: hLung_Laval_141


title: hLung_Laval_128


title: hLung_Laval_121


title: hLung_Laval_124


title: hLung_Laval_227


title: hLung_Laval_138


title: hLung_Laval_129


title: hLung_Laval_136


title: hLung_Laval_119


title: hLung_Laval_118


title: hLung_Laval_116


title: hLung_Laval_123


title: hLung_Laval_120


title: hLung_Laval_140


title: hLung_Laval_131


title: hLung_Laval_122


title: hLung_Laval_117


title: hLung_Laval_133


title: hLung_Laval_115


title: hLung_Laval_114


title: hLung_Laval_112


title: hLung_Laval_113


title: hLung_Laval_110


title: hLung_Laval_104


title: hLung_Laval_111


title: hLung_Laval_107


title: hLung_Laval_087


title: hLung_Laval_109


title: hLung_Laval_103


title: hLung_Laval_089


title: hLung_Laval_088


title: hLung_Laval_106


title: hLung_Laval_101


title: hLung_Laval_105


title: hLung_Laval_146


title: hLung_Laval_084


title: hLung_Laval_095


title: hLung_Laval_100


title: hLung_Laval_099


title: hLung_Laval_094


title: hLung_Laval_090


title: hLung_Laval_102


title: hLung_Laval_091


title: hLung_Laval_092


title: hLung_Laval_093


title: hLung_Laval_086


title: hLung_Laval_108


title: hLung_Laval_098


title: hLung_Laval_083


title: hLung_Laval_096


title: hLung_Laval_097


title: hLung_Laval_085


title: hLung_Laval_081


title: hLung_Laval_073


title: hLung_Laval_074


title: hLung_Laval_080


title: hLung_Laval_076


title: hLung_Laval_075


title: hLung_Laval_072


title: hLung_Laval_061


title: hLung_Laval_060


title: hLung_Laval_067


title: hLung_Laval_062


title: hLung_Laval_068


title: hLung_Laval_069


title: hLung_Laval_066


title: hLung_Laval_057


title: hLung_Laval_059


title: hLung_Laval_070


title: hLung_Laval_063


title: hLung_Laval_077


title: hLung_Laval_058


title: hLung_Laval_071


title: hLung_Laval_055


title: hLung_Laval_064


title: hLung_Laval_078


title: hLung_Laval_065


title: hLung_Laval_056


title: hLung_Laval_053


title: hLung_Laval_054


title: hLung_Laval_052


title: hLung_Laval_049


title: hLung_Laval_047


title: hLung_Laval_048


title: hLung_Laval_044


title: hLung_Laval_042


title: hLung_Laval_039


title: hLung_Laval_038


title: hLung_Laval_051


title: hLung_Laval_050


title: hLung_Laval_040


title: hLung_Laval_034


title: hLung_Laval_043


title: hLung_Laval_035


title: hLung_Laval_033


title: hLung_Laval_037


title: hLung_Laval_031


title: hLung_Laval_028


title: hLung_Laval_032


title: hLung_Laval_029


title: hLung_Laval_041


title: hLung_Laval_045


title: hLung_Laval_036


title: hLung_Laval_027


title: hLung_Laval_046


title: Ring1A/B cKO expressing I53A Ring1B #1 (OHT-)

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing I53A Ring1B construct #1 (OHT-untreated)

hyb_protocol: The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes, and then injected into a GeneChip Mouse Genome 430 2.0 cartridge. The arrays were incubated at 45°C for 16 hours in a rotating oven at 60 rpm.

scan_protocol: Fluorescence signals on arrays were scanned using the Affymetrix GeneChip Scaner 3000 and information about each probe on the chip was extracted from the image data by the Affymetrix image analysis software, GeneChip Operating Software (GCOS).

data_processing: The Affymetrix Expression Console was used to normalize data and determine signal intensity (RMA-Sketch).

organism: Mus musculus

label_protocol: The ds-cDNA derived from total RNA was incubated at 37℃ for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme mix to synthesize biotin-labeled cRNA.

growth_protocol: ES cells were cultured in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.

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

treatment_protocol: To deplete endogenous Ring1B, Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells stably expressing either of mock, WT or mutant Ring1B construct were treated with 4-hydoxytamoxifen (OHT) at a concentration of 800nM for 24 hours.

tag: genotype/variation

tag: expression

value: I53A Ring1B construct #1

tag: treatment

value: OHT-untreated

tag: cell type

value: Embryonic stem cells

tag: background mouse strain

value: 129/B6 hybrid


title: hLung_Laval_030


title: Ring1A/B cKO expressing I53A Ring1B #1 (OHT+)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing I53A Ring1B construct #1 (2 days after the start of OHT treatment)

value: OHT treatment


title: hLung_Laval_026


title: Ring1A/B cKO expressing I53S Ring1B #1 (OHT+)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing I53S Ring1B construct #1 (2 days after the start of OHT treatment)

value: I53S Ring1B construct #1


title: hLung_Laval_025


title: Ring1A/B cKO expressing I53S Ring1B #4 (OHT+)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing I53S Ring1B construct #4 (2 days after the start of OHT treatment)

value: I53S Ring1B construct #4


title: hLung_Laval_022


title: hLung_Laval_020


title: Ring1A/B cKO expressing I53S Ring1B #1 (OHT-)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing I53S Ring1B construct #1 (OHT-untreated)


title: Ring1A/B cKO expressing WT Ring1B #1 (OHT+)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing WT Ring1B construct #1 (2 days after the start of OHT treatment)

value: WT Ring1B construct #1


title: hLung_Laval_018


title: Ring1A/B cKO expressing WT Ring1B #1 (OHT-)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing WT Ring1B construct #1 (OHT-untreated)


title: Ring1A/B cKO expressing WT Ring1B #3 (OHT-)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing WT Ring1B construct #3 (OHT-untreated)

value: WT Ring1B construct #3


title: hLung_Laval_021


title: hLung_Laval_016


title: hLung_Laval_013


title: hLung_Laval_019


title: hLung_Laval_014


title: hLung_Laval_082


title: hLung_Laval_023


title: hLung_Laval_008


title: Ring1A/B cKO mock (OHT+)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing an empty vector (2 days after the start of OHT treatment: Ring1A/B-dKO)

value: an empty vector

value: OHT treatment:Ring1A/B-dKO


title: hLung_Laval_010


title: hLung_Laval_012


title: hLung_Laval_015


title: hLung_Laval_006


title: hLung_Laval_011


title: hLung_Laval_009


title: hLung_Laval_007


title: hLung_Laval_017


title: Ring1A/B cKO mock (OHT-)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing an empty vector (OHT-untreated: Ring1A(-/-))


title: hLung_Laval_005


title: Ring1A/B cKO expressing I53S Ring1B #4 (OHT-)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing I53S Ring1B construct #4 (OHT-untreated)


title: hLung_Laval_002


title: hLung_Laval_003


title: hLung_Laval_001


title: tetrahydrofolate synthase 2 mutant  6475C5_F2_2_071508

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

country: USA

institute: Baylor College of Medicine

description: Biological replicate 2 of 3. Dye swap 2

hyb_protocol: For hybridization, yeast tRNA and salmon testes DNA were added to labeled cDNA along with a formamide hybridization buffer. Samples were applied to slides, and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

scan_protocol: Arrays were scanned on a Axon instruments GenePix 4000B scanner.  Images were processed using GenePix Pro software (version 4.1)  and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

data_processing: Data normalization between and within array using LOWESS usingAgilent Genespring GX 11.5 software

organism: Limosilactobacillus reuteri

source_name: bacteria

label_protocol: 2 ug of total RNA were primed with 2.5 ug of random hexamers (Qiagen) at 70 degrees Celsius for 10 minutes. Reverse transcription was then carried out using Superscript III (Invitrogen) with 500 uM each dATP, dCTP, and dGTP, 300 uM dTTP, and 200 uM aminoallyl dUTP. After reverse transcription, RNA was removed by hydrolysis and cDNA was cleaned. cDNA was then labeled using CyDye Post-labeling reactive dye packs (Amersham).

growth_protocol: Bacterial cells were grown for 24h in MRS at 37C in anaerobic conditions

extract_protocol: At the specified times, 5 ml of bacterial were collected and mixed with an equal part of ice-cold methanol. Cell pellets were centrifuged, washed, and resuspended in 0.25 units/ul mutanolysin. After incubation at 37 degrees Celsius for 20 minutes, total RNA was collected according to the manufacturer's instructions with the Qiagen RNeasy Kit.

tag: strain

value: ATCC PTA 6475

tag: genotype

value: wild type

source_name: Bacteria


title: tetrahydrofolate synthase 2 mutant  6475C5_F2_3_070308

description: Biological replicate 2d of 3. Dye swap 2


title: tetrahydrofolate synthase 2 mutant  6475C5_F2_1_070108

description: Biological replicate 1 of 3. Dye swap 2


title: tetrahydrofolate synthase 1 mutant 6475C5_F1_3_070108_Redo

description: Biological replicate 3 of 3. Dye swap 3


title: tetrahydrofolate synthase 2 mutant  6475C3_F2_1_070108

description: Biological replicate 1 of 3. Dye swap 1


title: tetrahydrofolate synthase 2 mutant  6475C3_F2_2_071508

description: Biological replicate 2 of 3. Dye swap 1


title: tetrahydrofolate synthase 1 mutant 6475C5_F1_2_060608


title: tetrahydrofolate synthase 1 mutant 6475C5_F1_2_062508Redo

description: Biological replicate 2 of 3. Dye swap 2


title: tetrahydrofolate synthase 1 mutant 6475C3_F1_3_062508Redo

description: Biological replicate 3 of 3. Dye swap 1


title: tetrahydrofolate synthase 1 mutant 6475C5_F1_1_060608

description: Biological replicate 1 of 3. Dye swap 2


title: tetrahydrofolate synthase 1 mutant 6475C3_F1_2_070108Redo

description: Biological replicate 2 of 3. Dye swap 1


title: tetrahydrofolate synthase 2 mutant  6475C3_F2_3_070308

description: Biological replicate 3 of 3. Dye swap 1


title: tetrahydrofolate synthase 1 mutant 6475C3_F1_1_060608

description: Biological replicate 1 of 3. Dye swap 1


title: hLung_Laval_079


title: HCT116_DMSO_72hr_rep6

status: Public on Jun 10 2012

type: genomic

city: Chapel Hill

first: Derek

last: Chiang

state: NC

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

institute: University of North Carolina

hyb_protocol: Genomic DNA was bisulfite converted with the Zymo Research EZ DNA Methylation kit.  Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged with the Illumina HiScan scanner using standard settings

data_processing: Mean background-corrected and normalized signal intensities of the methylation (M) and unmethylated (U) estimates for each CpG locus were extracted using Illumina BeadStudio software

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Genomic DNA from colorectal cancer cell line HCT116 treated with 1 micromolar 5-azacytidine

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA mini kit, according to the manufacturer's protocol

tag: disease

value: colorectal cancer

tag: cell line


title: hLung_Laval_004


title: Cholangiocarcinoma Q09_MayoCC027T

source_name: Genomic DNA from Cholangiocarcinoma Q09_MayoCC027T

value: cholangiocarcinoma

tag: idh1/2 genotype

value: wildtype


title: HCT116_DKO_WGA_rep2_glioblstoma study

source_name: Genomic DNA from HCT116 DNMT1;DNMT3 double knockout cell line

value: HCT116 DNMT1;DNMT3 double knockout


title: HCT116_DKO_WGA_rep7_glioblstoma study


title: HCT116_DKO_WGA_rep8_glioblstoma study


title: HCT116_1uM_5azadC_72hr_rep6_glioblstoma study


title: HCT116_DMSO_72hr_rep6_glioblstoma study

source_name: Genomic DNA from colorectal cancer cell line HCT116


title: HCT116_DKO_WGA_rep5_glioblstoma study


title: Cholangiocarcinoma Q04_MayoCC045T

source_name: Genomic DNA from Cholangiocarcinoma Q04_MayoCC045T


title: HCT116_DMSO_72hr_rep8_glioblstoma study


title: HCT116_DMSO_72hr_rep7_glioblstoma study


title: Cholangiocarcinoma Q07_MayoCC043T

source_name: Genomic DNA from Cholangiocarcinoma Q07_MayoCC043T


title: HCT116_1uM_5azadC_72hr_rep8_glioblstoma study


title: Cholangiocarcinoma Q02_MayoCC002T

source_name: Genomic DNA from Cholangiocarcinoma Q02_MayoCC002T


title: Cholangiocarcinoma Q10_MayoCC049T

source_name: Genomic DNA from Cholangiocarcinoma Q10_MayoCC049T


title: HCT116_1uM_5azadC_72hr_rep7_glioblstoma study


title: Cholangiocarcinoma Q12_MayoCC003T

source_name: Genomic DNA from Cholangiocarcinoma Q12_MayoCC003T


title: HCT116_DKO_WGA_rep3_glioblstoma study


title: hLung_Laval_024

value: lung

value: non-tumorous


title: Cholangiocarcinoma Q11_MayoCC026T

source_name: Genomic DNA from Cholangiocarcinoma Q11_MayoCC026T


title: Cholangiocarcinoma Q08_MayoCC033T

source_name: Genomic DNA from Cholangiocarcinoma Q08_MayoCC033T


title: Ring1A/B cKO expressing WT Ring1B #3 (OHT+)

description: Ring1A(-/-);Ring1B(fl/fl);Rosa26::CreERT2 ES cells expressing WT Ring1B construct #3 (2 days after the start of OHT treatment)

value: Embryonic stem cells


title: Cholangiocarcinoma Q03_MayoCC019T

source_name: Genomic DNA from Cholangiocarcinoma Q03_MayoCC019T


title: HCT116_DKO_WGA_rep1_glioblstoma study


title: Cholangiocarcinoma Q01_MayoCC047T

source_name: Genomic DNA from Cholangiocarcinoma Q01_MayoCC047T


title: ccRCC tumor of patient T22 (Illumina)

city: Dallas

first: Samuel

last: Peña-Llopis

address: 6000 Harry Hines Blvd., NB5.102

department: Internal Medicine - Oncology Division

institute: UT Southwestern Medical Center

description: Genomic DNA extracted from a ccRCC tumor was hybridized with the Illumina Human 1M-Duo DNA Analysis BeadChip.

hyb_protocol: Standard Illumina Beadchip protocol.

scan_protocol: Standard Illumina Beadchip protocol.

data_processing: Samples were analyzed with the Genotyping module of GenomeStudio (Illumina).

label: C-Bio and A-DNP

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T22 (Illumina)

label_protocol: Standard Illumina Beadchip protocol.

extract_protocol: A flash-frozen tumor tissue of clear-cell renal cell carcinoma was homogenized in Ambion's Lysis/binding buffer using an RNase-free pestle with alternating freeze/thaw cycles (dry and wet ice) and subsequently passed through a QIAshredder column (Qiagen). Genomic and mitochondrial DNA was extracted using Allprep columns (Qiagen).

tag: patient id

value: Clear-cell renal cell carcinoma (ccRCC) tumor

tag: gender

value: Male

tag: age

tag: disease state

value: Clear-cell renal cell carcinoma

tag: pathologic tnm staging

tag: Stage

value: III

tag: fuhrman grade

tag: bap1 status

tag: pbrm1 status

tag: vhl status

value: mutant


title: HCT116_DKO_WGA_rep6_glioblstoma study


title: Blood sample of patient T22 (Illumina)

description: Genomic DNA from a blood sample was hybridized with the Illumina Human 1M-Duo DNA Analysis BeadChip.

source_name: SNP array of blood sample of patient T22 (Illumina)

extract_protocol: Genomic DNA was extracted from the buffy coat using QIAamp DNA Blood Midi kit (Qiagen).

tag: tissue

value: Blood sample


title: HCT116_DKO_WGA_rep4_glioblstoma study


title: HCT116_1uM_5azadC_72hr_rep3_glioblstoma study


title: HCT116_DMSO_72hr_rep5_glioblstoma study


title: HCT116_DMSO_72hr_rep2_glioblstoma study


title: HCT116_1uM_5azadC_72hr_rep1_glioblstoma study


title: HCT116_1uM_5azadC_72hr_rep5_glioblstoma study


title: HCT116_DMSO_72hr_rep3_glioblstoma study


title: Glioblastoma N01_119

source_name: Genomic DNA from Glioblastoma N01_119

value: glioblastoma


title: HCT116_DMSO_72hr_rep4_glioblstoma study


title: Glioblastoma M02_69

source_name: Genomic DNA from Glioblastoma M02_69


title: HCT116_DMSO_72hr_rep1_glioblstoma study


title: Glioblastoma M04_57

source_name: Genomic DNA from Glioblastoma M04_57


title: Glioblastoma N03_61

source_name: Genomic DNA from Glioblastoma N03_61


title: Glioblastoma L07_34

source_name: Genomic DNA from Glioblastoma L07_34


title: Glioblastoma N09_231

source_name: Genomic DNA from Glioblastoma N09_231


title: Glioblastoma M11_118

source_name: Genomic DNA from Glioblastoma M11_118


title: Glioblastoma N10_102

source_name: Genomic DNA from Glioblastoma N10_102


title: Glioblastoma M08_224

source_name: Genomic DNA from Glioblastoma M08_224


title: Glioblastoma M10_100

source_name: Genomic DNA from Glioblastoma M10_100


title: Glioblastoma M03_217

source_name: Genomic DNA from Glioblastoma M03_217


title: Glioblastoma L11_71

source_name: Genomic DNA from Glioblastoma L11_71


title: Glioblastoma L04_187

source_name: Genomic DNA from Glioblastoma L04_187


title: Glioblastoma L09_127

source_name: Genomic DNA from Glioblastoma L09_127


title: HCT116_1uM_5azadC_72hr_rep4_glioblstoma study

source_name: Genomic DNA from colorectal cancer cell line HCT116 treated with 1 micromolar 5-azacytidine


title: Glioblastoma L01_80

source_name: Genomic DNA from Glioblastoma L01_80


title: HCT116_1uM_5azadC_72hr_rep2_glioblstoma study


title: Glioblastoma J07_73

source_name: Genomic DNA from Glioblastoma J07_73


title: Glioblastoma J08_248

source_name: Genomic DNA from Glioblastoma J08_248


title: Glioblastoma K12_238

source_name: Genomic DNA from Glioblastoma K12_238


title: Glioblastoma K11_83

source_name: Genomic DNA from Glioblastoma K11_83


title: Glioblastoma J09_87

source_name: Genomic DNA from Glioblastoma J09_87


title: Glioblastoma K02_72

source_name: Genomic DNA from Glioblastoma K02_72


title: Glioblastoma K10_63

source_name: Genomic DNA from Glioblastoma K10_63


title: Glioblastoma K09_209

source_name: Genomic DNA from Glioblastoma K09_209


title: Glioblastoma H06_204

source_name: Genomic DNA from Glioblastoma H06_204


title: Glioblastoma H03_206

source_name: Genomic DNA from Glioblastoma H03_206


title: Glioblastoma L02_226

source_name: Genomic DNA from Glioblastoma L02_226


title: Glioblastoma N06_58

source_name: Genomic DNA from Glioblastoma N06_58


title: Glioblastoma G02_85

source_name: Genomic DNA from Glioblastoma G02_85


title: Glioblastoma G09_221

source_name: Genomic DNA from Glioblastoma G09_221


title: Glioblastoma F08_150

source_name: Genomic DNA from Glioblastoma F08_150


title: Glioblastoma M07_49

source_name: Genomic DNA from Glioblastoma M07_49


title: Glioblastoma N12_140

source_name: Genomic DNA from Glioblastoma N12_140


title: Glioblastoma G04_208

source_name: Genomic DNA from Glioblastoma G04_208


title: Glioblastoma K06_96

source_name: Genomic DNA from Glioblastoma K06_96


title: Glioblastoma G05_220

source_name: Genomic DNA from Glioblastoma G05_220


title: Glioblastoma N08_158

source_name: Genomic DNA from Glioblastoma N08_158


title: Glioblastoma L05_101

source_name: Genomic DNA from Glioblastoma L05_101


title: Glioblastoma K07_232

source_name: Genomic DNA from Glioblastoma K07_232


title: Glioblastoma G12_40

source_name: Genomic DNA from Glioblastoma G12_40


title: Glioblastoma N04_152

source_name: Genomic DNA from Glioblastoma N04_152


title: Glioblastoma N05_233

source_name: Genomic DNA from Glioblastoma N05_233


title: Glioblastoma H09_94

source_name: Genomic DNA from Glioblastoma H09_94


title: Glioblastoma M01_174

source_name: Genomic DNA from Glioblastoma M01_174


title: Glioblastoma M06_215

source_name: Genomic DNA from Glioblastoma M06_215


title: Glioblastoma J10_156

source_name: Genomic DNA from Glioblastoma J10_156


title: Glioblastoma H05_165

source_name: Genomic DNA from Glioblastoma H05_165


title: Glioblastoma H07_219

source_name: Genomic DNA from Glioblastoma H07_219


title: Glioblastoma L08_180

source_name: Genomic DNA from Glioblastoma L08_180


title: Glioblastoma J06_173

source_name: Genomic DNA from Glioblastoma J06_173


title: Glioblastoma G08_155

source_name: Genomic DNA from Glioblastoma G08_155


title: Glioblastoma J02_182

source_name: Genomic DNA from Glioblastoma J02_182


title: Glioblastoma L12_194

source_name: Genomic DNA from Glioblastoma L12_194


title: Glioblastoma F05_203

source_name: Genomic DNA from Glioblastoma F05_203


title: Glioblastoma H04_188

source_name: Genomic DNA from Glioblastoma H04_188


title: Glioblastoma J12_185

source_name: Genomic DNA from Glioblastoma J12_185


title: SssI_Methylated_rep3_cholangiocarcinoma_study

source_name: Genomic DNA from HCT116 DNMT1;DNMT3 double knockout cell line, treated with M.SssI CpG methyltransferase


title: Glioblastoma H11_36

source_name: Genomic DNA from Glioblastoma H11_36


title: Glioblastoma K03_139

source_name: Genomic DNA from Glioblastoma K03_139


title: Glioblastoma F04_199

source_name: Genomic DNA from Glioblastoma F04_199


title: Glioblastoma G03_170

source_name: Genomic DNA from Glioblastoma G03_170


title: HCT116_1uM_5azadC_72hr_rep4_cholangiocarcinoma_study

source_name: Genomic DNA from colorectal cancer cell line HCT116 treated with 1 micromolar 5-azacytidine


title: SssI_Methylated_rep2_cholangiocarcinoma_study


title: HCT116_DMSO_72hr_rep5_cholangiocarcinoma_study

source_name: Genomic DNA from colorectal cancer cell line HCT116


title: HCT116_1uM_5azadC_72hr_rep3_cholangiocarcinoma_study


title: HCT116_DKO_rep4_cholangiocarcinoma_study

source_name: Genomic DNA from HCT116 DNMT1;DNMT3 double knockout cell line


title: Glioblastoma K05_154

source_name: Genomic DNA from Glioblastoma K05_154


title: HCT116_DKO_rep2_cholangiocarcinoma_study


title: SssI_Methylated_rep1_cholangiocarcinoma_study


title: HCT116_DMSO_72hr_rep4_cholangiocarcinoma_study


title: HCT116_DKO_rep1_cholangiocarcinoma_study


title: HCT116_DKO_rep3_cholangiocarcinoma_study


title: HCT116_1uM_5azadC_72hr_rep1_cholangiocarcinoma_study


title: HCT116_DMSO_72hr_rep2_cholangiocarcinoma_study


title: HCT116_DMSO_72hr_rep1_cholangiocarcinoma_study


title: HCT116_DMSO_72hr_rep3_cholangiocarcinoma_study


title: Cholangiocarcinoma E4_6158

source_name: Genomic DNA from Cholangiocarcinoma E4_6158


title: HCT116_1uM_5azadC_72hr_rep2_cholangiocarcinoma_study


title: Cholangiocarcinoma D12_5293

source_name: Genomic DNA from Cholangiocarcinoma D12_5293


title: Cholangiocarcinoma P06_CC5275

source_name: Genomic DNA from Cholangiocarcinoma P06_CC5275


title: Cholangiocarcinoma D3_3358

source_name: Genomic DNA from Cholangiocarcinoma D3_3358


title: Cholangiocarcinoma P10_6579T

source_name: Genomic DNA from Cholangiocarcinoma P10_6579T


title: Glioblastoma F01_109

source_name: Genomic DNA from Glioblastoma F01_109


title: Cholangiocarcinoma P08_6637T

source_name: Genomic DNA from Cholangiocarcinoma P08_6637T


title: SssI_Methylated_rep4_cholangiocarcinoma_study


title: Cholangiocarcinoma E12_4503

source_name: Genomic DNA from Cholangiocarcinoma E12_4503


title: Cholangiocarcinoma D4_6137

source_name: Genomic DNA from Cholangiocarcinoma D4_6137


title: Cholangiocarcinoma D7_4413

source_name: Genomic DNA from Cholangiocarcinoma D7_4413


title: Cholangiocarcinoma P03_6938T

source_name: Genomic DNA from Cholangiocarcinoma P03_6938T


title: Cholangiocarcinoma D5_4319

source_name: Genomic DNA from Cholangiocarcinoma D5_4319


title: Cholangiocarcinoma E2_3076

source_name: Genomic DNA from Cholangiocarcinoma E2_3076


title: Cholangiocarcinoma B12_6170

source_name: Genomic DNA from Cholangiocarcinoma B12_6170


title: Cholangiocarcinoma B10_5044

source_name: Genomic DNA from Cholangiocarcinoma B10_5044


title: Cholangiocarcinoma B5_5446

source_name: Genomic DNA from Cholangiocarcinoma B5_5446


title: Cholangiocarcinoma B6_6104

source_name: Genomic DNA from Cholangiocarcinoma B6_6104


title: Cholangiocarcinoma D2_4081

source_name: Genomic DNA from Cholangiocarcinoma D2_4081


title: Cholangiocarcinoma E11_3039

source_name: Genomic DNA from Cholangiocarcinoma E11_3039


title: Cholangiocarcinoma A8_6521

source_name: Genomic DNA from Cholangiocarcinoma A8_6521


title: Cholangiocarcinoma P02_7471T

source_name: Genomic DNA from Cholangiocarcinoma P02_7471T


title: Cholangiocarcinoma P05_5850T

source_name: Genomic DNA from Cholangiocarcinoma P05_5850T


title: Cholangiocarcinoma E9_6120

source_name: Genomic DNA from Cholangiocarcinoma E9_6120


title: Glioblastoma F12_214

source_name: Genomic DNA from Glioblastoma F12_214


title: Cholangiocarcinoma B1_5113

source_name: Genomic DNA from Cholangiocarcinoma B1_5113


title: Cholangiocarcinoma P01_CC6523

source_name: Genomic DNA from Cholangiocarcinoma P01_CC6523


title: Cholangiocarcinoma A7_5264

source_name: Genomic DNA from Cholangiocarcinoma A7_5264


title: Cholangiocarcinoma A11_4411

source_name: Genomic DNA from Cholangiocarcinoma A11_4411


title: Cholangiocarcinoma P12_6746T

source_name: Genomic DNA from Cholangiocarcinoma P12_6746T


title: Cholangiocarcinoma E7_8137

source_name: Genomic DNA from Cholangiocarcinoma E7_8137


title: Cholangiocarcinoma B11_5207

source_name: Genomic DNA from Cholangiocarcinoma B11_5207


title: Cholangiocarcinoma B3_7138

source_name: Genomic DNA from Cholangiocarcinoma B3_7138


title: Cholangiocarcinoma B8_7078

source_name: Genomic DNA from Cholangiocarcinoma B8_7078


title: Cholangiocarcinoma D9_7141

source_name: Genomic DNA from Cholangiocarcinoma D9_7141


title: Cholangiocarcinoma D1_3110

source_name: Genomic DNA from Cholangiocarcinoma D1_3110


title: Cholangiocarcinoma A2_4129

source_name: Genomic DNA from Cholangiocarcinoma A2_4129


title: Cholangiocarcinoma A4_5364

source_name: Genomic DNA from Cholangiocarcinoma A4_5364


title: Mouse tumorgraft from metastasis, cohort 1 of patient T183

hyb_protocol: Arrays were washed and hybridized using Affymetrix Fluidics Station 450.

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

data_processing: CEL files were pre-processed and normalized using the RMA algorithm through the Affy package of R/Bioconductor.

label: Biotin

source_name: Gene expression profiling of mouse tumorgraft from metastasis, cohort 1 of patient T183

label_protocol: RNA was reverse-transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix).

extract_protocol: Tissues were homogenized with an RNase-free pestle alternating freeze/thaw cycles and subsequently passed through a QIAshredder column (Qiagen). RNA fraction was extracted using mirVana (Ambion) kit.


title: Cholangiocarcinoma A6_7258

source_name: Genomic DNA from Cholangiocarcinoma A6_7258


title: Cholangiocarcinoma A10_6284

source_name: Genomic DNA from Cholangiocarcinoma A10_6284


title: Cholangiocarcinoma E5_7255

source_name: Genomic DNA from Cholangiocarcinoma E5_7255


title: Cholangiocarcinoma P11_982018B

source_name: Genomic DNA from Cholangiocarcinoma P11_982018B


title: Cholangiocarcinoma P07_6288T

source_name: Genomic DNA from Cholangiocarcinoma P07_6288T


title: Mouse tumorgraft, cohort 4 of patient T166

source_name: Gene expression profiling of mouse tumorgraft, cohort 4 of patient T166

value: Mouse tumorgraft, cohort 4


title: Mouse tumorgraft, cohort 0 of patient T166

source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T166

value: Mouse tumorgraft, cohort 0


title: Mouse tumorgraft, cohort 0 of patient T165

source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T165

value: wild type


title: Mouse tumorgraft, cohort 1 of patient T164

source_name: Gene expression profiling of mouse tumorgraft, cohort 1 of patient T164

value: Mouse tumorgraft, cohort 1


title: Mouse tumorgraft, cohort 2 of patient T158

source_name: Gene expression profiling of mouse tumorgraft, cohort 2 of patient T158

value: Mouse tumorgraft, cohort 2

value: Female


title: Mouse tumorgraft, cohort 1 of patient T158

source_name: Gene expression profiling of mouse tumorgraft, cohort 1 of patient T158


title: Mouse tumorgraft, cohort 8 of patient T166

source_name: Gene expression profiling of mouse tumorgraft, cohort 8 of patient T166

value: Mouse tumorgraft, cohort 8


title: Mouse tumorgraft, cohort 7 of patient T144

source_name: Gene expression profiling of mouse tumorgraft, cohort 7 of patient T144

value: Mouse tumorgraft, cohort 7


title: Mouse tumorgraft, cohort 3 of patient T144

source_name: Gene expression profiling of mouse tumorgraft, cohort 3 of patient T144

value: Mouse tumorgraft, cohort 3


title: Mouse tumorgraft, cohort 0 of patient T144

source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T144


title: Mouse tumorgraft, cohort 9 of patient T143

source_name: Gene expression profiling of mouse tumorgraft, cohort 9 of patient T143

value: Mouse tumorgraft, cohort 9


title: Mouse tumorgraft, cohort 4 of patient T143

source_name: Gene expression profiling of mouse tumorgraft, cohort 4 of patient T143


data_processing:
CHP files were generated from CEL files by Affymetrix's Genotyping Console 4.0 using Birdseed v2 algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

source_name: SNP array of mouse tumorgraft, cohort 4 of patient T166

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.

extract_protocol: Tissues were homogenized with an RNase-free pestle alternating freeze/thaw cycles and subsequently passed through a QIAshredder column (Qiagen). Genomic and mitochondrial DNA was extracted using Allprep columns (Qiagen). Blood DNA was extracted using QIAamp DNA Blood Midi kit (Qiagen).


source_name: SNP array of mouse tumorgraft, cohort 0 of patient T144


source_name: SNP array of mouse tumorgraft, cohort 1 of patient T164


source_name: SNP array of mouse tumorgraft, cohort 2 of patient T158


source_name: SNP array of mouse tumorgraft, cohort 3 of patient T144


source_name: SNP array of mouse tumorgraft, cohort 9 of patient T143


title: Mouse tumorgraft, cohort 0 of patient T143

source_name: SNP array of mouse tumorgraft, cohort 0 of patient T143


source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T143


title: Mouse tumorgraft, cohort 1 of patient T142

source_name: SNP array of mouse tumorgraft, cohort 1 of patient T142


source_name: SNP array of mouse tumorgraft from metastasis, cohort 1 of patient T183

value: Mouse tumorgraft from metastasis, cohort 1


source_name: SNP array of mouse tumorgraft, cohort 4 of patient T143


title: Mouse tumorgraft from metastasis, cohort 0 of patient T183

source_name: SNP array of mouse tumorgraft from metastasis, cohort 0 of patient T183

value: Male


source_name: SNP array of mouse tumorgraft, cohort 8 of patient T166

value: Clear-cell renal cell carcinoma


title: Mouse tumorgraft, cohort 4 of patient T164

source_name: SNP array of mouse tumorgraft, cohort 4 of patient T164


source_name: SNP array of mouse tumorgraft, cohort 7 of patient T144


source_name: SNP array of mouse tumorgraft, cohort 0 of patient T166


title: Mouse tumorgraft, cohort 0 of patient T84

source_name: SNP array of mouse tumorgraft, cohort 0 of patient T84


title: Mouse tumorgraft, cohort 2 of patient T142

source_name: Gene expression profiling of mouse tumorgraft, cohort 2 of patient T142


source_name: Gene expression profiling of mouse tumorgraft, cohort 1 of patient T142


title: Mouse tumorgraft, cohort 0 of patient T127

source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T127


title: Mouse tumorgraft, cohort 0 of patient T79

source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T79


source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T84


title: Mouse tumorgraft, cohort 2 of patient T127

source_name: Gene expression profiling of mouse tumorgraft, cohort 2 of patient T127


title: Mouse tumorgraft, cohort 8 of patient T26

source_name: Gene expression profiling of mouse tumorgraft, cohort 8 of patient T26


source_name: SNP array of mouse tumorgraft, cohort 0 of patient T127


source_name: SNP array of mouse tumorgraft, cohort 0 of patient T79


title: Mouse tumorgraft, cohort 4 of patient T26

source_name: Gene expression profiling of mouse tumorgraft, cohort 4 of patient T26


source_name: SNP array of mouse tumorgraft, cohort 4 of patient T26


source_name: SNP array of mouse tumorgraft, cohort 8 of patient T26


title: Mouse tumorgraft, cohort 0 of patient T22

source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T22


title: Mouse tumorgraft, cohort 0 of patient T26

source_name: SNP array of mouse tumorgraft, cohort 0 of patient T26


source_name: SNP array of mouse tumorgraft, cohort 2 of patient T142


title: Blood sample of patient T183

source_name: SNP array of Blood sample of patient T183


title: ccRCC tumor of patient T183

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T183

value: Clear-cell renal cell carcinoma (ccRCC) tumor

value: IV


title: ccRCC tumor of patient T166

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T166

value: III

value: mutant


title: ccRCC tumor of patient T165

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T165


title: Mouse tumorgraft, cohort 0 of patient T165

source_name: SNP array of mouse tumorgraft, cohort 0 of patient T165


title: ccRCC tumor of patient T183

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T183


source_name: Gene expression profiling of mouse tumorgraft, cohort 0 of patient T26


title: Mouse tumorgraft, cohort 1 of patient T158

source_name: SNP array of mouse tumorgraft, cohort 1 of patient T158


title: ccRCC tumor of patient T166

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T166


source_name: SNP array of mouse tumorgraft, cohort 2 of patient T127


title: Normal cortex of patient T166

source_name: SNP array of normal cortex of patient T166

value: Normal cortex


title: Normal cortex of patient T164

source_name: Gene expression profiling of normal cortex of patient T164


title: ccRCC tumor of patient T163

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T163

value: I


title: Normal cortex of patient T163

source_name: Gene expression profiling of normal cortex of patient T163

value: wild type


title: Normal cortex of patient T166

source_name: Gene expression profiling of normal cortex of patient T166


title: ccRCC tumor of patient T164

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T164


title: Normal cortex of patient T158

source_name: Gene expression profiling of normal cortex of patient T158


title: Normal cortex of patient T164

source_name: SNP array of normal cortex of patient T164


title: ccRCC tumor of patient T144

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T144


title: ccRCC tumor of patient T143

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T143


title: ccRCC tumor of patient T165

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T165


title: ccRCC tumor of patient T164

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T164


title: Normal cortex of patient T158

source_name: SNP array of normal cortex of patient T158


title: Normal cortex of patient T163

source_name: SNP array of normal cortex of patient T163


title: Normal cortex of patient T144

source_name: Gene expression profiling of normal cortex of patient T144


title: ccRCC tumor of patient T158

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T158


title: Normal cortex of patient T142

source_name: Gene expression profiling of normal cortex of patient T142


title: ccRCC tumor of patient T163

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T163


title: ccRCC tumor of patient T144

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T144


title: Blood sample of patient T165

source_name: SNP array of Blood sample of patient T165

value: Blood sample


title: ccRCC tumor of patient T127

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T127


title: ccRCC tumor of patient T84

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T84


title: ccRCC tumor of patient T142

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T142


title: ccRCC tumor of patient T158

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T158


title: Normal cortex of patient T127

source_name: Gene expression profiling of normal cortex of patient T127


title: Normal cortex of patient T127

source_name: SNP array of normal cortex of patient T127


title: ccRCC tumor of patient T142

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T142


title: Normal cortex of patient T79

source_name: Gene expression profiling of normal cortex of patient T79


title: Normal cortex of patient T144

source_name: SNP array of normal cortex of patient T144


title: ccRCC tumor of patient T22

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T22


title: ccRCC tumor of patient 1524

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 1524


title: Normal cortex of patient 1524

source_name: Gene expression profiling of normal cortex of patient 1524


title: Normal cortex of patient T142

source_name: SNP array of normal cortex of patient T142


title: ccRCC tumor of patient T127

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T127


title: ccRCC tumor of patient T79

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T79


title: ccRCC tumor of patient 1393

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 1393


title: ccRCC tumor of patient T143

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T143


title: ccRCC tumor of patient T26

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T26


title: Normal cortex of patient 1393

source_name: Gene expression profiling of normal cortex of patient 1393


title: ccRCC tumor of patient 325

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 325


title: ccRCC tumor of patient 324

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 324


title: Normal cortex of patient 325

source_name: Gene expression profiling of normal cortex of patient 325


title: FVB_skin_R3

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: Replicate 3.

hyb_protocol: The labeled DNA was added to a hybridization cocktail and then the sample was injected into the array (GeneChip Mouse Gene 1.0 ST Array). Washing and staining steps were carried out using GeneChip Fluidics Station 450.

scan_protocol: The probe arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara CA).

data_processing: Signal intensities from each array were analyzed using Partek Genomic Suite version 6.4 (Partek, Saint Louis MI). Raw intensity probe values were normalized using robust multiarray analysis background correction (RMA). A two-way ANOVA was performed to identify differentially expressed genes.

source_name: FVB/N control virgin mice, skin

label_protocol: cDNA synthesis, amplification, and gene expression profiling were performed according to the manufacturer´s instructions. Specifically, 1 µg of total RNA was used to generate double-stranded cDNA by reverse transcription using an oligo(dT) primer containing a T7 RNA polymerase promoter followed by an in vitro transcription to obtain cRNA molecules. A second cDNA synthesis was performed incorporating dUTP nucleotides to the newly generated strand. Then, cDNA fragmentation was performed using a combination of uracil DNA glycosylase (UDG) and apurinic/apirymidinic endonuclease 1 (APE1). Following fragmentation, the resulting fragmented DNA was labeled using terminal deoxynucleotidyl transferase (TdT) in the presence of biotinylated nucleotides.

extract_protocol: Biopsies were immediately stored in RNAlater Solution (Ambion) at 4°C overnight. Tissue was recovered from RNAlater solution with sterile forceps, quickly blotted to remove excess RNAlater and immediately snap frozen in liquid nitrogen. Total RNA was extracted from snap-frozen tissue using standard procedures (TRIzol reagent, Invitrogen).

value: FVB/N

tag: sample type

value: control

value: female

value: 1.5 months

value: skin biopsy


title: FVB_skin_R1

description: Replicate 1.

tag: strain


title: ccRCC tumor of patient T26

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T26


title: Normal cortex of patient 324

source_name: Gene expression profiling of normal cortex of patient 324


title: ccRCC tumor of patient 265

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 265

value: Female


title: FVB_skin_R2

description: Replicate 2.


title: FVB_cvx_R3

description: Replicate 3.

source_name: FVB/N control virgin mice, cervix

value: cervix biopsy


title: Normal cortex of patient 265

source_name: Gene expression profiling of normal cortex of patient 265


title: Normal cortex of patient T84

source_name: SNP array of normal cortex of patient T84

value: Male


title: ccRCC tumor of patient T84

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T84

value: Clear-cell renal cell carcinoma


title: ccRCC tumor of patient T79

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T79

value: Clear-cell renal cell carcinoma (ccRCC) tumor


title: Normal cortex of patient T79

source_name: SNP array of normal cortex of patient T79


source_name: SNP array of Metastasis of ccRCC tumor of patient T183

value: Metastasis of ccRCC tumor

value: IV


title: ccRCC tumor of patient 260

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 260

value: mutant


title: ccRCC tumor of patient 325

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 325


title: Normal cortex of patient 260

source_name: Gene expression profiling of normal cortex of patient 260

value: Normal cortex


title: FVB_cvx_R2

description: Replicate 2.


title: Blood sample of patient T26

source_name: SNP array of Blood sample of patient T26


title: ccRCC tumor of patient 233

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 233


title: Normal cortex of patient 1393

source_name: SNP array of normal cortex of patient 1393


title: Normal cortex of patient 325

source_name: SNP array of normal cortex of patient 325


title: ccRCC tumor of patient 1393

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 1393


title: Normal cortex of patient 233

source_name: Gene expression profiling of normal cortex of patient 233


title: Normal cortex of patient 209

source_name: Gene expression profiling of normal cortex of patient 209


title: E7_Skin_R3

description: Replicate 3.

source_name: Transgenic E7 mouse, skin

value: K14E7 transgenic


title: FVB_cvx_R1

description: Replicate 1.

source_name: FVB/N control virgin mice, cervix


title: ccRCC tumor of patient 209

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 209

value: I

value: wild type


title: E7_Skin_R2

description: Replicate 2.


title: ccRCC tumor of patient 111

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 111


title: E7_Skin_R1

description: Replicate 1.


title: ccRCC tumor of patient 131

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 131


title: ccRCC tumor of patient 131

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 131


title: Normal cortex of patient 131

source_name: Gene expression profiling of normal cortex of patient 131


title: Normal cortex of patient 265

source_name: SNP array of normal cortex of patient 265


title: Normal cortex of patient 324

source_name: SNP array of normal cortex of patient 324


title: Normal cortex of patient 111

source_name: Gene expression profiling of normal cortex of patient 111


title: ccRCC tumor of patient 324

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 324


title: Normal cortex of patient 260

source_name: SNP array of normal cortex of patient 260


title: E7_Cervix_R3

description: Replicate 3.

source_name: Transgenic E7 mouse, cervix


title: E7_Cervix_R2

description: Replicate 2.


title: ccRCC tumor of patient 265

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 265


title: Normal cortex of patient 83

source_name: Gene expression profiling of normal cortex of patient 83


title: ccRCC tumor of patient 75

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 75

value: II


title: ccRCC tumor of patient 233

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 233


title: ccRCC tumor of patient 83

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 83

value: loss


title: Normal cortex of patient 75

source_name: Gene expression profiling of normal cortex of patient 75


title: Normal cortex of patient 131

source_name: SNP array of normal cortex of patient 131


title: ccRCC tumor of patient 42

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 42


title: E7_Cervix_R1

description: Replicate 1.

value: female


title: Normal cortex of patient 42

source_name: Gene expression profiling of normal cortex of patient 42


title: Control siRNA -E2 vs. PES1 siRNA +E2

city: Beijing

first: cheng

last: long

address: 27 Tai-Ping Lu Rd

country: China

institute: Beijing Institute of Biotechnology

description: sip+/c-

hyb_protocol: Labeled DNA was resuspended in 80 μl of hybridization buffer containing 3×SSC, 0.2% SDS, 5×Denhart’s, and 25% formamide. The hybridization was performed at 42°C overnight and then washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Images were scanned with a confocal LuxScanTM scanner and quantified with LuxScan TM software (CapitalBio Corp, Beijing, China).

data_processing: For individual channel data extract, faint spots were removed for which intensities were below 400 unit after background subtracted in both channels (Cy3 and Cy5). A space- and intensity-dependent normalization based on a LOWESS program was employed (using the R statistical software package). To determine the significant differentially expressed genes, Significance Analysis of Microarrays (SAM, version 3.02) were performed.

source_name: Control siRNA -E2

label_protocol: The purified cDNA was labeled with Cy5-dCTP or Cy3-dCTP (GE Healthcare Cat. No. PA 55021/ PA53021).

growth_protocol: Cells were cultured in medium containing phenol red-free DMEM supplemented with 10% charcoal dextran-treated FBS (Hyclone).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: After cultured for 3 days, cells were treated for E2 (10nM) for 24h, or untreated

tag: protocol

value: transfected with control siRNA

tag: agent

value: control (treated without E2)

source_name: PES1 siRNA +E2

value: transfected with PES1 siRNA

value: E2 (for 24hr)


title: Normal cortex of patient 233

source_name: SNP array of normal cortex of patient 233

value: Female


title: ccRCC tumor of patient 26

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 26

value: Clear-cell renal cell carcinoma


title: Control siRNA -E2 vs. PES1 siRNA -E2

description: c-/sip-

tag: cell line

source_name: PES1 siRNA -E2


title: Normal cortex of patient 26

source_name: Gene expression profiling of normal cortex of patient 26


title: ccRCC tumor of patient 14

source_name: Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 14

value: Clear-cell renal cell carcinoma (ccRCC) tumor


title: CHCC5086_versus_CHCC5376_Milk_pH5.7

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

hyb_protocol: According to the Amersham protocol the Cy3 and Cy5 labelled cDNA were combined and lyophilized. Hereafter they were resuspended in 7uL of nuclease free water and, 5uL of hybdridization buffer (4x), and 8uL of formamide was added. This 20uL solution was applied to the array under a 24x24mm LifterSlip (Erie Scientific Company, Portsmouth, NH) and put in an airtight box containing paper towels soaked with NaCl-saturated water. Arrays were hybridized for 16-20h at 42ºC, and then washed using the UltraGAPS protocol (Corning B.V.).

scan_protocol: Arrays were scanned using the GenePix 4100A Personal Scanner with GenePix Pro 6.0 software (Axon Instruments Inc., Union City, CA). The photo multiplier tube (PMT) sensitivity values of the scan were adjusted around 660 for Cy5 and 520 for Cy3 to obtain only few saturated spots on each array and about equal total signal for each dye.

data_processing:
A grid with 130um spots was laid over the array and was manually adjusted to fit small irregularities in spotting. Spots clearly covered by for example dust particles were flagged “Bad”. The intensity of all spots was then calculated using the “Analyze” function. Spots with very weak signals in both channels were also flagged “Bad”. These were spots where the signal-to-noise ratio [SNR] < 1 in both channels, or where [% > B + 2SD] < 20 in both channels. All other spots were considered “Found” and had a “Flag” value of >= 0. All data was exported from GenePix Pro in tab-delimited format.
In the further analysis the variables of feature (spot) intensity minus the background intensity around the spot was used, i.e. [F635 median – B635]=Cy5 and [F532 median – B532]=Cy3. The log2(ratio) of this was calculated as log2(Cy5/Cy3). Some spots may have a significant signal in one channel but no signal in the other channel. The latter may result in a negative value due to noise and thus and illegal log2(ratio). To avoid this a macro in Excel 2000 (Microsoft Corporation, Redmond, WA) was used to change [F635 median – B635] and [F532 median – B532] values of <10 to 10 for “Found” spots (the signal scale goes from 0, no signal, to 65535, saturated signal). For these spots the log2(ratio) was re-calculated. The corrected data was exported from Excel and imported into Acuity 4.0 (Axon) where they were ratio-normalized based on the “Found” spots.
In Acuity a dataset was created. For the array only genes were included where 1) 2 of the 2 replicate spots were “Found”, 2) <30% of the pixels in “Found” spots, in both channels, were saturated, and 3) the Cy3 or Cy5 signal (see above) was >200.

organism: Streptococcus thermophilus

label_protocol: 10ug of total RNA was lyophilized in a speed-vac. The copying into cDNA and labeling with either Cy3 (reference) or Cy5 (test) was done using the CyScribe Post-Labelling Kit using manufacturer’s protocol (Amersham Biosciences, Hillerød, Denmark). 1uL of random nonamer was used for priming.

growth_protocol: See under Characteristics.

extract_protocol: At pH 5.7 samples of 0.67mL were collected in 1.33mL RNAprotect according to protocol (QIAGEN, Valencia, CA). Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) except for the following: the 200uL TE buffer contained 15mg/mL of lysozyme, 15uL of proteinase K at 20mg/mL, and 2uL of mutanolysin at 25U/uL with vortexing every 10s at 37ºC for the 2min. The quality and concentration of RNA was determined using the RNA 6000 Nano Kit on the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Routinely, 20-50ug of total RNA was obtained. Only high quality total RNA, as indicated by two sharp rRNA peaks, was used.

treatment_protocol: See under Characteristics.

value: incoulated at 1% stationary culture into 9.5% boiled Skimmed Milk Powder at 37ºC. Sample harvested at pH 5.7.


title: ccRCC tumor of patient 111

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 111


title: Control siRNA -E2 vs. Control siRNA +E2

description: c-/c+

source_name: Control siRNA +E2


title: Normal cortex of patient 14

source_name: Gene expression profiling of normal cortex of patient 14


title: Heart ventricle, poor swimmer, fish 7

status: Public on Jun 09 2012

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays.

scan_protocol: Arrays were scanned with a GenePix 4100A DNA microarray scanner at a resolution of 5 microns.

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1 and GenePix Pro 6.0. After removal of flagged spots, Lowess normalization was performed.

organism: Salmo salar

source_name: Heart ventricle of challenged salmon, poor swimmer

label_protocol: Amplified and labeled according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol using the Agilent Quick Amp Labelling Kit.

growth_protocol: Salmon (average weight 100g) were kept in tanks with seawater.

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with PureLink RNA mini kits.

treatment_protocol: A cohabitation challenge test started when 20% of IPN-infected challenger fish were added to the experimental tank. A similar proportion of uninfected smolts were added to the unchallenged tank, keeping similar densities in both tanks. Challenger fish were previously marked by a fin clip and injected with 5 ml of ~3 x 106 TCID50/ml of IPNV.

tag: group

value: poor swimmer

value: heart ventricle

tag: developmental stage

value: post-smolt

tag: treatment

value: infectious pancreatic necrosis virus (IPNV) challenge

source_name: Heart ventricle of un-challenged salmon (n=9)

value: no challenge

value: reference


title: PHH IFNgamma 24 hours donor 160

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: The Hybridization and Wash Kit (Affymetrix) was used to hybridize all samples. (TIME, TEMP????)

scan_protocol: SCANNER TYPE

data_processing: Microarray data were preprocessed using standard RMA algorithm as implemented in the OLIGO package of Bioconductor libraries of R statistical environment.

source_name: primary human hepatocytes treated with 1000 IU/ml interferon gamma for 24 hours, donor #160

label_protocol: 500 ng of total RNA was reverse transcribed and biotinylated with the whole-transcript Expression Kit (Ambion) and whole-transcript Terminal Labeling Kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: Primary human hepatocytes (PHH) were isolated from liver resections obtained from non-infected patients at described previously 15. Freshly isolated PHH were seeded on 6-well-plates precoated with collagen (BD Biosciences) and maintained in culture in William's E medium (Sigma) supplemented with 1% Glutamax (Gibco), 1% insulin transferrin selenium (Gibco), 10-7 M dexamethasone (Sigma), 0.15% BSA (Sigma), and 10% FBS (PAN Biotec).

extract_protocol: Total RNA was extracted from the PHH using Qiazol reagent and RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction

treatment_protocol: PHHs were treated with 1000U/mL of human IFN-alpha (Roferon, Roche) or human IFN-gamma (BioLegend) for 6 or 24 hours.

tag: cell type

value: isolated primary human hepatocytes

value: IFNgamma

tag: time

tag: donor


title: Heart ventricle, poor swimmer, fish 9


title: Heart ventricle, poor swimmer, fish 6


title: PHH IFNgamma 24 hours donor 156

source_name: primary human hepatocytes treated with 1000 IU/ml interferon gamma for 24 hours, donor #156


title: Heart ventricle, poor swimmer, fish 5


title: Heart ventricle, poor swimmer, fish 4


title: PHH IFNgamma 6 hours donor 160

source_name: primary human hepatocytes treated with 1000 IU/ml interferon gamma for 6 hours, donor #160


title: ccRCC tumor of patient 260

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 260

tag: patient id

tag: gender

tag: age

tag: disease state

tag: pathologic tnm staging

tag: Stage

value: wild type

value: mutant


title: PHH IFNalpha 24 hours donor 160

source_name: primary human hepatocytes treated with 1000 IU/ml interferon alpha for 24 hours, donor #160


title: Heart ventricle, poor swimmer, fish 2

tag: tissue

tag: sample type


title: PHH IFNgamma 6 hours donor 156

source_name: primary human hepatocytes treated with 1000 IU/ml interferon gamma for 6 hours, donor #156


title: PHH IFNalpha 6 hours donor 160

source_name: primary human hepatocytes treated with 1000 IU/ml interferon alpha for 6 hours, donor #160

value: IFNalpha


title: PHH untreated donor 156

source_name: primary human hepatocytes, untreated, donor #156

value: untreated

value: control


title: Heart ventricle, poor swimmer, fish 1


title: Heart ventricle, good swimmer, fish 9

source_name: Heart ventricle of challenged salmon, good swimmer

value: good swimmer


title: PHH IFNalpha 24 hours donor 156

source_name: primary human hepatocytes treated with 1000 IU/ml interferon alpha for 24 hours, donor #156


title: Heart ventricle, good swimmer, fish 7


title: PHH untreated donor 160

source_name: primary human hepatocytes, untreated, donor #160


title: Heart ventricle, poor swimmer, fish 3


title: Heart ventricle, good swimmer, fish 6


title: Normal cortex of patient 111

source_name: SNP array of normal cortex of patient 111

value: Normal cortex

value: Female

value: Clear-cell renal cell carcinoma

tag: bap1 status

tag: pbrm1 status

tag: vhl status


title: Heart ventricle, good swimmer, fish 8

tag: group


title: C2C12_Plin2_siRNA_oleate

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.3).

source_name: cultured C2C12 myotubes, transfected with Plin2 siRNA, treatment with oleic acid

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: C2C12 cells (LGC standards, Teddington, USA) were maintained in DMEM (Invitrogen, Breda, The Netherlands) containing antibiotics supplemented with 10% FCS, grown on ECM matrigel (Sigma, St. Louis, USA) coated cell culture plates, and differentiated over the course of a week in DMEM supplemented with 2% FCS (differentiation media).

extract_protocol: Purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) 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: Cells were treated with 200µM fatty acids (20h) (oleic acid or palmitic acid conjugated to BSA, ratio BSA to FA 1:2.5), or only BSA as a control. For RNAi experiments, cells were transfected with 10 nM Stealth RNAi oligos using Lipofectamine RNAiMAX (Invitrogen, Breda, The Netherlands) as transfection reagent.

tag: cell line


title: Heart ventricle, good swimmer, fish 5

tag: developmental stage

tag: treatment


title: Heart ventricle, poor swimmer, fish 8

value: poor swimmer


title: PHH IFNalpha 6 hours donor 156

source_name: primary human hepatocytes treated with 1000 IU/ml interferon alpha for 6 hours, donor #156

tag: cell type

tag: time


title: Leukaemia drug resistant VLB100 microparticles

city: Sydney

first: Ritu

last: Jaiswal

address: 92 - 94 Parramatta Rd

country: Australia

institute: The University of Sydney

description: Microparticle from drug resistant donor cell (VLBMP)

hyb_protocol: RNA labelling and hybridization was done using Affymetrix™ Fluidics Station 450.

scan_protocol: Gene chips were scanned using GeneChip® Scanner 3000 7G.

data_processing: Data were processed with AffymetrixTM miRNA QCTool software and following the default workflow as described in the user manual. Sgnal intensities calculated by Wilcoxon-Rank Sum test, followed by background adjustment based on the GC content of ‘anti-genomic’ probes, quantile normalization, addition of a small constant (value 16) to avoid negative signal after background-GC correction, and finally applying median summarization to all probe set in each sample

source_name: Leukaemia drug resistant MP

growth_protocol: Microparticles from resistant leukaemia (VLBMP) breast cancer cells (DXMP) were  coincubated with their sensitve counterparts CEM or MCF-7 cells, respectively, for 4 h in complete culture medium at 37°C and 5% CO2.

treatment_protocol: Unbound Microparticels were removed by washing with PBS and centrifuging at 500 g for 5 min at 25°C after 4 h from the MP co-incubated cells (CEM+VLBMP or MCF+DXMP). The control sensitive cells (CEM or MCF-7), the donor resistant cells (VLB or DX) and microparticles isolated from them (VLBMP or DXMP) were also washed with PBS as decribed.

value: VLB100 microparticle


title: C2C12_Plin2_siRNA_control

source_name: cultured C2C12 myotubes, transfected with Plin2 siRNA, control treatment (BSA only)


title: Heart ventricle, good swimmer, fish 3

value: heart ventricle

value: post-smolt

source_name: Heart ventricle of un-challenged salmon (n=9)


title: Heart ventricle, good swimmer, fish 4

value: infectious pancreatic necrosis virus (IPNV) challenge

value: no challenge


title: Heart ventricle, good swimmer, fish 2

value: reference


title: Normal cortex of patient 75

source_name: SNP array of normal cortex of patient 75

tag: patient id


title: Heart ventricle, good swimmer, fish 1


title: Leukaemia drug resistant cell VLB100

description: Drug resistant donor cell (VLB)

source_name: Leukaemia drug resistant cell

label_protocol: RNA labelling and hybridization was done using Affymetrix™ Fluidics Station 450.

value: total RNA


title: Leukaemia coculture CEM + VLB100 microparticles

description: CEM+VLBMP (senstive cell+drug resistant microparticle)

source_name: Leukaemia cells

value: CEM


title: ccRCC tumor of patient 75

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 75

value: Clear-cell renal cell carcinoma (ccRCC) tumor

tag: gender

value: II

tag: fuhrman grade

value: wild type

value: mutant


title: C2C12_scrambled_siRNA_control

source_name: cultured C2C12 myotubes, transfected with scrambled (control) siRNA, control treatment (BSA only)


title: C2C12_scrambled_siRNA_palmitate

source_name: cultured C2C12 myotubes, transfected with scrambled (control) siRNA, treatment with palmitic acid


title: C2C12_scrambled_siRNA_oleate

source_name: cultured C2C12 myotubes, transfected with scrambled (control) siRNA, treatment with oleic acid


title: C2C12_Plin2_siRNA_palmitate

source_name: cultured C2C12 myotubes, transfected with Plin2 siRNA, treatment with palmitic acid


title: Acute hepatitis C patient 6

hyb_protocol: The Hybridization, Wash and Stain Kit (Affymetrix) was used to hybridize all samples for 17 hours at 45°C in Affymetrix hybridization oven 645. The arrays were washed and stained on Fluidics station 450 using wash protocol FS450_0004 (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the arrays.

data_processing: Microarray data were preprocessed using standard RMA algorithm as implemented in the AFFY package of Bioconductor libraries of R statistical environment. Batch effects observed between the human liver samples processed and hybridized at different times were corrected using the ComBat algorithm (Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007;8:118-27.)

source_name: liver biopsy, acute hepatitis C, patient 6

label_protocol: 1 ug of total RNA was reverse transcribed, amplified, labelled and fragmented with GeneChip 3'IVT Express Kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: All patients were recruited in the Hepatology Outpatient Clinic of the University Hospital Basel, Switzerland. From October 2007 to December 2010, 6 patients with AHC (between 0-6 months after the HCV transmission) gave written informed consent to participate in this study and donated a liver biopsy specimen for research purposes. The study was approved by the Ethics Committee of Basel. Liver biopsies from 16 patients with CHC and 4 normal liver tissue samples were used for comparative analysis. These samples have been obtained during a previous study that has been published 7. The data reported in that paper have been deposited in the Gene Expression Omnibus database, www.ncbi.nlm.nih.gov/geo (accession no. GSE11190).

extract_protocol: Total RNA was extracted from the liver samples using Qiazol reagent and miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction

value: liver biopsy

tag: disease state

value: acute hepatitis


title: ccRCC tumor of patient 83

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 83

value: Female

tag: age

tag: pathologic tnm staging

value: I

value: loss


title: Healthy liver sample patient3

source_name: liver biopsy, healthy liver, patient 3

tag: tissue

value: healthy


title: Acute hepatitis C patient 5

source_name: liver biopsy, acute hepatitis C, patient 5


title: Healthy liver sample patient4

source_name: liver biopsy, healthy liver, patient 4


title: Breast drug resistant DX microparticles

description: Microparticle from drug resistant donor cell (DXMP)

source_name: Breast drug resistant cell

tag: sample type

value: DX microparticle

value: DX


title: Leukaemia drug sensitve cell CEM

description: Leukeamia drug sensitve parental cell (CEM)

source_name: Leukaemia drug sensitve cell


title: ccRCC tumor of patient 42

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 42

value: Male

value: Clear-cell renal cell carcinoma

tag: Stage

tag: bap1 status


title: Normal cortex of patient 42

source_name: SNP array of normal cortex of patient 42

value: Normal cortex

tag: pbrm1 status

tag: vhl status


title: Breast drug resistant cell DX

description: Drug resistant donor cell (DX)

value: total RNA

tag: cell line


title: Breast coculture MCF-7 + DX microparticles

description: MCF+DXMP (senstive cell+drug resistant microparticle)

source_name: Breast cancer cell


title: Acute hepatitis C patient 3

source_name: liver biopsy, acute hepatitis C, patient 3


title: Acute hepatitis C patient 4

source_name: liver biopsy, acute hepatitis C, patient 4


title: Normal cortex of patient 83

source_name: SNP array of normal cortex of patient 83


title: ccRCC tumor of patient 14

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 14


title: Breast cancer drug sensitve cell MCF-7

description: Breast cancer drug sensitve parental cell (MCF-7)

source_name: Breast cancer drug sensitve cell


title: ccRCC tumor of patient 26

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient 26


title: Acute hepatitis C patient 1

source_name: liver biopsy, acute hepatitis C, patient 1


title: Acute hepatitis C patient 2

source_name: liver biopsy, acute hepatitis C, patient 2


title: Blood sample of patient T22 (Affymetrix)

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: CHP files were generated from CEL files by Affymetrix's Genotyping Console 4.0 using Birdseed v2 algorithm.

source_name: SNP array of blood sample of patient T22 (Affymetrix)

value: Blood sample


title: Melanoma_metastasis METMEL291

status: Public on Jun 08 2012

city: Nashville

first: Leon

last: Raskin

state: TN

address: 2525 West End Avenue, Suite 300

department: Medicine

institute: Vanderbilt University

description: amplified using Nugen WT-Ovation™

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Expression data on 76 samples and 54,675 probes on U133 Plus 2.0 array were first subjected for quality assessment by creating the density plot of the log-intensity and RNA degradation plot corresponding to each sample. For all 76 samples, MAS 5.0-calculated signal intensities were normalized using the quantile normalization procedure implemented in robust multiarray analysis and the normalized data were log 2 transformed. Filtering was done to exclude probe sets that were not expressed or probe sets that exhibited low variability across samples. Expression values were required to be above the lower quartile of all expression measurements in at least 25% of samples, and the interquartile range across the samples on log 2 scale was required to be at least 0.5. After preprocessing and quality assessment, 74 samples and 44,137 probe sets were subjected to further analysis.

source_name: Frozen melanoma metastasis

label_protocol: The RNA samples were labeled with IVT labelling kit according to manufacturer's instructions.

extract_protocol: Frozen blocks were microdissected and total RNA was extracted using TRIzol protocol and Qiagen RNeasy purification kit according to the manufacturer's instructions.

value: f

tag: age at diagnosis

tag: diagnosis

value: REGIONAL LYMPH NODE METASTASIS

tag: regional metastases

value: YES

tag: distant metastases

value: NO

tag: braf mutation status

value: WT

tag: nras mutation status


title: Melanoma_metastasis METMEL361

description: amplified using Nugen WT-Ovation™

tag: gender

value: m

value: SUBCUTANIOUS SOFT TISSUE METASTASIS


title: Melanoma_metastasis METMEL200708

description: amplified using Nugen WT-Ovation™


title: Melanoma_metastasis METMEL308

description: amplified using Nugen WT-Ovation™


title: Normal cortex of patient 26

source_name: SNP array of normal cortex of patient 26

tag: patient id

value: Female

tag: disease state

value: wild type


title: Melanoma_metastasis METMEL200707

description: amplified using Nugen WT-Ovation™

value: DISTANT METASTASIS


title: Melanoma_metastasis METMEL381

description: amplified using Nugen WT-Ovation™


title: Normal cortex of patient 14

source_name: SNP array of normal cortex of patient 14

tag: age


title: Melanoma_metastasis METMEL261

description: amplified using Nugen WT-Ovation™


title: Melanoma_metastasis METMEL200703

description: amplified using Nugen WT-Ovation™


title: Melanoma_metastasis METMEL200701

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL429

description: amplified using Nugen WT-Ovation™

source_name: Frozen half of the melanoma punch biopsy

value: NODULAR MELANOMA


title: Mouse tumorgraft, cohort 0 of patient T22 (Affymetrix)

source_name: SNP array of mouse tumorgraft, cohort 0 of patient T22 (Affymetrix)

extract_protocol: Flash-frozen tissue was homogenized in Ambion's Lysis/binding buffer using an RNase-free pestle with alternating freeze/thaw cycles (dry and wet ice) and subsequently passed through a QIAshredder column (Qiagen). Genomic and mitochondrial DNA was extracted using Allprep columns (Qiagen).

tag: tissue

value: Mouse tumorgraft, cohort 0

value: mutant


title: Melanoma_metastasis METMEL240

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL420

description: amplified using Nugen WT-Ovation™

value: LMM


title: Primary_melanoma MEL430

description: amplified using Nugen WT-Ovation™

value: SSM


title: Primary_melanoma MEL380

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL375

description: amplified using Nugen WT-Ovation™


title: Melanoma_metastasis METMEL200705

description: amplified using Nugen WT-Ovation™


title: LoVo-negative

city: Tokyo

first: Yoko

last: Matsuda

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Pathology

institute: Nippon Medical School

description: Gene expression after 48hr in anti-GFP antibody treated colorectal cancer cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: human colorectal cancer cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LoVo and HCT-15 cells were plated at a density of 2.5 × 105 cells in a 60-mm dish, and grown overnight in RPIM 1640 medium supplemented with 10% FBS.

extract_protocol: Total RNA extraction from cells was performed using a High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Then 100 μg/ml of monoclonal anti-human FGFR2IIIc antibody was added in each dish. For control groups, an equal amount of anti-GFP antibody was added in another dish. Cells were incubated for 48hr at 37°C  under a humidified 5% CO2 atmosphere.

tag: cell type

value: human colorectal cancer cell

value: LoVo

tag: treatment

value: anti-GFP antibody treated


title: Melanoma_metastasis METMEL195

description: amplified using Nugen WT-Ovation™

value: REGIONAL LYMPH NODE METASTASIS


title: LoVo-FGFR Ab

description: Gene expression after 48hr in anti-FGFR2IIIc antibody treated colorectal cancer cells

value: anti-FGFR2IIIc antibody treated


title: Primary_melanoma MEL395

description: amplified using Nugen WT-Ovation™

value: NO


title: HCT-FGFR Ab


title: HCT-negative


title: Primary_melanoma MEL364

description: amplified using Nugen WT-Ovation™

value: f

value: WT


title: Week 60 3 aortic arch

city: Stockholm

first: Johan

middle: Lars Markus

last: Björkegren

state: Stockholm

address: Scheelesv. 2

department: The Department of Medical Biophysics and Biochemistry

country: Sweden

institute: The Vascular Biology Unit

description: Gene expression data from aortic arch at week 60

hyb_protocol: According to the standard Affymetrix protocols.

scan_protocol: According to the standard Affymetrix protocols using GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (Affymetrix) using default analysis settings.

source_name: Week 60 3 aortic arch

label_protocol: Biotinylated cRNA were prepared using the 2-cycle protocol according to the standard Affymetrix protocols.

extract_protocol: Aortas were perfused with RNAlater (Qiagen), and the aortic arch from above the third rib to the aortic root was removed and homogenized with FastPrep (Qbiogene). Total RNA was isolated with RNeasy Mini Kit (Qiagen) using a DNAse I treatment step. RNA quality was assessed with a Bioanalyzer 2100 (Agilent Technologies).

value: Atherosclerotic aortic arch

value: 60 wk

tag: genotype

value: Ldlr-/-, Apob100/100, Mttp flox/flox Mx1-Cre

tag: genetic background

value: mixed C57BL/6


title: Week 60 2 aortic arch

source_name: Week 60 2 aortic arch


title: Week 50 5 aortic arch

description: Gene expression data from aortic arch at week 50

source_name: Week 50 5 aortic arch

value: 50 wk


title: Primary_melanoma MEL385

description: amplified using Nugen WT-Ovation™

value: m


title: Week 50 3 aortic arch

source_name: Week 50 3 aortic arch


title: Primary_melanoma MEL362

description: amplified using Nugen WT-Ovation™

value: NODULAR MELANOMA


title: Primary_melanoma MEL339

description: amplified using Nugen WT-Ovation™

value: POLYPOID MELANOMA

value: YES


title: ccRCC tumor of patient T22 (Affymetrix)

source_name: SNP array of clear-cell renal cell carcinoma (ccRCC) tumor of patient T22 (Affymetrix)

value: Clear-cell renal cell carcinoma (ccRCC) tumor

value: Male

value: Clear-cell renal cell carcinoma

tag: pathologic tnm staging

tag: Stage

value: III

tag: fuhrman grade

tag: bap1 status

value: wild type

tag: pbrm1 status

tag: vhl status

value: mutant


title: Week 60 1 aortic arch

source_name: Week 60 1 aortic arch


title: Primary_melanoma MEL356

description: amplified using Nugen WT-Ovation™

tag: age at diagnosis

tag: diagnosis

value: SSM

tag: regional metastases

value: NO

tag: distant metastases

tag: braf mutation status


title: Week 60 4 aortic arch

source_name: Week 60 4 aortic arch

value: Atherosclerotic aortic arch

tag: age


title: chd1D_WT (2)

city: Santa Cruz

first: Grant

middle: A

last: Hartzog

state: CA

address: 349 Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

hyb_protocol: Purified Cy3 and Cy5 labeled samples were combined and mixed with hybridization buffer, respun through filter columns and then applied to spotted arrays under Lifterslips. These hybridized ~16 hours at 63ºC. The slides were then washed in hot 2xSSC/0.1% SDS, 2xSSC/0.1%SDS, 0.2xSSC and 0.05xSSC and then spun dry.

scan_protocol: Arrays were scanned with GenePix 6.0

data_processing: Log2 ratios were calculated from background subtracted median intensities and were LOESS normalized and summarized using Bioconductor

organism: Saccharomyces cerevisiae

source_name: Log phase yeast cultures with 30 minute heat shock

label_protocol: 15ug of total RNA was reverse transcribed using Invitrogen SuperScript II in the presence of Cy3 or Cy5 labeled dUTP for 2 hours at 42ºC. Reactions were stopped, RNA was hydrolyzed, labeled single-stranded cDNA was purified via Zymo DNA Clean & Concentrator columns.

growth_protocol: Yeast were grown to log phase in 50mL of YPD media at 30ºC.

extract_protocol: RNA was extracted via hot phenol, re-extracted with phenol-chloroform-isoamyl alcohol, re-extracted with chloroform and then ethanol precipitated. RNA was then DNase treated, re-extracted and re-precipitated.

treatment_protocol: Cells were heat shocked at 39ºC for 30 minutes (to maintain consistency with other samples prepared for Platform GPL1370; see [1]).

tag: strains

tag: genotype/variation

value: WT


title: Primary_melanoma MEL307

description: amplified using Nugen WT-Ovation™

tag: gender

tag: nras mutation status


title: Week 50 2 aortic arch

source_name: Week 50 2 aortic arch

tag: tissue

tag: genotype

value: Ldlr-/-, Apob100/100, Mttp flox/flox Mx1-Cre

tag: genetic background


title: chd1D_WT (1)


title: Primary_melanoma MEL326

description: amplified using Nugen WT-Ovation™

value: DERMAL  MELANOMA


title: Primary_melanoma MEL310

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL340

description: amplified using Nugen WT-Ovation™


title: Week 40 5 aortic arch

description: Gene expression data from aortic arch at week 40

source_name: Week 40 5 aortic arch

value: 40 wk

value: mixed C57BL/6


title: Week 40 4 aortic arch

source_name: Week 40 4 aortic arch


title: BF188_IVP

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

country: France

institute: INRA

description: Embryonic stage was defined by "Brachuyry" ISH on the embryonic disc (Hue et al. 2001). SCNT: somatic cell nuclear transfer. Donor cells: skin-ear fibroblasts from 3 different Holstein cows: 5538, 7711, 029. Syntax of the sample names: embryoName_ReproductionMode. Where the reproduction mode is either IVP, SCNT-0029, SCNT-771 and SCNT-5538.

hyb_protocol: Prehybridisation in ExpressHybTM Hybridization Solution (Clontech) at 68°C during 1h (14ml). Hybridisation using new ExpressHybTM Hybridization Solution (Clontech) at 68°C overnight (10ml). Arrays were washed four times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68°C for 30 min each. They were then exposed to phosphor-screens (Amersham) for 5 days.

scan_protocol: Scanner: STORM 760 from Molecular Dynamics - Raw data set : Feature extraction with Imagene 5.1 software from BioDiscovery (Proteigene)

data_processing: Intensity = Signal Mean - Normalization = Signal mean were log2 transformed and normalized by the mean of the all intensities on the array

organism: Bos taurus

source_name: reproduction mode: IVP

label_protocol: aRNA was retro-transcribed and directly labelled with [alpha-33P]dATP as described  (Degrelle et al., 2008). 500ng of aRNA was mixed with 500ng of random hexamers in a volume of 25µl. The mixture was incubated at 70°C for 10 min and chilled on ice. cDNA was synthesised by the addition of 5µl 10X PCR buffer, 5µl 25mM MgCl2, 5 µl 0,1 mM DTT, 2,5µl 10mM mix dGTP, dCTP and dTTP, 2,5µl water, 50 µCi [alpha-33P]dATP and 200U Superscript II (Invitrogen) at 42°C for 50min. The RNA template was removed by the addition of 1µl RNAse H- and incubation at 37°C for 20 min. Labelled targets were then purified on Sephadex columns (G-50).

extract_protocol: IVT amplified RNA from each sample was synthesized with the MessageAmpTM aRNA Kit (Ambion) according to Degrelle et al., 2008 (RT on 1µg total RNA, IVT during 10h). aRNA was purified on Mini Quick Spin RNA columns (Roche Diagnostic).

treatment_protocol: Tissues were collected and immediately snap-frozen. Total RNA from IVP and SCNT embryos were extracted with TrizolTM (Invitrogen). RNA quality was first verified by A260/280 absorbance ratios.

tag: embryo name

tag: Stage

value: embryonic

tag: somatic tissue

value: no

tag: reproduction mode

value: IVP


title: BF189_IVP


title: Week 40 3 aortic arch

source_name: Week 40 3 aortic arch


title: BF190_IVP


title: Week 50 4 aortic arch

source_name: Week 50 4 aortic arch

value: 50 wk


title: BF176_IVP


title: BF178_IVP


title: Primary_melanoma MEL298

description: amplified using Nugen WT-Ovation™

source_name: Frozen half of the melanoma punch biopsy

value: m

tag: age at diagnosis


title: BF153_IVP


title: Week 40 2 aortic arch

source_name: Week 40 2 aortic arch


title: Week 50 1 aortic arch

source_name: Week 50 1 aortic arch


title: Primary_melanoma MEL290

description: amplified using Nugen WT-Ovation™

value: f

tag: diagnosis


title: BCSD80_SCNT0029

source_name: reproduction mode: SCNT-0029


title: Week 30 6 aortic arch

description: Gene expression data from aortic arch at week 30

source_name: Week 30 6 aortic arch

value: 30 wk


title: BF152_IVP


title: BC30_SCNT7711

source_name: reproduction mode: SCNT-7711


title: Week 40 1 aortic arch

source_name: Week 40 1 aortic arch


title: BF156_IVP


title: BC279_SCNT5538

source_name: reproduction mode: SCNT-5538


title: BF169_IVP


title: Primary_melanoma MEL282

description: amplified using Nugen WT-Ovation™

tag: regional metastases


title: Primary_melanoma MEL294

description: amplified using Nugen WT-Ovation™

value: ACRAL MELANOMA

tag: distant metastases


title: BC2U41_SCNT7711


title: Primary_melanoma MEL283

description: amplified using Nugen WT-Ovation™

value: MIS

tag: braf mutation status


title: BF170_IVP


title: Week 30 4 aortic arch

source_name: Week 30 4 aortic arch

tag: age


title: Primary_melanoma MEL280

description: amplified using Nugen WT-Ovation™

value: NODULAR MELANOMA

value: YES


title: BC272_SCNT5538


title: Week 30 5 aortic arch

source_name: Week 30 5 aortic arch

value: Atherosclerotic aortic arch


title: Primary_melanoma MEL287

description: amplified using Nugen WT-Ovation™

value: SSM

value: NO

value: WT


title: BC273_SCNT5538


title: BC271_SCNT0029


title: BC275_SCNT5538


title: BC268_SCNT0029


title: Week 30 3 aortic arch

source_name: Week 30 3 aortic arch

value: Ldlr-/-, Apob100/100, Mttp flox/flox Mx1-Cre


title: Primary_melanoma MEL276

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL258

description: amplified using Nugen WT-Ovation™


title: BC255_SCNT0029


title: Primary_melanoma MEL275

description: amplified using Nugen WT-Ovation™


title: Week 30 1 aortic arch

source_name: Week 30 1 aortic arch

value: mixed C57BL/6


title: Primary_melanoma MEL257

description: amplified using Nugen WT-Ovation™


title: BC257_SCNT0029

value: embryonic


title: Primary_melanoma MEL272

description: amplified using Nugen WT-Ovation™


title: BC254_SCNT0029

value: no


title: BC250_SCNT0029


title: BC252_SCNT5538


title: Week 20 4 aortic arch

description: Gene expression data from aortic arch at week 20

source_name: Week 20 4 aortic arch

value: 20 wk


title: Week 20 1 aortic arch

source_name: Week 20 1 aortic arch


title: Primary_melanoma MEL244

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL243

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL250

description: amplified using Nugen WT-Ovation™


title: Week 30 2 aortic arch

source_name: Week 30 2 aortic arch


title: BC249_SCNT0029


title: BC256_SCNT0029


title: Week 10 6 aortic arch

description: Gene expression data from aortic arch at week 10

source_name: Week 10 6 aortic arch

value: 10 wk


title: Week 20 2 aortic arch

source_name: Week 20 2 aortic arch


title: Primary_melanoma MEL236

description: amplified using Nugen WT-Ovation™

source_name: Frozen half of the melanoma punch biopsy

value: m


title: Week 10 7 aortic arch

source_name: Week 10 7 aortic arch


title: Week 20 3 aortic arch

source_name: Week 20 3 aortic arch


title: chd1D_Rpb3

hyb_protocol: Labeled probes were hybridized onto an Agilent yeast 4x44 whole genome array. The arrays were scanned at 5 micron resolution with the Agilent array scanner. Image analysis and data normalization were performed as previously described [1].

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent High resolution C fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (IP/input) were calculated to produce the values given in the data table.

label_protocol: DNA samples were amplified, with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification method described previously [1].  2.5 micrograms of aRNA produced from the linear amplification were labeled via the amino-allyl method as described on www.microarrays.org.

growth_protocol: WT and mutant cells were grown to an OD of 0.5 in YPD media at 30°C.

extract_protocol: DNA was isolated from mononucleosomal cell extract or from an anti-Rpb3 immunoprecipitate of that extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: strain

tag: antibody


title: BC245_SCNT5538


title: Week 10 5 aortic arch

source_name: Week 10 5 aortic arch


title: BC243_SCNT5538


title: Primary_melanoma MEL213

description: amplified using Nugen WT-Ovation™

tag: gender

value: SPINDLE CELL MELANOMA


title: chd1D_Rpb3 dye flip

source_name: chd1D_Rpb3_input dye flip

tag: genotype/variation

source_name: chd1D_Rpb3_IP dye flip


title: Primary_melanoma MEL233

description: amplified using Nugen WT-Ovation™

value: f

tag: nras mutation status


title: Week 20 5 aortic arch

source_name: Week 20 5 aortic arch

tag: tissue

tag: genotype


title: Primary_melanoma MEL209

description: amplified using Nugen WT-Ovation™


title: BC242_SCNT5538

source_name: reproduction mode: SCNT-5538

tag: embryo name


title: wt_Rpb3

value: wild type


title: Week 10 3 aortic arch

source_name: Week 10 3 aortic arch

tag: genetic background


title: Week 10 4 aortic arch

source_name: Week 10 4 aortic arch


title: Primary_melanoma MEL197

description: amplified using Nugen WT-Ovation™


title: BC244_SCNT5538

tag: Stage

tag: somatic tissue


title: BC241_SCNT5538

tag: reproduction mode


title: Week 10 1 aortic arch

source_name: Week 10 1 aortic arch


title: BC202_SCNT0029

source_name: reproduction mode: SCNT-0029