title: Cultured chicken embryonic hepatocytes: 10 uM L-PFOS replicate 1

description: 10 uM L-PFOS replicate 1


title: Cultured chicken embryonic hepatocytes: DMSO control replicate 5

status: Public on Oct 29 2011

type: RNA

city: Ottawa

first: Jason

middle: M.

last: O'Brien

state: ON

address: 1125 Colonel By Drive, Raven Road

country: Canada

institute: Environment Canada

description: DMSO control replicate 5

hyb_protocol: Labelled sample and reference cRNA (825 ng each) was fragmented and then hybridized to arrays for 17 hours using Agilent Hybridization kits as per manufacturer’s direction

scan_protocol: Arrays scanned on an Agilent G2505B scanner at 5 um resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

data_processing: A reference design was used to analyse gene expression data. The design was blocked on the slide as Agilent slides contain four arrays per slide. Background fluorescence was measured using the (-)3xSLv1 probes. Probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent. Data were pre-processed using R (http://www.R-project.org).  The median signal intensities were normalized by the global LOWESS method using the transform.madata function in the microarray analysis of variance (MAANOVA) library. Ratio intensity plots, using complete and single linkages, were generated to identify arrays with poor quality. Differentially expressed genes were identified using the MAANOVA library.  The analysis of variance (ANOVA) model included the main effect of treatment and block effect of the microarray.  The Fs statistic, a shrinkage estimator, was used for the gene-specific variance components and the associated p-values for all the statistical tests were estimated using the permutation method (30,000 permutations with residual shuffling). These p-values were then adjusted for multiple comparisons using the false discovery rate approach (FDR). The least-squares means was used to estimate the fold changes for each pairwise comparison.

molecule: total RNA

organism: Gallus gallus

source_name: Cultured chicken embryonic heaptocytes: DMSO treated

label_protocol: Complementary RNA (cRNA) for each microarray hybridization was prepared from 150 ng of total RNA. cRNA from experimental samples was labelled with Cy5 and reference cRNA with Cy3 using Agilent Quick Amp labelling kits as per manufacturer’s instructions

extract_protocol: Total RNA was isolated from CEH using RNeasy 96 kits (Qiagen), including the on-column DNase treatment according to the manufacturer’s instructions

tag: agent

value: DMSO

tag: age of embryo

value: day 19

tag: cell type

value: hepatocytes

tag: exposure time

value: 24 hrs

source_name: Cultured chicken embryonic hepatocytes: reference pool

tag: reference

value: pool of equal parts of all control and treated samples


title: Cultured chicken embryonic hepatocytes: 10 uM L-PFOS replicate 2

description: 10 uM L-PFOS replicate 2

source_name: Cultured chicken embryonic heaptocytes: 10 uM L-PFOS treated

value: 10 uM L-PFOS


title: Cultured chicken embryonic hepatocytes: 10 uM L-PFOS replicate 3

description: 10 uM L-PFOS replicate 3


title: Cultured chicken embryonic hepatocytes: 40 uM L-PFOS replicate 3

description: 40 uM L-PFOS replicate 3

source_name: Cultured chicken embryonic heaptocytes: 40 uM L-PFOS treated

value: 40 uM L-PFOS


title: Cultured chicken embryonic hepatocytes: 10 uM L-PFOS replicate 4

description: 10 uM L-PFOS replicate 4


title: Cultured chicken embryonic hepatocytes: DMSO control replicate 4

description: DMSO control replicate 4


title: Cultured chicken embryonic hepatocytes: DMSO control replicate 2

description: DMSO control replicate 2


title: Cultured chicken embryonic hepatocytes: 40 uM L-PFOS replicate 4

description: 40 uM L-PFOS replicate 4


title: Cultured chicken embryonic hepatocytes: DMSO control replicate 3

description: DMSO control replicate 3


title: Cultured chicken embryonic hepatocytes: 10 uM T-PFOS replicate 2

description: 10 uM T-PFOS replicate 2

source_name: Cultured chicken embryonic heaptocytes: 10 uM T-PFOS treated

value: 10 uM T-PFOS


title: Subject 39 after LCD

status: Public on Sep 30 2011

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

description: Subject 39 after LCD

hyb_protocol: Sample preparation, hybridization, and microarray washing were performed according to manufacturer’s instructions (Agilent Technologies).

scan_protocol: Scanned using a GenePix 4000A Scanner (Axon Instruments-Molecular Devices).

data_processing: Microarray normalization was carried out by subtracting the median intensity background signal prior to intra-slide Loess normalization of log-transformed data (Goulphar Version 1.1.3 package). All data was then uploaded into the JMP Genomics Version 4.1 platform and further normalized using a quantile inter-slide intensity method.

organism: Homo sapiens

source_name: after LCD

label_protocol: According to Agilent instructions. RNA from study participant labeled with Cy5, RNA from reference pool labeled with Cy3.

growth_protocol: 8 week low calorie diet (LCD; 3.3 MJ/d; 800 kcal).

extract_protocol: Total RNA was extracted using the RNeasy total RNA Mini kit (Qiagen).

treatment_protocol: Subcutaneous adipose tissue samples from the periumbilical area were obtained by needle aspiration under local anaesthesia after an overnight fast at each of the time points. Biopsy samples were stored at -80°C until analysis.

tag: source material

value: study participant, subcutaneous adipose tissue, periumbilical area

tag: weight class

value: weight maintainer

tag: time

value: after LCD

source_name: reference RNA

value: commercial pool of human liver, heart, intestine tissue, skeletal muscle RNA


title: Cultured chicken embryonic hepatocytes: DMSO control replicate 1

description: DMSO control replicate 1


title: Subject 40 after LCD

description: Subject 40 after LCD

value: weight regainer


title: Subject 35 before LCD

description: Subject 35 before LCD

source_name: before LCD

value: before LCD


title: Subject 36 after LCD

description: Subject 36 after LCD


title: Subject 38 after LCD

description: Subject 38 after LCD


title: Subject 35 after LCD

description: Subject 35 after LCD


title: Subject 27 after LCD

description: Subject 27 after LCD


title: Subject 38 before LCD

description: Subject 38 before LCD


title: Subject 30 before LCD

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description: Subject 28 after LCD


title: Subject 40 before LCD

description: Subject 40 before LCD


title: Subject 37 after LCD

description: Subject 37 after LCD


title: Subject 34 before LCD

description: Subject 34 before LCD


title: Subject 37 before LCD

description: Subject 37 before LCD


title: Subject 31 after LCD

description: Subject 31 after LCD


title: Subject 36 before LCD

description: Subject 36 before LCD


title: Subject 34 after LCD

description: Subject 34 after LCD


title: Subject 29 after LCD

description: Subject 29 after LCD


title: Subject 33 before LCD

description: Subject 33 before LCD


title: Subject 30 after LCD

description: Subject 30 after LCD


title: Subject 32 after LCD

description: Subject 32 after LCD


title: Subject 39 before LCD

description: Subject 39 before LCD


title: Subject 33 after LCD

description: Subject 33 after LCD


title: Subject 28 before LCD

description: Subject 28 before LCD


title: Subject 29 before LCD

description: Subject 29 before LCD


title: Subject 31 before LCD

description: Subject 31 before LCD


title: Subject 32 before LCD

description: Subject 32 before LCD


title: Subject 27 before LCD

description: Subject 27 before LCD


title: Subject 26 after LCD

description: Subject 26 after LCD


title: Subject 25 before LCD

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title: Subject 24 before LCD

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title: Subject 24 after LCD

description: Subject 24 after LCD


title: Subject 19 after LCD

description: Subject 19 after LCD


title: Subject 26 before LCD

description: Subject 26 before LCD


title: Subject 22 before LCD

description: Subject 22 before LCD


title: Subject 20 after LCD

description: Subject 20 after LCD


title: Subject 21 before LCD

description: Subject 21 before LCD


title: Subject 21 after LCD

description: Subject 21 after LCD


title: Subject 23 before LCD

description: Subject 23 before LCD


title: Subject 23 after LCD

description: Subject 23 after LCD


title: Subject 18 after LCD

description: Subject 18 after LCD


title: Subject 18 before LCD

description: Subject 18 before LCD


title: Subject 19 before LCD

description: Subject 19 before LCD


title: Subject 22 after LCD

description: Subject 22 after LCD


title: Subject 15 after LCD

description: Subject 15 after LCD


title: Subject 25 after LCD

description: Subject 25 after LCD


title: Subject 17 before LCD

description: Subject 17 before LCD


title: Subject 17 after LCD

description: Subject 17 after LCD


title: Subject 14 after LCD

description: Subject 14 after LCD


title: Subject 15 before LCD

description: Subject 15 before LCD


title: Subject 16 after LCD

description: Subject 16 after LCD


title: Subject 12 after LCD

description: Subject 12 after LCD


title: Subject 20 before LCD

description: Subject 20 before LCD


title: Subject 8 after LCD

description: Subject 8 after LCD


title: Subject 10 before LCD

description: Subject 10 before LCD


title: Subject 14 before LCD

description: Subject 14 before LCD


title: Subject 11 after LCD

description: Subject 11 after LCD


title: Subject 6 before LCD

description: Subject 6 before LCD


title: Subject 13 before LCD

description: Subject 13 before LCD


title: Subject 9 before LCD

description: Subject 9 before LCD


title: Subject 16 before LCD

description: Subject 16 before LCD


title: Subject 10 after LCD

description: Subject 10 after LCD


title: Subject 11 before LCD

description: Subject 11 before LCD


title: Subject 13 after LCD

description: Subject 13 after LCD


title: Subject 8 before LCD

description: Subject 8 before LCD


title: Subject 4 after LCD

description: Subject 4 after LCD


title: Subject 9 after LCD

description: Subject 9 after LCD


title: Subject 12 before LCD

description: Subject 12 before LCD


title: Subject 7 before LCD

description: Subject 7 before LCD


title: Subject 7 after LCD

description: Subject 7 after LCD


title: Subject 3 before LCD

description: Subject 3 before LCD


title: Subject 4 before LCD

description: Subject 4 before LCD


title: Subject 5 after LCD

description: Subject 5 after LCD


title: Subject 5 before LCD

description: Subject 5 before LCD


title: LongSAGE Leishmania infantum chagasi

status: Public on Aug 10 2011

type: SAGE

anchor: NlaIII

city: TERESINA

first: ADELINO

middle: SOARES

last: LIMA NETO

state: PIAUI

address: RUA GOV. ARTUR DE VASCONCELOS, 151 CENTRO SUL

department: LEISHMANIOSES

country: Brazil

institute: INSTITUTO DE DOENÇAS TROPICAIS NATAN PORTELLA

description: leishmania infantum chagasi is the causative agent of visceral leishmaniasis in the New World.

data_processing: Automatic tag detection and counting was performed with software SAGE 2000 v4.5

organism: Leishmania chagasi

source_name: Leishmania infantum chagasi promastigote cells

growth_protocol: Leishmania i. chagasi promastigotes were cultured in Schneiders Insect Medium supplemented with 10% (v/v) fetal bovine serum (FBS), at 25 ºC and pH 7.2

extract_protocol: Library was constructed using the LongSAGE procedure with the NlaIII anchoring enzyme (CATG).

treatment_protocol: untreated cells

value: promastigotes (flagellated form within the sand fly vector)


title: Subject 2 after LCD

description: Subject 2 after LCD


title: IRRc_1

status: Public on Sep 13 2011

city: Oslo

first: Erta

last: kalanxhi

address: Montebello 0310

country: Norway

institute: Oslo University Hospital

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: performed with Illumina BeadStudio 3.1.3.0 Gene Expression Module 3.4.0

label: biotin, Cy3

source_name: control F11hTERT

label_protocol: Performed with Illumina® TotalPrep RNA Amplification Kit

growth_protocol: The cells were grown in DMEM supplied with 1% L-Glutamine and Penicillin/ Streptomycin and 20% FBS and kept at 37°C and 5% CO2.

extract_protocol: Total RNA from 4 independent experiments was isolated from cells irradiated with 2.0 Gy and the respective controls 2 h after irradiation using Pure Link RNA mini kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Irradiated cells were irradiated with 2Gy g-radiation. Unirradiated cells were used as controls Extraction of RNA was done 2 h after irradiation.

tag: cell line

value: immortalized hTERT

tag: treatment

value: control


title: Subject 1 after LCD

description: Subject 1 after LCD


title: IRRc_4

description: replicate 4


title: IRR_3

description: replicate 3

source_name: 2 Gy irradiated F11hTERT

value: 2 Gy irradiated


title: HSC young female , biological rep1

status: Public on May 06 2011

city: Lund

first: Gudmundur

last: Norddahl

address: Tornavagen 10

country: Sweden

institute: Lund University

hyb_protocol: RNA hybridized to MOE430_2. Chips according to manufacturer manual

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000

data_processing: Probe level expression values and normalization were calculated using RMAExpress and further analysis was done using dChip

label: biotin

organism: Mus musculus

source_name: HSC young female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4000 to 7000 cell

growth_protocol: Primary Cells directly sorted for RNA extraction

extract_protocol: Total RNA extraction was performed with QIAGEN microRNeasy kit according to the manufacturer's instructions.

tag: background strain

tag: genotype

value: wild type

tag: tissue

value: Mouse bone marrow

tag: age

value: 9-12 weeks

tag: gender

value: female


title: Subject 3 after LCD

description: Subject 3 after LCD


title: IRRc_2

description: replicate 2


title: sh-CTL_rep1

status: Public on Jun 30 2011

city: seoul

first: jiyoung

last: kim

address: Heusokdong

country: South Korea

institute: Chung-Ang University

description: Tet-on system

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2 Gene Expression Module v1.5.4.Array data were filtered by detection p-value < 0.05 (similar to signal to noise) and the selected probe signal values were transformed by logarithm and normalized by quantile method.

source_name: sh-CTL

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: K562 cells in RPMI1640 medium supplemented with 5 % fetal bovine serum (FBS) and 0.05 % antibiotics at 37 C in a 5 % CO2 atmosphere

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

treatment_protocol: Stable cells were treated 1 ug/ml doxyclcline for 48 h.

tag: genotype/variation

value: sh-CTL control


title: IRRc_3

description: replicate 3


title: sh-JMJD1B_rep3

description: Tet-on system

value: JMJD1B knock-down


title: IRR_1

description: replicate 1


title: Subject 2 before LCD

description: Subject 2 before LCD


title: HSC young female , biological rep3


title: IRR_4

description: replicate 4


title: sh-JMJD1B_rep1

description: Tet-on system

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2 Gene Expression Module v1.5.4. Array data were filtered by detection p-value < 0.05 (similar to signal to noise) and the selected probe signal values were transformed by logarithm and normalized by quantile method.


title: Subject 6 after LCD

description: Subject 6 after LCD


title: sh-JMJD1B_rep2

description: Tet-on system


title: AML_GE_40

status: Public on Dec 03 2010

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

country: USA

institute: University of Miiami

description: Sample name: 14969

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: RMA normalization using the RMA algorithm found in the oligo package (version 1.8.3)(Carvalho et al.) in BioConductor

source_name: AML blast cells

label_protocol: Random priming with 7-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Total RNA extracted with Qiagen's Rneasy Plus Mini kit per manufacturer's instructions. cDNA  synthesis carried out as previously described (Figueroa et al. PLoS One, 2008)

tag: sex (male.1_female.2)

tag: hemoglobin

tag: platelets

value: WT


title: IRR_2

description: replicate 2

tag: cell type


title: AML_GE_227

description: Sample name: 18329


title: AML_GE_174

description: Sample name: 17588


title: AML_GE_64

description: Sample name: 15330


title: Subject 1 before LCD

description: Subject 1 before LCD

value: study participant, subcutaneous adipose tissue, periumbilical area


title: HSC young female , biological rep2


title: sh-CTL_rep2

description: Tet-on system


title: BDC into NOD.RAG-/- (24 hrs.) purified beta cells

status: Public on Feb 16 2011

city: Saint Louis

first: Emil

last: Unanue

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

hyb_protocol: Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G, GCOS

data_processing:
GCOS, Expression Console, and DNAStar Arraystar 4.0
affymetrix-algorithm-name = RMA
affymetrix-algorithm-version = 1.0
affymetrix-algorithm-param-Background correction method = RMA Background Correction
affymetrix-algorithm-param-Normalization method = Quantile
affymetrix-algorithm-param-Summarization method = Median polish

label: Biotin

source_name: purified beta cells, BDC T cell transfer into NOD.RAG-/- strain, 24 hrs.

label_protocol: Affymetrix® GeneChip® WT Sense Target Labeling

extract_protocol: Ambion RNAqeuous Micro Kit

value: RAG-/-

tag: strain

value: NOD

tag: organ

value: Pancreas


title: AML_GE_301

description: Sample name: 19537


title: AML_GE_300

description: Sample name: 19528


title: AML_GE_151

description: Sample name: 17268


title: AML_GE_46

description: Sample name: 15056

value: MUT


title: AML_GE_94

description: Sample name: 15835


title: AML_GE_86

description: Sample name: 15763


title: AML_GE_118

description: Sample name: 16327


title: AML_GE_58

description: Sample name: 15267


title: AML_GE_297

description: Sample name: 19512


title: AML_GE_71

description: Sample name: 15438


title: AML_GE_78

description: Sample name: 15544


title: AML_GE_335

description: Sample name: 20573


title: AML_GE_106

description: Sample name: 16182


title: AML_GE_235

description: Sample name: 18448


title: AML_GE_225

description: Sample name: 18298


title: AML_GE_45

description: Sample name: 15051


title: AML_GE_110

description: Sample name: 16249


title: AML_GE_290

description: Sample name: 19386


title: AML_GE_145

description: Sample name: 17065


title: AML_GE_89

description: Sample name: 15780


title: AML_GE_201

description: Sample name: 17928


title: AML_GE_146

description: Sample name: 17076


title: AML_GE_266

description: Sample name: 19047


title: AML_GE_141

description: Sample name: 16916


title: AML_GE_124

description: Sample name: 16475


title: AML_GE_260

description: Sample name: 18948


title: AML_GE_276

description: Sample name: 19182


title: AML_GE_226

description: Sample name: 18310


title: AML_GE_257

description: Sample name: 18871


title: AML_GE_56

description: Sample name: 15251


title: AML_GE_261

description: Sample name: 18951


title: AML_GE_136

description: Sample name: 16745


title: AML_GE_88

description: Sample name: 15766


title: AML_GE_30

description: Sample name: 14707


title: AML_GE_205

description: Sample name: 18025


title: AML_GE_239

description: Sample name: 18504


title: AML_GE_191

description: Sample name: 17781


title: AML_GE_32

description: Sample name: 14732


title: AML_GE_96

description: Sample name: 15923


title: AML_GE_268

description: Sample name: 19079


title: AML_GE_100

description: Sample name: 15948


title: AML_GE_39

description: Sample name: 14891


title: AML_GE_287

description: Sample name: 19356


title: AML_GE_199

description: Sample name: 17919


title: AML_GE_326

description: Sample name: 20119


title: AML_GE_306

description: Sample name: 19621


title: AML_GE_113

description: Sample name: 16276


title: AML_GE_236

description: Sample name: 18457


title: AML_GE_87

description: Sample name: 15765


title: AML_GE_103

description: Sample name: 16054


title: AML_GE_321

description: Sample name: 20018


title: AML_GE_331

description: Sample name: 20198


title: AML_GE_20

description: Sample name: 14490


title: AML_GE_282

description: Sample name: 19274


title: AML_GE_159

description: Sample name: 17384


title: AML_GE_286

description: Sample name: 19352


title: AML_GE_307

description: Sample name: 19694


title: AML_GE_339

description: Sample name: 20623


title: AML_GE_17

description: Sample name: 14397


title: AML_GE_47

description: Sample name: 15065


title: AML_GE_336

description: Sample name: 20599


title: AML_GE_341

description: Sample name: 20655


title: AML_GE_329

description: Sample name: 20164


title: AML_GE_12

description: Sample name: 14314


title: AML_GE_195

description: Sample name: 17814


title: AML_GE_348

description: Sample name: 20800


title: AML_GE_334

description: Sample name: 20560


title: AML_GE_217

description: Sample name: 18187


title: AML_GE_160

description: Sample name: 17385


title: AML_GE_24

description: Sample name: 14556


title: AML_GE_246

description: Sample name: 18736


title: AML_GE_304

description: Sample name: 19603


title: AML_GE_218

description: Sample name: 18191


title: AML_GE_182

description: Sample name: 17692


title: AML_GE_351

description: Sample name: 20861


title: AML_GE_200

description: Sample name: 17924


title: AML_GE_148

description: Sample name: 17197


title: AML_GE_44

description: Sample name: 15040


title: AML_GE_134

description: Sample name: 16728


title: AML_GE_54

description: Sample name: 15203


title: AML_GE_74

description: Sample name: 15465


title: AML_GE_270

description: Sample name: 19115


title: AML_GE_214

description: Sample name: 18131


title: AML_GE_323

description: Sample name: 20026


title: AML_GE_281

description: Sample name: 19265


title: AML_GE_70

description: Sample name: 15434


title: AML_GE_42

description: Sample name: 15036


title: AML_GE_170

description: Sample name: 17550


title: AML_GE_285

description: Sample name: 19341


title: AML_GE_221

description: Sample name: 18215


title: AML_GE_59

description: Sample name: 15268


title: AML_GE_50

description: Sample name: 15122


title: AML_GE_250

description: Sample name: 18767


title: AML_GE_14

description: Sample name: 14348


title: AML_GE_177

description: Sample name: 17640


title: AML_GE_41

description: Sample name: 15025


title: AML_GE_318

description: Sample name: 19992


title: AML_GE_34

description: Sample name: 14751


title: AML_GE_154

description: Sample name: 17298


title: AML_GE_4

description: Sample name: 13970


title: AML_GE_153

description: Sample name: 17277


title: AML_GE_309

description: Sample name: 19750


title: AML_GE_320

description: Sample name: 20005


title: AML_GE_315

description: Sample name: 19814


title: AML_GE_6

description: Sample name: 14025


title: AML_GE_105

description: Sample name: 16123


title: AML_GE_133

description: Sample name: 16724


title: AML_GE_277

description: Sample name: 19194


title: AML_GE_97

description: Sample name: 15927


title: AML_GE_23

description: Sample name: 14512


title: AML_GE_173

description: Sample name: 17571


title: AML_GE_243

description: Sample name: 18573


title: AML_GE_28

description: Sample name: 14677


title: AML_GE_327

description: Sample name: 20145


title: AML_GE_206

description: Sample name: 18026


title: AML_GE_288

description: Sample name: 19369


title: AML_GE_242

description: Sample name: 18570


title: AML_GE_294

description: Sample name: 19490


title: AML_GE_317

description: Sample name: 19987


title: AML_GE_233

description: Sample name: 18407


title: AML_GE_295

description: Sample name: 19496


title: AML_GE_265

description: Sample name: 19039


title: AML_GE_73

description: Sample name: 15453


title: AML_GE_102

description: Sample name: 16037


title: AML_GE_76

description: Sample name: 15492


title: AML_GE_298

description: Sample name: 19515


title: AML_GE_22

description: Sample name: 14506


title: AML_GE_93

description: Sample name: 15834


title: AML_GE_21

description: Sample name: 14497


title: AML_GE_72

description: Sample name: 15448


title: AML_GE_212

description: Sample name: 18105


title: AML_GE_228

description: Sample name: 18330


title: AML_GE_165

description: Sample name: 17425


title: AML_GE_350

description: Sample name: 20860


title: AML_GE_289

description: Sample name: 19380


title: AML_GE_271

description: Sample name: 19128


title: AML_GE_132

description: Sample name: 16677


title: AML_GE_333

description: Sample name: 20228


title: AML_GE_183

description: Sample name: 17732


title: AML_GE_85

description: Sample name: 15747


title: AML_GE_175

description: Sample name: 17623


title: AML_GE_8

description: Sample name: 14055


title: AML_GE_98

description: Sample name: 15934


title: AML_GE_210

description: Sample name: 18081


title: AML_GE_193

description: Sample name: 17791


title: AML_GE_299

description: Sample name: 19525


title: AML_GE_167

description: Sample name: 17497


title: AML_GE_11

description: Sample name: 14278


title: AML_GE_107

description: Sample name: 16189


title: AML_GE_283

description: Sample name: 19319


title: AML_GE_296

description: Sample name: 19511


title: AML_GE_119

description: Sample name: 16369


title: AML_GE_247

description: Sample name: 18749


title: AML_GE_258

description: Sample name: 18889


title: AML_GE_279

description: Sample name: 19225


title: AML_GE_158

description: Sample name: 17374


title: AML_GE_150

description: Sample name: 17228


title: AML_GE_36

description: Sample name: 14834


title: AML_GE_92

description: Sample name: 15827


title: AML_GE_198

description: Sample name: 17859


title: AML_GE_169

description: Sample name: 17535


title: AML_GE_2

description: Sample name: 13895


title: AML_GE_180

description: Sample name: 17681


title: AML_GE_163

description: Sample name: 17410


title: AML_GE_229

description: Sample name: 18339


title: AML_GE_187

description: Sample name: 17754


title: AML_GE_241

description: Sample name: 18555


title: AML_GE_181

description: Sample name: 17687


title: AML_GE_13

description: Sample name: 14343


title: AML_GE_220

description: Sample name: 18211


title: AML_GE_184

description: Sample name: 17739


title: AML_GE_190

description: Sample name: 17771


title: AML_GE_253

description: Sample name: 18806


title: AML_GE_112

description: Sample name: 16255


title: AML_GE_152

description: Sample name: 17270


title: AML_GE_3

description: Sample name: 13946


title: AML_GE_256

description: Sample name: 18865


title: AML_GE_69

description: Sample name: 15429


title: AML_GE_77

description: Sample name: 15517


title: NBM_GE_5

description: Sample name: NBM_5

source_name: Normal CD34+ bone marrow cells


title: AML_GE_255

description: Sample name: 18855


title: AML_GE_264

description: Sample name: 19034


title: AML_GE_114

description: Sample name: 16304


title: AML_GE_139

description: Sample name: 16819


title: AML_GE_204

description: Sample name: 17974


title: NBM_GE_4

description: Sample name: NBM_4


title: AML_GE_26

description: Sample name: 14571


title: AML_GE_230

description: Sample name: 18345


title: NBM_GE_3

description: Sample name: NBM_3


title: AML_GE_115

description: Sample name: 16307


title: AML_GE_131

description: Sample name: 16665


title: AML_GE_237

description: Sample name: 18466


title: AML_GE_215

description: Sample name: 18171


title: AML_GE_15

description: Sample name: 14355


title: NBM_GE_1

description: Sample name: NBM_1


title: AML_GE_1

description: Sample name: 13479


title: AML_GE_19

description: Sample name: 14443


title: NBM_GE_2

description: Sample name: NBM_2


title: AML_GE_35

description: Sample name: 14787


title: AML_GE_9

description: Sample name: 14111


title: AML_GE_272

description: Sample name: 19132


title: AML_GE_156

description: Sample name: 17333


title: AML_GE_65

description: Sample name: 15334


title: AML_GE_43

description: Sample name: 15038


title: AML_GE_189

description: Sample name: 17770


title: AML_GE_303

description: Sample name: 19585


title: AML_GE_291

description: Sample name: 19390


title: AML_GE_161

description: Sample name: 17388


title: AML_GE_109

description: Sample name: 16226


title: AML_GE_63

description: Sample name: 15329


title: AML_GE_208

description: Sample name: 18045


title: AML_GE_108

description: Sample name: 16223


title: AML_GE_162

description: Sample name: 17389


title: AML_GE_178

description: Sample name: 17658


title: AML_GE_324

description: Sample name: 20058


title: AML_GE_90

description: Sample name: 15800


title: AML_GE_213

description: Sample name: 18106


title: AML_GE_340

description: Sample name: 20633


title: AML_GE_319

description: Sample name: 19993


title: AML_GE_245

description: Sample name: 18695


title: AML_GE_38

description: Sample name: 14877


title: AML_GE_62

description: Sample name: 15328


title: AML_GE_274

description: Sample name: 19172


title: AML_GE_68

description: Sample name: 15424


title: AML_GE_316

description: Sample name: 19827


title: AML_GE_308

description: Sample name: 19735


title: AML_GE_346

description: Sample name: 20780


title: AML_GE_49

description: Sample name: 15104


title: AML_GE_280

description: Sample name: 19244


title: AML_GE_231

description: Sample name: 18373


title: AML_GE_314

description: Sample name: 19807


title: AML_GE_143

description: Sample name: 16998


title: AML_GE_202

description: Sample name: 17950


title: AML_GE_179

description: Sample name: 17665


title: AML_GE_322

description: Sample name: 20025


title: AML_GE_352

description: Sample name: 20869


title: AML_GE_353

description: Sample name: 20889


title: AML_GE_66

description: Sample name: 15388


title: AML_GE_275

description: Sample name: 19179


title: AML_GE_345

description: Sample name: 20713


title: AML_GE_269

description: Sample name: 19080


title: AML_GE_358

description: Sample name: 20974


title: AML_GE_186

description: Sample name: 17745


title: AML_GE_144

description: Sample name: 17030


title: AML_GE_138

description: Sample name: 16772


title: AML_GE_343

description: Sample name: 20671


title: AML_GE_137

description: Sample name: 16758


title: AML_GE_292

description: Sample name: 19429


title: AML_GE_129

description: Sample name: 16596


title: AML_GE_192

description: Sample name: 17785


title: AML_GE_48

description: Sample name: 15094


title: AML_GE_216

description: Sample name: 18180


title: AML_GE_25

description: Sample name: 14559


title: AML_GE_126

description: Sample name: 16509


title: AML_GE_211

description: Sample name: 18086


title: AML_GE_293

description: Sample name: 19430


title: AML_GE_312

description: Sample name: 19779


title: AML_GE_302

description: Sample name: 19561


title: AML_GE_219

description: Sample name: 18200


title: AML_GE_284

description: Sample name: 19334


title: AML_GE_238

description: Sample name: 18492


title: AML_GE_240

description: Sample name: 18551


title: AML_GE_310

description: Sample name: 19762


title: AML_GE_52

description: Sample name: 15159


title: AML_GE_168

description: Sample name: 17511


title: AML_GE_338

description: Sample name: 20621


title: AML_GE_147

description: Sample name: 17136


title: AML_GE_37

description: Sample name: 14873


title: AML_GE_172

description: Sample name: 17570


title: AML_GE_248

description: Sample name: 18761


title: AML_GE_55

description: Sample name: 15250


title: AML_GE_251

description: Sample name: 18780


title: AML_GE_305

description: Sample name: 19616


title: AML_GE_128

description: Sample name: 16579


title: AML_GE_332

description: Sample name: 20207


title: AML_GE_33

description: Sample name: 14742


title: AML_GE_222

description: Sample name: 18235


title: AML_GE_117

description: Sample name: 16320


title: AML_GE_209

description: Sample name: 18064


title: AML_GE_278

description: Sample name: 19211


title: AML_GE_75

description: Sample name: 15480


title: AML_GE_328

description: Sample name: 20156


title: AML_GE_142

description: Sample name: 16995


title: AML_GE_79

description: Sample name: 15568


title: AML_GE_344

description: Sample name: 20685


title: AML_GE_164

description: Sample name: 17424


title: AML_GE_349

description: Sample name: 20806


title: AML_GE_101

description: Sample name: 15962


title: AML_GE_356

description: Sample name: 20962


title: AML_GE_325

description: Sample name: 20062


title: AML_GE_84

description: Sample name: 15746


title: AML_GE_10

description: Sample name: 14239


title: AML_GE_357

description: Sample name: 20972


title: AML_GE_337

description: Sample name: 20607


title: AML_GE_31

description: Sample name: 14715


title: AML_GE_224

description: Sample name: 18285


title: AML_GE_263

description: Sample name: 18985


title: AML_GE_330

description: Sample name: 20180


title: AML_GE_254

description: Sample name: 18837


title: AML_GE_355

description: Sample name: 20950


title: AML_GE_347

description: Sample name: 20790


title: AML_GE_5

description: Sample name: 13986


title: AML_GE_18

description: Sample name: 14437


title: AML_GE_185

description: Sample name: 17742


title: AML_GE_273

description: Sample name: 19134


title: AML_GE_194

description: Sample name: 17801


title: AML_GE_354

description: Sample name: 20923


title: AML_GE_80

description: Sample name: 15571


title: AML_GE_313

description: Sample name: 19798


title: AML_GE_111

description: Sample name: 16253


title: AML_GE_311

description: Sample name: 19778


title: AML_GE_166

description: Sample name: 17456


title: AML_GE_244

description: Sample name: 18689


title: AML_GE_262

description: Sample name: 18968


title: AML_GE_61

description: Sample name: 15303


title: AML_GE_342

description: Sample name: 20665


title: AML_GE_60

description: Sample name: 15277


title: AML_GE_122

description: Sample name: 16446


title: AML_GE_51

description: Sample name: 15155


title: AML_GE_81

description: Sample name: 15599


title: AML_GE_157

description: Sample name: 17372


title: AML_GE_197

description: Sample name: 17831


title: AML_GE_57

description: Sample name: 15256


title: AML_GE_149

description: Sample name: 17224


title: AML_GE_203

description: Sample name: 17973


title: AML_GE_223

description: Sample name: 18271


title: AML_GE_125

description: Sample name: 16492


title: AML_GE_259

description: Sample name: 18896


title: AML_GE_116

description: Sample name: 16308


title: AML_GE_267

description: Sample name: 19057


title: AML_GE_232

description: Sample name: 18374


title: AML_GE_234

description: Sample name: 18425


title: AML_GE_249

description: Sample name: 18763


title: AML_GE_53

description: Sample name: 15175


title: AML_GE_252

description: Sample name: 18790


title: AML_GE_29

description: Sample name: 14687


title: AML_GE_196

description: Sample name: 17815


title: AML_GE_67

description: Sample name: 15394


title: AML_GE_7

description: Sample name: 14026


title: AML_GE_121

description: Sample name: 16427


title: AML_GE_82

description: Sample name: 15644


title: AML_GE_188

description: Sample name: 17758


title: AML_GE_127

description: Sample name: 16554


title: AML_GE_207

description: Sample name: 18037


title: AML_GE_83

description: Sample name: 15705


title: AML_GE_176

description: Sample name: 17632


title: AML_GE_91

description: Sample name: 15819


title: AML_GE_155

description: Sample name: 17311


title: AML_GE_104

description: Sample name: 16070


title: AML_GE_171

description: Sample name: 17567


title: AML_GE_95

description: Sample name: 15838


title: AML_GE_16

description: Sample name: 14396


title: AML_GE_140

description: Sample name: 16888


title: AML_GE_120

description: Sample name: 16408


title: AML_GE_123

description: Sample name: 16466


title: AML_GE_27

description: Sample name: 14585


title: NBM_#9

type: genomic

description: Sample name: F50.CD34.POS

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167. Each array was centered around the lowest point between the two modes.

molecule: genomic DNA

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: fraction

value: MspI representation of genomic DNA

value: HpaII representation of genomic DNA


title: NBM_#7

description: Sample name: M48


title: NBM_#4

description: Sample name: M42


title: NBM_#3

description: Sample name: M46


title: AML_382

description: Sample name: 20972


title: AML_377

description: Sample name: 20869


title: AML_378

description: Sample name: 20889

value: Mut


title: AML_GE_130

description: Sample name: 16637


title: AML_379

description: Sample name: 20923


title: AML_381

description: Sample name: 20962


title: NBM_#11

description: Sample name: F32.CD34.POS


title: NBM_#6

description: Sample name: S-BM-D


title: NBM_#8

description: Sample name: F34.CD34.POS


title: AML_GE_135

description: Sample name: 16738


title: NBM_#2

description: Sample name: M49


title: NBM_#10

description: Sample name: F28.CD34.POS


title: AML_373

description: Sample name: 20800


title: AML_383

description: Sample name: 20974


title: NBM_#1

description: Sample name: F55


title: NBM_#5

description: Sample name: M45


title: AML_380

description: Sample name: 20950


title: AML_376

description: Sample name: 20861


title: AML_374

description: Sample name: 20806


title: AML_370

description: Sample name: 20713


title: AML_372

description: Sample name: 20790


title: AML_369

description: Sample name: 20685


title: AML_368

description: Sample name: 20671


title: AML_GE_99

description: Sample name: 15940


title: AML_375

description: Sample name: 20860


title: AML_365

description: Sample name: 20633


title: AML_366

description: Sample name: 20655


title: AML_371

description: Sample name: 20780


title: AML_367

description: Sample name: 20665


title: AML_359

description: Sample name: 20560


title: AML_356

description: Sample name: 20198


title: AML_364

description: Sample name: 20623


title: AML_360

description: Sample name: 20573


title: AML_363

description: Sample name: 20621


title: AML_357

description: Sample name: 20207


title: AML_361

description: Sample name: 20599


title: AML_358

description: Sample name: 20228


title: AML_354

description: Sample name: 20164


title: AML_351

description: Sample name: 20122


title: AML_355

description: Sample name: 20180


title: AML_348

description: Sample name: 20058


title: AML_362

description: Sample name: 20607


title: AML_346

description: Sample name: 20018


title: AML_350

description: Sample name: 20119


title: AML_347

description: Sample name: 20025


title: AML_343

description: Sample name: 19992


title: AML_345

description: Sample name: 20005


title: AML_349

description: Sample name: 20062


title: AML_353

description: Sample name: 20156


title: AML_352

description: Sample name: 20145


title: AML_339

description: Sample name: 19807


title: AML_338

description: Sample name: 19798


title: AML_330

description: Sample name: 19616


title: AML_341

description: Sample name: 19827


title: AML_342

description: Sample name: 19987


title: AML_344

description: Sample name: 19993


title: AML_340

description: Sample name: 19814


title: AML_337

description: Sample name: 19779


title: AML_336

description: Sample name: 19778


title: AML_332

description: Sample name: 19694


title: AML_334

description: Sample name: 19750


title: AML_331

description: Sample name: 19621


title: AML_335

description: Sample name: 19762


title: AML_329

description: Sample name: 19603


title: AML_326

description: Sample name: 19537


title: AML_321

description: Sample name: 19511


title: AML_325

description: Sample name: 19528


title: AML_333

description: Sample name: 19735


title: AML_322

description: Sample name: 19512


title: AML_317

description: Sample name: 19429


title: AML_318

description: Sample name: 19430


title: AML_315

description: Sample name: 19386


title: AML_328

description: Sample name: 19585


title: AML_319

description: Sample name: 19490


title: AML_323

description: Sample name: 19515


title: AML_327

description: Sample name: 19561


title: AML_316

description: Sample name: 19390


title: AML_314

description: Sample name: 19380


title: AML_324

description: Sample name: 19525


title: AML_312

description: Sample name: 19356


title: AML_320

description: Sample name: 19496


title: AML_308

description: Sample name: 19319


title: AML_311

description: Sample name: 19352


title: AML_303

description: Sample name: 19211


title: AML_310

description: Sample name: 19341


title: AML_313

description: Sample name: 19369


title: AML_304

description: Sample name: 19225


title: AML_309

description: Sample name: 19334


title: AML_300

description: Sample name: 19179


title: AML_301

description: Sample name: 19182


title: AML_299

description: Sample name: 19172


title: AML_306

description: Sample name: 19265


title: AML_298

description: Sample name: 19135


title: AML_296

description: Sample name: 19132


title: AML_305

description: Sample name: 19244


title: AML_302

description: Sample name: 19194


title: AML_297

description: Sample name: 19134


title: AML_293

description: Sample name: 19080


title: AML_295

description: Sample name: 19128


title: AML_286

description: Sample name: 18985


title: AML_290

description: Sample name: 19047


title: AML_292

description: Sample name: 19079


title: AML_294

description: Sample name: 19115


title: AML_287

description: Sample name: 19014


title: AML_291

description: Sample name: 19057


title: AML_284

description: Sample name: 18951


title: AML_288

description: Sample name: 19034


title: AML_283

description: Sample name: 18948


title: AML_274

description: Sample name: 18790


title: AML_278

description: Sample name: 18865


title: AML_282

description: Sample name: 18917


title: AML_275

description: Sample name: 18806


title: AML_279

description: Sample name: 18871


title: AML_307

description: Sample name: 19274


title: AML_280

description: Sample name: 18889


title: AML_271

description: Sample name: 18761


title: AML_276

description: Sample name: 18837


title: AML_281

description: Sample name: 18896


title: AML_289

description: Sample name: 19039


title: AML_268

description: Sample name: 18695


title: AML_277

description: Sample name: 18855


title: AML_273

description: Sample name: 18780


title: AML_285

description: Sample name: 18968


title: AML_269

description: Sample name: 18736


title: AML_270

description: Sample name: 18749


title: AML_265

description: Sample name: 18570


title: AML_261

description: Sample name: 18488


title: AML_260

description: Sample name: 18466


title: AML_257

description: Sample name: 18448


title: AML_264

description: Sample name: 18555


title: AML_256

description: Sample name: 18425


title: AML_258

description: Sample name: 18456


title: AML_262

description: Sample name: 18492


title: AML_254

description: Sample name: 18374


title: AML_253

description: Sample name: 18373


title: AML_266

description: Sample name: 18573


title: AML_250

description: Sample name: 18330


title: AML_251

description: Sample name: 18339


title: AML_249

description: Sample name: 18329


title: AML_259

description: Sample name: 18457


title: AML_263

description: Sample name: 18551


title: AML_267

description: Sample name: 18689


title: AML_246

description: Sample name: 18297


title: AML_252

description: Sample name: 18345


title: AML_245

description: Sample name: 18285


title: AML_244

description: Sample name: 18271


title: AML_242

description: Sample name: 18215


title: AML_255

description: Sample name: 18407


title: AML_241

description: Sample name: 18211


title: AML_238

description: Sample name: 18187


title: AML_232

description: Sample name: 18086


title: AML_235

description: Sample name: 18131


title: AML_248

description: Sample name: 18310


title: AML_230

description: Sample name: 18064


title: AML_234

description: Sample name: 18106


title: AML_240

description: Sample name: 18200


title: AML_226

description: Sample name: 18025


title: AML_236

description: Sample name: 18171


title: AML_233

description: Sample name: 18105


title: AML_237

description: Sample name: 18180


title: AML_223

description: Sample name: 17973


title: AML_239

description: Sample name: 18191


title: AML_243

description: Sample name: 18235


title: AML_229

description: Sample name: 18045


title: AML_225

description: Sample name: 18011


title: AML_227

description: Sample name: 18026


title: AML_218

description: Sample name: 17859


title: AML_247

description: Sample name: 18298


title: AML_228

description: Sample name: 18037


title: AML_219

description: Sample name: 17919


title: AML_221

description: Sample name: 17928


title: AML_224

description: Sample name: 17974


title: AML_217

description: Sample name: 17831


title: AML_215

description: Sample name: 17814


title: AML_222

description: Sample name: 17950


title: AML_231

description: Sample name: 18081


title: AML_216

description: Sample name: 17815


title: AML_220

description: Sample name: 17924


title: AML_272

description: Sample name: 18767


title: AML_209

description: Sample name: 17770


title: AML_213

description: Sample name: 17791


title: AML_199

description: Sample name: 17665


title: AML_208

description: Sample name: 17758


title: AML_203

description: Sample name: 17732


title: AML_198

description: Sample name: 17658


title: AML_191

description: Sample name: 17568


title: AML_207

description: Sample name: 17754


title: AML_202

description: Sample name: 17692


title: AML_201

description: Sample name: 17687


title: AML_214

description: Sample name: 17801


title: AML_210

description: Sample name: 17771


title: AML_204

description: Sample name: 17739


title: AML_211

description: Sample name: 17781


title: AML_200

description: Sample name: 17681


title: AML_197

description: Sample name: 17640


title: AML_195

description: Sample name: 17623


title: AML_212

description: Sample name: 17785


title: AML_205

description: Sample name: 17742


title: AML_196

description: Sample name: 17632


title: AML_194

description: Sample name: 17588


title: AML_192

description: Sample name: 17570


title: AML_190

description: Sample name: 17567


title: AML_184

description: Sample name: 17425


title: AML_189

description: Sample name: 17550


title: AML_188

description: Sample name: 17535


title: AML_193

description: Sample name: 17571


title: AML_187

description: Sample name: 17511


title: AML_185

description: Sample name: 17456


title: AML_178

description: Sample name: 17385


title: AML_181

description: Sample name: 17402


title: AML_186

description: Sample name: 17497


title: AML_180

description: Sample name: 17389


title: AML_176

description: Sample name: 17374


title: AML_183

description: Sample name: 17424


title: AML_177

description: Sample name: 17384


title: AML_172

description: Sample name: 17298


title: AML_164

description: Sample name: 17197


title: AML_179

description: Sample name: 17388


title: AML_168

description: Sample name: 17268


title: AML_175

description: Sample name: 17372


title: AML_166

description: Sample name: 17228


title: AML_174

description: Sample name: 17333


title: AML_170

description: Sample name: 17277


title: AML_182

description: Sample name: 17410


title: AML_162

description: Sample name: 17147


title: AML_167

description: Sample name: 17267


title: AML_171

description: Sample name: 17289


title: AML_173

description: Sample name: 17311


title: AML_169

description: Sample name: 17270


title: AML_165

description: Sample name: 17224


title: AML_163

description: Sample name: 17193


title: AML_156

description: Sample name: 16916


title: AML_160

description: Sample name: 17076


title: AML_155

description: Sample name: 16888


title: AML_158

description: Sample name: 16998


title: AML_151

description: Sample name: 16758


title: AML_159

description: Sample name: 17030


title: AML_150

description: Sample name: 16745


title: AML_152

description: Sample name: 16772


title: AML_153

description: Sample name: 16819


title: AML_154

description: Sample name: 16887


title: AML_161

description: Sample name: 17136


title: AML_157

description: Sample name: 16995


title: AML_149

description: Sample name: 16728


title: AML_138

description: Sample name: 16475


title: AML_144

description: Sample name: 16665


title: AML_146

description: Sample name: 16713


title: AML_137

description: Sample name: 16446


title: AML_140

description: Sample name: 16509


title: AML_134

description: Sample name: 16369


title: AML_139

description: Sample name: 16492


title: AML_145

description: Sample name: 16677


title: AML_143

description: Sample name: 16596


title: AML_136

description: Sample name: 16426


title: AML_141

description: Sample name: 16554


title: AML_142

description: Sample name: 16579


title: AML_147

description: Sample name: 16717


title: AML_148

description: Sample name: 16724


title: AML_135

description: Sample name: 16408


title: AML_206

description: Sample name: 17745


title: AML_131

description: Sample name: 16326


title: AML_127

description: Sample name: 16304


title: AML_133

description: Sample name: 16345


title: AML_129

description: Sample name: 16308


title: AML_125

description: Sample name: 16255


title: AML_128

description: Sample name: 16307


title: AML_122

description: Sample name: 16226


title: AML_126

description: Sample name: 16276


title: AML_132

description: Sample name: 16327


title: AML_124

description: Sample name: 16253


title: AML_120

description: Sample name: 16189


title: AML_130

description: Sample name: 16320


title: AML_121

description: Sample name: 16223


title: AML_123

description: Sample name: 16249


title: AML_117

description: Sample name: 16070


title: AML_115

description: Sample name: 16037


title: AML_116

description: Sample name: 16054


title: AML_114

description: Sample name: 16005


title: AML_118

description: Sample name: 16123


title: AML_107

description: Sample name: 15835


title: AML_108

description: Sample name: 15838


title: AML_112

description: Sample name: 15948


title: AML_106

description: Sample name: 15834


title: AML_113

description: Sample name: 15962


title: AML_110

description: Sample name: 15927


title: AML_105

description: Sample name: 15827


title: AML_109

description: Sample name: 15923


title: AML_119

description: Sample name: 16182


title: AML_104

description: Sample name: 15819


title: AML_101

description: Sample name: 15780


title: AML_100

description: Sample name: 15773


title: AML_103

description: Sample name: 15809


title: AML_111

description: Sample name: 15934


title: AML_95

description: Sample name: 15746


title: AML_97

description: Sample name: 15763


title: AML_96

description: Sample name: 15747


title: AML_102

description: Sample name: 15800


title: AML_98

description: Sample name: 15765


title: AML_99

description: Sample name: 15766


title: AML_91

description: Sample name: 15599


title: AML_94

description: Sample name: 15744


title: AML_90

description: Sample name: 15571


title: AML_89

description: Sample name: 15568


title: AML_92

description: Sample name: 15670


title: AML_93

description: Sample name: 15705


title: AML_86

description: Sample name: 15517


title: AML_81

description: Sample name: 15448


title: AML_83

description: Sample name: 15465


title: AML_88

description: Sample name: 15544


title: AML_77

description: Sample name: 15424


title: AML_85

description: Sample name: 15492


title: AML_84

description: Sample name: 15480


title: AML_87

description: Sample name: 15523


title: AML_82

description: Sample name: 15453


title: AML_75

description: Sample name: 15388


title: AML_72

description: Sample name: 15329


title: AML_76

description: Sample name: 15394


title: AML_80

description: Sample name: 15438


title: AML_68

description: Sample name: 15268


title: AML_79

description: Sample name: 15434


title: AML_61

description: Sample name: 15182


title: AML_74

description: Sample name: 15334


title: AML_73

description: Sample name: 15330


title: AML_58

description: Sample name: 15155


title: AML_71

description: Sample name: 15328


title: AML_65

description: Sample name: 15251


title: AML_56

description: Sample name: 15104


title: AML_69

description: Sample name: 15277


title: AML_70

description: Sample name: 15303


title: AML_66

description: Sample name: 15256


title: AML_64

description: Sample name: 15250


title: AML_51

description: Sample name: 15040


title: AML_54

description: Sample name: 15065


title: AML_50

description: Sample name: 15038


title: AML_78

description: Sample name: 15429


title: AML_49

description: Sample name: 15036


title: AML_53

description: Sample name: 15056


title: AML_63

description: Sample name: 15234


title: AML_67

description: Sample name: 15267


title: AML_62

description: Sample name: 15203


title: AML_60

description: Sample name: 15175


title: AML_57

description: Sample name: 15122


title: AML_52

description: Sample name: 15051


title: AML_59

description: Sample name: 15159


title: AML_45

description: Sample name: 14969


title: AML_41

description: Sample name: 14873


title: AML_44

description: Sample name: 14965


title: AML_47

description: Sample name: 14997


title: AML_48

description: Sample name: 15025


title: AML_55

description: Sample name: 15094


title: AML_27

description: Sample name: 14556


title: AML_46

description: Sample name: 14993


title: AML_40

description: Sample name: 14834


title: AML_43

description: Sample name: 14921


title: AML_39

description: Sample name: 14787


title: AML_31

description: Sample name: 14665


title: AML_32

description: Sample name: 14677


title: AML_36

description: Sample name: 14742


title: AML_42

description: Sample name: 14877


title: AML_37

description: Sample name: 14751


title: AML_34

description: Sample name: 14715


title: AML_38

description: Sample name: 14786


title: AML_33

description: Sample name: 14707


title: AML_30

description: Sample name: 14585


title: AML_29

description: Sample name: 14571


title: AML_21

description: Sample name: 14437


title: AML_24

description: Sample name: 14497


title: AML_28

description: Sample name: 14559


title: AML_35

description: Sample name: 14732


title: AML_22

description: Sample name: 14443


title: AML_14

description: Sample name: 14278


title: AML_26

description: Sample name: 14512


title: AML_18

description: Sample name: 14355


title: AML_16

description: Sample name: 14343


title: AML_20

description: Sample name: 14397


title: Analysing of Chromosome VIII of EC-C1 strains (S. cerevisiae)

status: Public on Aug 03 2010

city: Taipei

first: Jun-Yi

last: Leu

address: 128 Academia Road, Section 2, Nankang

department: Insititute of Molecular Biolody

country: Taiwan

institute: Academia Sinica

description: The genomic DNA of rearranged chromosome VIII was extracted from the gel of pulsed field gel electrophoresis, and analyzed by array-CGH to identify amplified chromosomal region on chromosome VIII

hyb_protocol: The hybridization protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

scan_protocol: Scanned on an Molecular Device AXON 4000B (version GenePix 6.0) and got .gpr files

data_processing: Subtracted background. Dividing by ch2 (control) was used to transform data (Agilent GeneSpring 7.3.1 software)

organism: Saccharomyces cerevisiae

source_name: EC9 diploid strain, EC9 ChrVIII DNA Fragment

label_protocol: The label protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

growth_protocol: Grow in YPD medium

extract_protocol: After PFGE, The rearranged ChrVIII DNA (~650kb) was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit.

value: EC9 diploid strain

source_name: w303 diploid strain, control

extract_protocol:
Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit
 Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit.

value: w303 diploid strain (JYL1127 X JYL1128)


title: AML_23

description: Sample name: 14490


title: AML_17

description: Sample name: 14348


title: AML_25

description: Sample name: 14506


title: AML_19

description: Sample name: 14396


title: AML_15

description: Sample name: 14314


title: AML_8

description: Sample name: 14025


title: AML_3

description: Sample name: 13936


title: AML_5

description: Sample name: 13965


title: AML_1

description: Sample name: 13479


title: AML_6

description: Sample name: 13970


title: AML_12

description: Sample name: 14111


title: AML_13

description: Sample name: 14239


title: AML_10

description: Sample name: 14028


title: AML_7

description: Sample name: 13986


title: AML_4

description: Sample name: 13946


title: AML_9

description: Sample name: 14026


title: AML_11

description: Sample name: 14108


title: AML_2

description: Sample name: 13895


title: UMARY-1583-FCTX-CpG

status: Public on Apr 20 2010

city: Bethesda

first: J Raphael

last: Gibbs

state: MD

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

description: Human Brain Tissue: FCTX

hyb_protocol: Two bead types correspond to each CpG locus, one to the methylated (C) state, and the other to the unmethylated (T) state. After extension, the BeadChip was fluorescently stained.

scan_protocol: Illumina Beadstation BeadArray laser confocal scanner to measure the intensities of unmethylated and methylated bead types for each locus.

data_processing: Beadstudio Methylation Module v3.2.0, no normalization (analysis performed on the non-normalized data).

label: C-Bio and A-DNP

source_name: Human Brain Tissue: FCTX

label_protocol: 1ug of genomic DNA underwent bisulfite conversion using the WZ-96 DNA Methylation Kit according to the manufacturer’s protocol (Zymo Research Corp, Orange, CA). Incubation conditions used during conversion were as follows: (95°C for 30 seconds, 50°C for 1 hour) for 16 cycles, hold overnight at 4°C. Unmethylated cytosines were chemically deaminated to uracil in the presence of bisulfite, while methylated cytosines were refractory to the effects of bisulfite and remained as cytosines. Methylation was then detected as a C/T nucleotide polymorphism at each CpG site. After bisulfite conversion, each sample was whole-genome amplified, fragmented, and hybridized to the BeadChip. DNA molecules anneal to locus-specific DNA oligomers.

extract_protocol: Genomic DNA for the Infinium methylation assay was extracted using phenol-chloroform and ethanol precipitation. DNA concentration was determined using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE), and DNA extraction was repeated using a new tissue aliquot for samples with DNA concentration less than 50ng/ul, or with a 260/280 ratio less than 1.7.

value: frontal cortex

value: male

tag: age (y)

tag: pmi (hr)

tag: tissuebank

value: UMARY

value: FCTX


title: UMARY-4903-FCTX-CpG

description: Human Brain Tissue: FCTX

value: female


title: UMARY-5079-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1903-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1935-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5028-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4786-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1614-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1710-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4263-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1611-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1902-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4789-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1907-FCTX-CpG

description: Human Brain Tissue: FCTX


title: Uninfected 1 hr STS

status: Public on Jun 12 2010

first: Douglas Scott

last: Merrell

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77295.gif

hyb_protocol: not provided

scan_protocol: Agilent

data_processing: Agilent

source_name: 1.0 _g amplified Uninfected HeLa cell cDNA

label_protocol: not provided

extract_protocol: not provided

tag: cell line

value: HeLa

source_name: 1.0 _g amplified Uninfected 1 hr STS cDNA

tag: length of treatment

value: 1 h

tag: infection

value: not infected

tag: treatment

value: treated with Stautosporine


title: BLSA-745-FCTX-CpG

description: Human Brain Tissue: FCTX

tag: tissue

value: BLSA


title: UMARY-4729-FCTX-CpG

description: Human Brain Tissue: FCTX

tag: gender


title: UMARY-1865-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1939-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4636-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4598-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4549-FCTX-CpG

description: Human Brain Tissue: FCTX


title: Uninfected 2 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77303.gif

source_name: 1.0 _g amplified Uninfected 2 hr STS cDNA

value: 2 h


title: UMARY-4540-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1940-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5078-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1802-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4841-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1556-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1570-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-602-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1889-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1839-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5081-FCTX-CpG

description: Human Brain Tissue: FCTX


title: Uninfected 2.75 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77290.gif

source_name: 1.0 _g amplified Uninfected 2.75 hr STS cDNA


title: Uninfected 1 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77291.gif

source_name: 1.0 _g amplified Uninfected 1 hr cDNA

value: untreated


title: 2457T-infected 2.75 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77294.gif

source_name: 1.0 _g amplified 2457T-infected 2.75 hr cDNA

value: infected with Shigella flexneri serotype 2a strain 2457T


title: BLSA-2000-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1579-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1830-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1603-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-2020-FCTX-CpG

description: Human Brain Tissue: FCTX


title: Uninfected 0.5 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77287.gif

source_name: 1.0 _g amplified Uninfected 0.5 hr STS cDNA


title: BLSA-2037-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-2093-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-2069-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1883-FCTX-CpG

description: Human Brain Tissue: FCTX


title: 2457T-infected 2 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77304.gif

source_name: 1.0 _g amplified 2457T-infected 2 hr STS cDNA


title: UMARY-871-FCTX-CpG

description: Human Brain Tissue: FCTX


title: Uninfected 2.75 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77305.gif

source_name: 1.0 _g amplified Uninfected 2.75 hr cDNA


title: 2457T-Infected 0.5 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77288.gif

source_name: 1.0 _g amplified 2457T-Infected 0.5 hr STS cDNA


title: 2457T-infected 2 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77300.gif

source_name: 1.0 _g amplified 2457T-infected 2 hr cDNA


title: 2457T-infected 1 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77296.gif

source_name: 1.0 _g amplified 2457T-infected 1 hr STS cDNA


title: BLSA-1595-FCTX-CpG

description: Human Brain Tissue: FCTX


title: 2457T-infected 1 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77292.gif

source_name: .6175 _g amplified Uninfected HeLa cell cDNA

source_name: .6175 _g amplified 2457T-infected 1 hr cDNA


title: BLSA-827-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1640-FCTX-CpG

description: Human Brain Tissue: FCTX


title: Uninfected 2 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77299.gif

source_name: 1.0 _g amplified Uninfected 2 hr cDNA


title: BLSA-2066-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1713-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1924-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4640-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4593-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-2102-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1825-FCTX-CpG

description: Human Brain Tissue: FCTX


title: 2457T-infected 2.75 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77298.gif

source_name: 1.0 _g amplified 2457T-infected 2.75 hr STS cDNA


title: BLSA-1961-FCTX-CpG

description: Human Brain Tissue: FCTX

source_name: Human Brain Tissue: FCTX


title: BLSA-1838-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1454-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1862-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1917-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1867-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1805-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4788-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1866-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4542-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-933-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1775-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1105-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1465-FCTX-CpG

description: Human Brain Tissue: FCTX


title: BLSA-1672-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1827-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1326-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-705-FCTX-CpG

description: Human Brain Tissue: FCTX

value: JHU


title: UMARY-880-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1541-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1544-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1037-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-879-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1571-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-994-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1209-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1134-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1502-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-142-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1584-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1847-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-1361-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1578-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1648-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1260-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1028-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-712-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-995-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1064-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-1344-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1612-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1846-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1545-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1535-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-713-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-604-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1230-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1795-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1540-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4924-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1715-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4782-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1078-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4726-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4590-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1079-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1849-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-993-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5086-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1936-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-710-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4543-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1226-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1104-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1797-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1136-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1613-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4842-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1170-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5024-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4916-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1792-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1498-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1486-FCTX-CpG

description: Human Brain Tissue: FCTX


title: JHU-719-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1079-CRBLM-CpG

description: Human Brain Tissue: CRBLM

source_name: Human Brain Tissue: CRBLM

value: cerebellum


title: UMARY-1158-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4590-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4786-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1571-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4788-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1076-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1133-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5087-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-871-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-993-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-914-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1454-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1545-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1614-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1540-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1935-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1846-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4789-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-384-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1936-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-705-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1064-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1496-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4842-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4545-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1556-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4593-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4640-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1206-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4727-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-2069-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1134-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4726-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5024-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-745-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1839-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1830-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4782-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1889-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1595-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1883-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-2102-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1867-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5078-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-2037-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-1344-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4543-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1465-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1862-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4725-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1713-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4542-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1541-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4916-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1260-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1326-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4924-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1583-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-602-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1825-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1865-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5079-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-142-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-927-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1840-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1902-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1849-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1105-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1712-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4841-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1838-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4636-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1907-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1613-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-827-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1866-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-2093-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4540-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1579-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1672-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1578-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1903-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1640-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1104-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1795-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1535-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1924-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4263-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1827-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1611-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1939-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1797-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-1361-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-933-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1961-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4903-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1209-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4598-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1847-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5028-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4729-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4915-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5081-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1114-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-1775-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: BLSA-2020-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-710-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1715-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1226-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-712-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1170-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1940-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1230-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1570-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1206-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4549-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1498-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-719-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1136-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: JHU-384-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-914-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5086-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1158-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5087-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1792-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: Primary skin fibroblasts infected with empty retroviral vector SFCVneo replicate 2

status: Public on Mar 05 2010

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

description: Gene expression data from cultured primary skin fibroblasts isolated from 10 days old chicken embryos and infected with empty SFCVneo retroviral construct.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Bioconductor (version 2.3) using Affymetrix default annotation and GC-RMA as normalization method.

source_name: Cultured primary skin fibroblasts isolated from 10 days old chicken embryos and infected with empty SFCVneo retroviral construct.

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

extract_protocol: Approximately 3 millions (subconfluent 10cm plate) of cultured cells were dissolved in 2 ml TRIzol reagent and total RNA was extracted according to manufacturer's protocol.

value: primary skin fibroblast

tag: age

value: embryo, 10 days


title: Primary skin fibroblasts infected with retroviral construct SFCVneo-EGR4 replicate 1

description: Gene expression data from cultured primary skin fibroblasts isolated from 10 days old chicken embryos and infected with SFCVneo-EGR4 retroviral construct.

source_name: Cultured primary skin fibroblasts isolated from 10 days old chicken embryos and infected with SFCVneo-EGR4 retroviral construct.


title: Primary skin fibroblasts infected with empty retroviral vector SFCVneo replicate 1


title: UMARY-1133-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: Primary skin fibroblasts infected with retroviral construct SFCVneo-EGR4 replicate 2


title: Primary skin fibroblasts infected with retroviral construct SFCVneo-EGR4 replicate 3


title: normal mammary gland FVBmg.18PI.Normal.Cy5

status: Public on Jun 29 2009

city: St. Louis

first: Robert

last: Lesurf

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

description: RNA isolated from whole flash frozen mammary tissue/tumor.

hyb_protocol: Following fragmentation, 750ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122A) according to the protocols provided by the manufacturer.

scan_protocol: Array was scanned using Agilent's dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantified using Agilent's Feature Extraction software (Palo Alto, CA).

data_processing: Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.

source_name: Stratagene universal mouse reference

label_protocol: 500ng of total RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp aRNA kit, Ambion) according to manufacturer's protocol.  Cy3-labeled aRNA was prepared from 10ug aRNA using Cy Post-labeling Reactive Dye Pack (Amersham Biosciences).

extract_protocol: No extraction

tag: sample identifier

tag: sample type

value: Stratagene universal mouse reference

source_name: Normal tissue from whole murine mammary gland

label_protocol: 500ng of total RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp aRNA kit, Ambion) according to manufacturer's protocol. Cy5-labeled aRNA was prepared from 10ug aRNA using Cy Post-labeling Reactive Dye Pack (Amersham Biosciences).

extract_protocol: RNeasy Midi Kit (Qiagen)

value: FVBmg.18PI; Sex:Female; Strain:FVB/N

tag: genetic background

value: FVB/N


title: Nkx03

status: Public on Oct 11 2008

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

hyb_protocol: Cy5-labeled samples were hybridized with n equimolar amount of rat reference RNA labeled with Cy3 to a DNA chip containing the version 3 rat microarray (Operon Biotechnologies) printed with 27,649 spots corresponding to 27,095 annotated genes   After hybridization, slides were washed sequentially.  Details of hybridization and washing protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

scan_protocol: Scanned on a Gene Pix 5000 scanner in the Duke University Microarray Core facility.

data_processing: The data were processed using GenePix Pro 5 software and uploaded to the Duke Institute for Genome Sciences and Policy Express Data Repository (http://data.genome.duke.edu/schislerMCB2008)  Data were normalized using per-chip and per-spot intensity-dependent LOWESS normalization with a threshold of 0.01.

organism: Rattus norvegicus

source_name: Rat reference

label_protocol: 500 ng of total RNA from five independent groups of AdCMV-Nkx6.1- and AdCMV-βGAL-treated islets were used for two rounds of amplification and labeled with Cy5.  Details of amplification and labeling protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

growth_protocol: Pancreatic islets were harvested from male Sprague-Dawley rats weighing approximately 250 g under a protocol approved by the Duke University Institutional Animal Care and Use Committee. Approximately 200 rat islets per condition were cultured in 2 ml of RPMI medium (10% fetal calf serum, 8 mM glucose).

extract_protocol: Total RNA was prepared from rat islets and was purified using the RNeasy microkit (Qiagen)  in accordance with the manufacturer’s instructions which included DNase treatment to eliminate genomic contamination. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer.

treatment_protocol: Islet pools were treated with viruses at a concentration of 5E9 particles/ml medium for 18 h. Virus-containing medium was replaced with fresh culture medium, and islets were cultured for an additional 60 h, with fresh medium daily

tag: pool of rat RNA

source_name: Isolated pancreatic islets of langerhans

tag: 500 ng used for 2 rounds of RNA amplification


title: normal mammary gland FVBmg.10.Normal.Cy5

value: FVBmg.10; Sex:Female; Strain:FVB/N

value: Normal tissue from whole murine mammary gland


title: Primary skin fibroblasts infected with empty retroviral vector SFCVneo replicate 3


title: Nkx05


title: NIC tumor T.NICp1.Tumor.Cy5

source_name: NIC tumor pool from whole murine mammary gland

value: T.NICp1; Type:Pool from 5 NIC tumors (equal amounts); Sex:Female; Strain:FVB/N

value: female


title: bGAL03

tag: AdCMV-βGAL


title: Nkx02


title: Nkx04


title: normal mammary gland FVBmg.10.Normal.Cy3

value: normal mammary gland


title: bGAL01


title: Malignant 6NC

status: Public on Oct 01 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Microarray experiments were carried out as one-color hybridizations on human catalog 8-plex 15K miRNA microarrays (AMADID 016436) from Agilent Technologies. Analyses were done initially with matched malignant and non-malignant sample pairs.

hyb_protocol: Labeled samples were hybridized on human catalog 8-plex 15K miRNA microarrays (AMADID 016436) from Agilent Technologies encoding probes for 470 human and 64 human viral microRNAs from the Sanger database v9.1. Microarrays were washed according to the supplier’s protocol.

scan_protocol: Microarrays were scanned at 5 µm resolution with DNA microarray laser scanner (Agilent Technologies) and processed according to the supplier’s protocol.

data_processing: Features were extracted with an image analysis tool version A.9.5.3 using default protocols and settings (Agilent Technologies). Data analysis was carried out on the Rosetta Inpharmics gene expression data management and analysis system Resolver Version 7.0. Intensity experiments were created with the Intensity Experiment Manager from Resolver by combining all hybridizations derived from malignant and non-malignant samples, respectively. ‘In silico’ ratio profiles and ratio experiments were generated by the Ratio Experiment Wizard after selection of either malignant and non-malignant samples derived from individual patients or by combining malignant and non-malignant intensity experiments. A two-sample Students t-test was applied on all intensity profiles, while a one-sample t-test was applied to the ratio experiments comprising individual patients. Principal Component Analysis (PCA) was used for data reduction on either experiment or reporter level. Cluster analysis was done on features or reporter levels with the 2D Matrix Wizard from Resolver with an agglomerative algorithm using average link as heuristic criteria and Manhattan distance as metric similarity measure on both, intensity profiles and ratio experiments. All analysis criteria were combined making the microarray results extremely robust and highly reproducible.

source_name: human kidney

label_protocol: An amount of 100 ng total RNA was dephosphorylated with Calf Intestine Alkaline Phosphatase (GE Healthcare, Chalfont St. Giles, United Kingdom), denaturated with DMSO and used as RNA acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3’, 5’-cytidine bisphosphate having a single Cy3 label attached to the 3’ phosphate of the nucleotide (Cy3-pCp). The labeling reaction was column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.

extract_protocol: Immediately after nephrectomy matched malignant and non-malignant specimens from the same kidney were collected in RNAlater Stabilization Reagent (Qiagen, Hilden, Germany), stored at room temperature for 2 h, subsequently overnight at 4°C and at -80°C until RNA isolation. Total RNA including small and micro RNAs were isolated from about 50 mg of tissue using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. This approach combines phenol/guanidine thiocyanate-based tissue lysis and silika membrane-based binding with purification of isolated total RNA including micro and small RNAs. Briefly, samples were homogenized in Qiazol lysis buffer with the TissueLyser (Qiagen) twice for 1 min at 30 Hz. After a centrifugation and phase separation step RNA was immobilized at the silika-membrane of the kit including spin column several times washed, and eluted with water. The RNA was stored at -80°C. The total RNA yield and the ratio of absorbance at 260 nm to 280 nm (A260/A280 ratio) were measured with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Montchanin, DE, USA). The integrity of total RNA was assessed with the 2100 Bioanalyzer and the RNA 6000 Nano LabChip kit (Agilent Technologies, Santa Clara, CA, USA). The Agilent 2100 Expert software B.02.05 was used to generate the RNA Integrity Number (RIN) as criterion of the RNA quality. Furthermore, the ratio of miRNA fraction to small RNA in isolated total RNA was monitored by use of the Agilent Small RNA kit.

tag: kidney carcinoma

tag: Kidney tissue samples were derived from adult patients undergoing radical nephrectomy. Tumor types were clear renal cell carcinoma. Tumor classification and stage were established according to the 2002 TNM System and the 2004 WHO Classification.


title: Non-malignant 11NN

tag: kidney non-malignant sample

tag: Matched kidney tissue samples were derived from adult patients undergoing radical nephrectomy. Tumor types were clear renal cell carcinoma. Tumor classification and stage were established according to the 2002 TNM System and the 2004 WHO Classification.


title: bGAL02


title: Non-malignant 13NN


title: Malignant 4NC


title: Malignant 14C


title: Non-malignant 5NN


title: bGAL05


title: NIC tumor T.NICp2.Tumor.Cy5

value: T.NICp2; Type:Pool from 5 NIC tumors (equal amounts); Sex:Female; Strain:FVB/N

value: NIC tumor pool from whole murine mammary gland


title: Nkx01


title: NIC tumor T.NICp1.Tumor.Cy3


title: Non-malignant 41NN


title: normal mammary gland FVBmg.18PI.Normal.Cy3


title: Malignant 12NC


title: NIC tumor T.NICp2.Tumor.Cy3


title: Non-malignant 3NN


title: Malignant 40NC


title: Malignant 34NC


title: bGAL04


title: Non-malignant 9NN


title: Malignant 42NC


title: Non-malignant 1NN


title: Mutant Histone H2B^30-37 replicate 1

status: Public on Apr 08 2006

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Mutant yeast strain Histone H2B^30-37

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Yeast RNA

label_protocol: Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Cells were grown to mid-log phase (OD600=0.5-0.7) in rich media (YPD).  Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: PY020 (mutant Histone H2B^30-37)


title: Wild-type for Histone H2B^30-37 replicate 1

description: Wild-type yeast strain

tag: PY014 (wild-type Histone H2B)


title: Mutant Histone H2B^3-37 replicate 2

description: Mutant yeast strain Histone H2B^3-37

tag: PY021 (mutant Histone H2B^3-37)


title: Mutant Histone H2B^30-37 replicate 2

description: Mutant yeast strain Histone H2B^30-37


title: Mutant Histone H2B^3-37 replicate 3

description: Mutant yeast strain Histone H2B^3-37


title: Mutant Histone H2B^3-37 replicate 1

description: Mutant yeast strain Histone H2B^3-37


title: adult head_AA22_experimentywtemp1

status: Public on Dec 07 2007

city: Southampton

first: Herman

last: Wijnen

state: Hampshire

address: Life Sciences Building 85 - Highfield Campus

department: Centre for Biological Sciences

country: United Kingdom

institute: University of Southampton

data_processing: Bioconductor Robust Multi-array Average

organism: Drosophila melanogaster

source_name: adult head

label_protocol: Approximately 25 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: initially 25 C DD, then 12-hr 18 C/12-hr 25 C thermocycle in constant darkness

extract_protocol: Flies were immediately frozen on dry ice. Approximately 100-200 heads were isolated on sieves after breaking the frozen flies

treatment_protocol: 25 C in constant darkness (after 12-hr 18 C/12-hr 25 C thermocycle in constant darkness)

tag: y w stock


title: Non-malignant 23NN


title: Mutant Histone H2B^30-37 replicate 3

description: Mutant yeast strain Histone H2B^30-37


title: Non-malignant 17NN


title: Malignant 28NC


title: Malignant 10NC


title: Malignant 2NC


title: Malignant 24NC


title: Malignant 18NC


title: Mutant Histone H2B K->G replicate 3

description: Mutant yeast strain Histone H2B K->G

tag: PY029 (mutant Histone H2B K->G)