title: sda+ LB (T3) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85584.gif

source_name: wild type in LB at T3 (run 2)


title: loaded-bone-6d-sample-rep1

status: Public on Jun 12 2010

type: RNA

city: Indianapolis

first: Charles

middle: H

last: Turner

state: IN

address: 723 W. Michigan St. SL 220C

department: Biomedical Engineering

country: USA

institute: Indiana University Purdue University Indiapanolis

description: exon expression data of loaded bone in rat

hyb_protocol: Labeled DNA were hybridized for 17 hr at 45C on Rat Exon 1.0 St Genechips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned using Affymetrix GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Partek Genomics Suite.  RMA was used to import raw data, and a 2-way ANOVA was used to identify differentially expressed transcripts.
probe_group_file: RaEx-1_0-st-v1.r2.pgf
meta-probeset_file: RaEx-1_0-st-v1.r2.dt1.rn4.core.mps

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: right forelimb (loaded) from rat

label_protocol: Biotinylated DNA were prepared according to the Affymetrix standard WT protocol using 1ug pretreated with Ribominus (Invitrogen)

extract_protocol: Trizol followed by Qiagen Rneasy and DNA-free kit (Ambion)

treatment_protocol: Right forelimb of each animal was loaded daily.  At the indicated time point (4h, 12h, 1d, 2d, 4d, 6d, 8d, 12d, 16d, 24d, or 32d) ulnae were dissected and snap frozen until RNA isolation.

tag: tissue

value: bone (ulna)

tag: stimulation

value: loaded

tag: time point

tag: replicate


title: Tomato Heat Tolerant Control rep-3

city: Varanasi

first: Ashutosh

last: Rai

state: Uttar Pradesh

address: Post Box-1. Jakhini Shahanshapur

department: Crop Improvment

country: India

institute: Indian Institute of Vegetable Research

description:
SAMPLE 21
Gene expression data from Tomato Heat Tolerant untreated plants

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Affymetrix Expression Console and RMA version 1.0 as normalization method.

organism: Solanum lycopersicum

source_name: Leave at flowering stage in normal growth condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were sown in plastic pots at optimal conditions for tomato plants.

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

treatment_protocol: Sample 1,2,3,7,8,9,13,14,15,19,20,21 were grown in normal growth conditions without any stress in green house. While sample 4,5,6, and 10,11,12 were subjected to water stress by with holding water for 7 days. Sample 16,17,18 and 22,23,24 were subjected to 40C for 60 min in growth chamber befor sample collection.

tag: genotype

value: Heat Tolerant Genotype


title: Tomato Heat Tolerant Control rep-2

description:
SAMPLE 20
Gene expression data from Tomato Heat Tolerant untreated plants


title: loaded-bone-12h-sample-rep2


title: Tomato Heat Tolerant Control rep-1

description:
SAMPLE 19
Gene expression data from Tomato Heat Tolerant untreated plants


title: Tomato Heat Susceptible Treated rep-1

description:
SAMPLE 16
Gene expression data from Tomato Heat Susceptible treated plants

source_name: Leave at flowering stage at High temperature (40C) stress condition

value: Heat Susceptible Genotype


title: Tomato Heat Susceptible Treated rep-3

description:
SAMPLE 18
Gene expression data from Tomato Heat Susceptible treated plants


title: Tomato Heat Susceptible Treated rep-2

description:
SAMPLE 17
Gene expression data from Tomato Heat Susceptible treated plants


title: Tomato Heat Susceptible Control rep-2

description:
SAMPLE 14
Gene expression data from Tomato Heat Susceptible untreated plants


title: Tomato Heat Susceptible Control rep-3

description:
SAMPLE 15
Gene expression data from Tomato Heat Susceptible untreated plants


title: control-bone-12h-sample-rep5

description: exon expression data of untreated bone in rat

source_name: left forelimb (untreated) from rat

value: control


title: loaded-bone-12h-sample-rep3


title: control-bone-12h-sample-rep4


title: loaded-bone-12h-sample-rep1


title: control-bone-12h-sample-rep3


title: Tomato Drought Tolerant Treated rep-3

description:
SAMPLE 12
Gene expression data from Tomato Drought Tolerant treated plants

source_name: Leave at flowering stage at water stress condition

value: Drought Tolerant Genotype


title: Tomato Heat Susceptible Control rep-1

description:
SAMPLE 13
Gene expression data from Tomato Heat Susceptible untreated plants


title: control-bone-12h-sample-rep2


title: Tomato Drought Tolerant Treated rep-2

description:
SAMPLE 11
Gene expression data from Tomato Drought Tolerant treated plants


title: Tomato Drought Tolerant Treated rep-1

description:
SAMPLE 10
Gene expression data from Tomato Drought Tolerant treated plants


title: sda- LB (T0) run 2

city: Stanford

first: Sharon

last: Hoover

state: CA

address: 337 Campus Drive, Lokey 105

department: Department of Biology

institute: Stanford University

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85581.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Bacillus subtilis

source_name: Reference pool

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Reference pool

source_name: sda- in LB at T0 (run 2)

tag: measurement

value: time(change) T0 h

tag: mutated gene

value: delta-sda

tag: growth condition

value: Mn-

tag: experiment type

value: replicate 2


title: Tomato Drought Susceptible Treated rep-3

description:
SAMPLE 6
Gene expression data from Tomato Drought Susceptible treated plants

value: Drought Susceptible Genotype


title: Tomato Drought Tolerant Control rep-3

description:
SAMPLE 9
Gene expression data from Tomato Drought Tolerant untreated plants


title: loaded-bone-4h-sample-rep5

description: exon expression data of loaded bone in rat


title: Tomato Drought Susceptible Treated rep-2

description:
SAMPLE 5
Gene expression data from Tomato Drought Susceptible treated plants


title: loaded-bone-4h-sample-rep1


title: Tomato Drought Susceptible Control rep-3

description:
SAMPLE 3
Gene expression data from Tomato Drought Susceptible untreated plants


title: Tomato Drought Tolerant Control rep-2

description:
SAMPLE 8
Gene expression data from Tomato Drought Tolerant untreated plants


title: Tomato Drought Tolerant Control rep-1

description:
SAMPLE 7
Gene expression data from Tomato Drought Tolerant untreated plants


title: loaded-bone-4h-sample-rep3


title: loaded-bone-4h-sample-rep2


title: control-bone-12h-sample-rep1


title: control-bone-4h-sample-rep3


title: control-bone-4h-sample-rep2


title: control-bone-4h-sample-rep5


title: loaded-bone-4h-sample-rep4


title: control-bone-4h-sample-rep4


title: Tomato Drought Susceptible Control rep-2

description:
SAMPLE 2
Gene expression data from Tomato Drought Susceptible untreated plants


title: Tomato Drought Susceptible Control rep-1

description:
SAMPLE 1
Gene expression data from Tomato Drought Susceptible untreated plants


title: Tomato Drought Susceptible Treated rep-1

description:
SAMPLE 4
Gene expression data from Tomato Drought Susceptible treated plants


title: RA-treated 48 hr

status: Public on Jun 11 2010

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

description: Gene expression data from RA-treated keratinocytes.

hyb_protocol: Labeled probe, 15  g, was hybridized to Hu133Av2 arrays (Affymetrix).

scan_protocol: Arrays were washed, stained with anti-biotin streptavidin-phycoerythrin labeled antibody and scanned using the Agilent GeneArray Scanner system (Hewlett-Packard)

data_processing: Affymetrix Microsuite 5.0

organism: Homo sapiens

source_name: Human epidermal keratinocyte cultures

label_protocol: Approximately 5 to 8  micro-g of total RNA was reverse transcribed, amplified and labeled as recommended by Affymetrix

growth_protocol: Keratinocytes were grown without feeder cells in Keratinocyte Serum-Free Medium (Gibco), supplemented with 0.025 mg/ml bovine pituitary extract, 0.2 ng/ml epidermal growth factor, 0.4 mM CaCl2 and 1% penicillin/streptomycin (Growth media) at 37°C, in 5% CO2. At ~30% confluency, they are switched to Phenol Red-free Keratinocyte Serum Free-Media (Invitrogen) supplemented only with 1% penicillin/streptomycin (KBM) 24 h prior to commencing experiments.

extract_protocol: RNeasy kits (Qiagen) according to the manufacturer's instructions

treatment_protocol: Keratinocytes were treated with 1 microM RA (Sigma), or with 1 mM T3 (3,3',5-triiodo-L-thyronine sodium salt; Sigma) diluted in 0.1 N NaOH  for 1, 4, 24, 48 and 72 hr.

tag: cell type

value: Growing keratinocytes


title: RA-treated 24 hr


title: T3-treated 24 hr

description: Gene expression data from T3-treated keratinocytes.


title: T3-treated 1 hr


title: RA-treated 1 hr


title: T3-treated 72 hr


title: Control 72 hr

description: Gene expression data from untreated keratinocytes.


title: T3-treated 4 hr


title: Control 48 hr


title: control-bone-4h-sample-rep1

description: exon expression data of untreated bone in rat


title: Control 24 hr


title: RA-treated 4 hr


title: matUPD15 SAMPLE 2B_Replicate2

type: genomic

first: Andrew

middle: J

last: Sharp

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: patient with complete matUPD15 and a clinical diagnosis of Prader-Willi syndrome

hyb_protocol: Roche Nimblegen hybridization protocol

scan_protocol: scanned on an G2565 Agilent scanner at 5 microm resolution.

data_processing: Array images were analysed using NimbleScan v2.5 software (Roche NimbleGen, Madison WI, USA) with default parameters incorporating spatial correction. The probe log2 ratios were subsequently quantile normalized and potential outliers were replaced by the median probe intensity of four neighboring probes.

molecule: genomic DNA

label_protocol: immunoprecipitated DNA was labelled by random priming using Cy5-conjugated random nonamers (TriLink BioTechnologies, San Diego CA, USA)

extract_protocol: genomic DNA extracted from peripheral blood samples

treatment_protocol: 15 microg of DNA was sonicated to generate fragments 200-800bp in size (Branson 450D Sonifier, Danbury, CT, USA), incubated with 10microg of anti 5-methyl cytidine (Diagenode, Liege, Belgium), immunoprecipitated using Protein A sepharose beads (Life Technologies, Carlsbad CA, USA), and purified by phenol:chloroform extraction.

value: peripheral blood

tag: antibody

tag: disease state

value: Prader-Willi syndrome

source_name: 2B_input sonicated DNA_R2

label_protocol: input DNA was labelled by random priming using Cy3-conjugated random nonamers (TriLink BioTechnologies, San Diego CA, USA)


title: matUPD15 SAMPLE 2B_Replicate1

source_name: 2B_input sonicated DNA_R1

treatment_protocol: 15 microg of DNA was sonicated to generate fragments 200-800bp in size (Branson 450D Sonifier, Danbury, CT, USA)


title: matUPD15 SAMPLE 1A_Replicate1

source_name: 1A_input sonicated DNA_R1


title: 7708-Trauma Day0

city: New Brunswick

first: Stephen

middle: F

last: Lowry

state: NJ

address: 125 Paterson St

department: Surgery

institute: UMDNJ

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Focus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GeneSpring GX11.0.1 - RMA - baseline transformation, log

source_name: Patient ICU

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

value: Leukocytes

tag: condition

value: ICU 1-5 Days


title: patUPD15 SAMPLE 4D_Replicate2

description: patient with complete patUPD15 associated with Angelman syndrome

value: Angelman syndrome

source_name: 4D_input sonicated DNA_R2


title: matUPD15 SAMPLE 3C_Replicate1

source_name: 3C_input sonicated DNA_R1


title: 7702-Trauma Day0


title: patUPD15 SAMPLE 5E_Replicate1

source_name: 5E_input sonicated DNA_R1


title: matUPD15 SAMPLE 1A_Replicate2

source_name: 1A_input sonicated DNA_R2


title: Control 1 hr


title: matUPD15 SAMPLE 3C_Replicate2

source_name: 3C_input sonicated DNA_R2


title: patUPD15 SAMPLE 4D_Replicate1

source_name: 4D_input sonicated DNA_R1


title: 7704-Trauma Day0


title: RA-treated 72 hr


title: 7702-Trauma Day1

value: ICU 5-7 Days


title: patUPD15 SAMPLE 6F_Replicate2

source_name: 6F_input sonicated DNA_R2


title: 2204 cortisol+LPS (24hr)

source_name: Healthy Volunteers

value: 24hr post Cortisol+LPS


title: patUPD15 SAMPLE 6F_Replicate1

source_name: 6F_input sonicated DNA_R1


title: T3-treated 48 hr


title: 2212 cortisol+LPS (24hr)


title: 2206 cortisol+LPS (24hr)


title: 2202 cortisol+LPS (6hr)

value: 12hr Cortisol + 6hr LPS


title: 2203 cortisol+LPS (6hr)


title: 7708-Trauma Day1


title: Control 4 hr


title: 2209 saline+LPS (24hr)

value: 24hr post saline+LPS


title: 2210 saline+LPS (24hr)


title: 2205 cortisol+LPS (6hr)


title: 7711-Trauma Day1


title: 2201 cortisol+LPS (6hr)


title: 2202 cortisol+LPS (24hr)


title: 2207 saline+LPS (24hr)


title: 2203 cortisol+LPS (24hr)


title: 930 saline+LPS (24hr)


title: 7711-Trauma Day0


title: 2208 saline+LPS (6hr)

value: 12hr saline + 6hr LPS


title: 2201 cortisol+LPS (24hr)


title: 2210 saline+LPS (6hr)


title: 927 saline+LPS (24hr)


title: 2207 saline+LPS (6hr)


title: 7713-Trauma Day0


title: 2204 cortisol+LPS (6hr)


title: 2206 cortisol+LPS (6hr)


title: 927 saline+LPS (6hr)


title: 2212 cortisol+LPS (6hr)


title: 7713-Trauma Day1


title: 2210 saline+LPS (0hr)

value: 6hr of saline


title: patUPD15 SAMPLE 5E_Replicate2

source_name: 5E_input sonicated DNA_R2


title: 2209 saline+LPS (0hr)


title: 930 saline+LPS (6hr)


title: leaf_Col-0_rep3

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description:
A refers to Col-0
A-3-LG_(ATH1-121501)

hyb_protocol: Fragmentation of the labeled aRNA prepares the target for hybridization to GeneChip® 3’ expression arrays with GeneChip® hybridization oven 640.

scan_protocol: Wash and stain the arrays with GeneChip® fluidics station 450, Scan the arrays with the GeneArray scanner 3000 by the GeneChip® Operating  Software (GCOS) or Command Console® (AGCC) Software.

data_processing: RMA data were obtained by using Partek GS 6.4.

organism: Arabidopsis thaliana

label_protocol: In Vitro Transcription to Synthesize Biotin-Modified aRNA with IVT Labeling Master Mix generates multiple copies of biotin-modified aRNA from  the double-stranded cDNA templates; this is the amplification step.aRNA Purification removes unincorporated NTPs, salts, enzymes, and  inorganic phosphate to improve the stability of the biotin-modified aRNA.

growth_protocol: 16 h light, 8 h dark, 21°C

extract_protocol: Extract and purify the total RNA by the Qiagen RNeasy Mini Kit.Reverse Transcription to Synthesize First-Strand cDNA is primed with  T7 oligo(dT) primer to synthesize cDNA containing a T7 promoter sequence.Second-Strand cDNA Synthesis converts the single-stranded cDNA into  a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA polymerase and RNase H to simultaneously degrade the RNA  and synthesize second strand cDNA.

treatment_protocol: no treatment

tag: genotype/variation

value: wild type

value: leaves

tag: age

value: 15 days


title: 931 saline+LPS (6hr)


title: leaf_chr11-1chr17-1_rep3

description:
B refers to chr11-1 chr17-1
B-3-LG_(ATH1-121501)

value: chr11-1 chr17-1 mutant


title: 921 saline+LPS (6hr)


title: leaf_chr11-1chr17-1_rep1

description:
B refers to chr11-1 chr17-1
B-1-LG_(ATH1-121501)


title: leaf_Col-0_rep1

description:
A refers to Col-0
A-1-LG_(ATH1-121501)


title: leaf_chr11-1chr17-1_rep2

description:
B refers to chr11-1 chr17-1
B-2-LG_(ATH1-121501)


title: leaf_Col-0_rep2

description:
A refers to Col-0
A-2-LG_(ATH1-121501)


title: 7414 microaerobiosis PSY 3

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum bll2758 mutant grown microaerobically

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com).

organism: Bradyrhizobium japonicum

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase which corresponded to an OD600 of 0.4 to 0.5 in microoxic cultures (PSY-arabinose medium)

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

value: microaerobiosis

tag: medium

value: PSY


title: 7414 microaerobiosis PSY 1

source_name: B. japonicum bll2758 mutant grown microaerobically


title: 2208 saline+LPS (0hr)

tag: tissue


title: 930 saline+LPS (0hr)


title: 7414 microaerobiosis PSY 2


title: mesenterc lymph nodes, Inf-Con

city: nanjing

first: fang

last: tian

state: jiangsu

address: hanzhong road No.140

institute: nanjing medical university

description: Gene expression data from mesenterc lymph nodes in Inf-Con group

hyb_protocol: fragmented (200 nt or less) cRNA was hybridized for 16 h at 45°C to Affymetrix porcine genome arrays

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3,000.

data_processing:
program-name = Expression Console
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0

organism: Sus scrofa

source_name: mesenterc lymph nodes in Inf-Con group

growth_protocol: The mesenteric lymph nodes surrounding the cecum from three pigs in each of the Vac-Cha and Inf-Con groups were isolated immediately and also stored in liquid nitrogen.

extract_protocol: Total RNA extraction from each mesenteric lymph node was performed with TRIzol reagent (Invitrogen Life Technologies) and purified with RNeasy mini kits (QIAGEN). cDNA was generated using One-Cycle Target Labeling and Control Reagents (Affymetrix), and cRNA was made with GeneChip® IVT Labeling Kit (Affymetrix).

tag: crossbred pigs

value: Landrace/Yorkshire/Duroc

tag: treatment protocol

value: infected with normal cercariae (control)

value: mesenteric lymph nodes

tag: sex

value: male


title: mesenterc lymph nodes,Vac-Cha

description: Gene expression data from the mesenterc lymph nodes in Vac-Cha group

source_name: mesenterc lymph nodes in Vac-Cha group

value: vaccinated with UV attenuated cercariae and challenged with normal cercariae


title: 6884_LF

city: Nashville

first: Xiaofei

last: Wang

state: TN

address: 3500 John A Merritt blvd

department: Biological Sciences

institute: Tennessee State University

description: Segmental copy number variation

hyb_protocol: Equal amounts of Cy3 labeled test sample and Cy5 labeled reference sample were mixed and hybridized to tiling array, by NimbleGen commercial service

scan_protocol: performed by NimbleGen

data_processing: Data were normalized with qspline algorithm. Segmentation analysis was performed using Olsen algorithm (performed by NimbleGen)

organism: Gallus gallus

label_protocol: 1 ug of test DNA were labeled with Cy3, and 1 ug of reference DNA were labeled with Cy5, using NimbelGen commercial service

extract_protocol: Blood DNA was extracted from whole blood anticoagulent 0.5 M EDTA. Samples were stored at -20 until DNA isoaltion. 100 ul of whole blood were mixed with lysis buffer (0.2x PBS, 0.02% SDS), digested with protease K, then extracted twice with phenol/chloroform/IAA, once with chloroform.

tag: breed

value: Leghorn

tag: gender

value: Female

value: Blood

value: Broiler

value: Male


title: 1003_RM

description: Segmental copy number variation

value: Rhode Island Red


title: 6191_BF

description: Segmental copy number variation


title: 6262_BM

description: Segmental copy number variation


title: 6951_LM

description: Segmental copy number variation


title: 1007_RM

description: Segmental copy number variation


title: 5849_BF

description: Segmental copy number variation


title: 6870_LF

description: Segmental copy number variation


title: 2916_BF

description: Segmental copy number variation


title: 6953_LM

description: Segmental copy number variation


title: Male Ethiopians Africa EthiopiaAm78 Human660W-Quad v1.0

status: Public on Jun 10 2010

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0   Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium  Human660W-Quad v1.0 Genotyping BeadChips (Illumina).
Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

label: C-Bio and A-DNP

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Ethiopians

tag: region

value: Africa

value: blood


title: Male Ethiopians Africa EthiopiaOr48c Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaAm77 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaTi63 Human660W-Quad v1.0


title: Male Samaritians Near East Samaritian988 Human660W-Quad v1.0

value: Samaritians

value: Near East


title: Male Ethiopians Africa EthiopiaTi7 Human660W-Quad v1.0


title: Male Samaritians Near East Samaritian990 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaTi61 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaAm76 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaAm59 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaAm58 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaTi5 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaTi69 Human660W-Quad v1.0


title: Male Samaritians Near East Samaritian983 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaOr53b Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaOr48 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaAm52 Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaAm50 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1430 Human660W-Quad v1.0

value: Saudis

value: Arabia


title: Male Ethiopians Africa EthiopiaOr45a Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaOr41c Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaOr42a Human660W-Quad v1.0


title: Male Ethiopians Africa EthiopiaOr44b Human660W-Quad v1.0


title: Male Saudis Arabia saudi1413 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1424 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1436 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1428b Human660W-Quad v1.0


title: Male Saudis Arabia saudi1434 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1432 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1411 Human660W-Quad v1.0


title: Male Syrians Near East syria361 Human660W-Quad v1.0

value: Syrians


title: Male Syrians Near East syria520 Human660W-Quad v1.0


title: Male Syrians Near East syria461 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1426 Human660W-Quad v1.0


title: Male Georgia Jews Caucasus GeorgJew125 Human660W-Quad v1.0

value: Georgia Jews

value: Caucasus


title: Male Georgia Jews Caucasus GeorgJew111 Human660W-Quad v1.0


title: Male Syrians Near East syria485 Human660W-Quad v1.0


title: Male Syrians Near East syria298 Human660W-Quad v1.0


title: Male Georgia Jews Caucasus GeorgJew105 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan560 Human660W-Quad v1.0

value: Jordanians


title: Male Georgia Jews Caucasus GeorgJew141 Human660W-Quad v1.0


title: Male Azerbaijan Jews Caucasus AzerbJew204 Human660W-Quad v1.0

value: Azerbaijan Jews


title: Male Jordanians Near East Jordan546 Human660W-Quad v1.0


title: Male Azerbaijan Jews Caucasus AzerbJew210 Human660W-Quad v1.0


title: Male Azerbaijan Jews Caucasus AzerbJew213 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan485 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan563 Human660W-Quad v1.0


title: Male Azerbaijan Jews Caucasus AzerbJew218 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan382 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan502 Human660W-Quad v1.0


title: Female Morocco Jews Africa MorJew2001 Human660W-Quad v1.0

value: Female

value: Morocco Jews


title: Male Jordanians Near East Jordan426 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan603 Human660W-Quad v1.0


title: Male Saudis Arabia saudi1403 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan387 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan384 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan646 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan62 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan214 Human660W-Quad v1.0


title: Female Jordanians Near East Jordan305 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan445 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan543 Human660W-Quad v1.0


title: Male Syrians Near East syria464 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan503 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan608 Human660W-Quad v1.0


title: Male Jordanians Near East Jordan307 Human660W-Quad v1.0


title: Male Moroccans Africa moroccoB17 Human660W-Quad v1.0

value: Moroccans


title: Male Azerbaijan Jews Caucasus GeorgJewtat2 Human660W-Quad v1.0

value: Male


title: Male Moroccans Africa moroccoC60 Human660W-Quad v1.0


title: Male Moroccans Africa moroccoE28 Human660W-Quad v1.0


title: Male Azerbaijan Jews Caucasus GeorgJewtat17 Human660W-Quad v1.0


title: Male Moroccans Africa moroccoE21 Human660W-Quad v1.0


title: Male Moroccans Africa moroccoC61 Human660W-Quad v1.0


title: Male Georgians Caucasus  mg72 Human610-Quad v1.0

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium Human610-Quad v1.0  Genotyping BeadChips (Illumina).
Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

value: Georgians


title: Male Moroccans Africa moroccoB93 Human660W-Quad v1.0


title: Male Moroccans Africa moroccoA57 Human660W-Quad v1.0


title: Female Azerbaijan Jews Caucasus GeorgJewtat14 Human660W-Quad v1.0


title: Male Georgians Caucasus  mg70 Human610-Quad v1.0


title: Male Georgians Caucasus  mg68 Human610-Quad v1.0


title: Male Moroccans Africa moroccoA98 Human660W-Quad v1.0


title: Male Georgians Caucasus  mg65 Human610-Quad v1.0


title: Male Georgians Caucasus  mg54 Human610-Quad v1.0


title: Male Georgians Caucasus  mg64 Human610-Quad v1.0


title: Male Georgians Caucasus  mg62 Human610-Quad v1.0


title: Male Georgians Caucasus  mg61 Human610-Quad v1.0


title: Male Jordanians Near East Jordan444 Human660W-Quad v1.0


title: Male Georgians Caucasus  mg51 Human610-Quad v1.0


title: Male Moroccans Africa moroccoA62 Human660W-Quad v1.0


title: Male Moroccans Africa moroccoA121 Human660W-Quad v1.0


title: Male Azerbaijan Jews Caucasus GeorgJewtat16 Human660W-Quad v1.0


title: Male Georgians Caucasus  mg40 Human610-Quad v1.0


title: Male Georgians Caucasus  mg43 Human610-Quad v1.0


title: Male Georgians Caucasus  mg49 Human610-Quad v1.0


title: Male Georgians Caucasus  mg22 Human610-Quad v1.0


title: Male Georgians Caucasus  mg31 Human610-Quad v1.0


title: Male Georgians Caucasus  mg5 Human610-Quad v1.0


title: Male Georgians Caucasus  mg47 Human610-Quad v1.0


title: Male Georgians Caucasus  mg34 Human610-Quad v1.0


title: Male Georgians Caucasus  mg23 Human610-Quad v1.0


title: Male Georgians Caucasus  mg27 Human610-Quad v1.0


title: Male Georgians Caucasus  mg20 Human610-Quad v1.0


title: Female Lezgins Caucasus  lez52 Human610-Quad v1.0

value: Lezgins


title: Male Lezgins Caucasus  lez33 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez38 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez40 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez49 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez44 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez24 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez25 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez31 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez37 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez42 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez36 Human610-Quad v1.0


title: Male Armenians Caucasus  arm26 Human610-Quad v1.0

value: Armenians


title: Male Armenians Caucasus  arm21 Human610-Quad v1.0

value: blood


title: Male Armenians Caucasus  arm11 Human610-Quad v1.0


title: Female Lezgins Caucasus  lez13 Human610-Quad v1.0


title: Female Lezgins Caucasus  lez9 Human610-Quad v1.0


title: Female Lezgins Caucasus  lez15 Human610-Quad v1.0


title: Male Lezgins Caucasus  lez3 Human610-Quad v1.0


title: Male Armenians Caucasus  arm19 Human610-Quad v1.0


title: Male Armenians Caucasus  arm23 Human610-Quad v1.0


title: Male Armenians Caucasus  arm14 Human610-Quad v1.0


title: Male Armenians Caucasus  arm18 Human610-Quad v1.0


title: Male Armenians Caucasus  arm20 Human610-Quad v1.0


title: Male Armenians Caucasus  arm13 Human610-Quad v1.0


title: Female Lezgins Caucasus  lez17 Human610-Quad v1.0


title: Male Armenians Caucasus  arm17 Human610-Quad v1.0


title: Male Armenians Caucasus  arm12 Human610-Quad v1.0


title: Male Armenians Caucasus  arm9 Human610-Quad v1.0


title: Male Armenians Caucasus  arm5 Human610-Quad v1.0


title: Male Armenians Caucasus  arm3 Human610-Quad v1.0


title: Male SAKILLI South Asia  SAKD75 Human610-Quad v1.0

value: SAKILLI

value: South Asia


title: Male SAKILLI South Asia  SAKD60 Human610-Quad v1.0


title: Male Armenians Caucasus  arm7 Human610-Quad v1.0


title: Male Armenians Caucasus  arm4 Human610-Quad v1.0


title: Male Armenians Caucasus  arm6 Human610-Quad v1.0


title: Male SAKILLI South Asia  SAKD72 Human610-Quad v1.0


title: Male NORTH KANNADI South Asia  KNTK386 Human610-Quad v1.0

value: NORTH KANNADI


title: Male MALAYAN South Asia  MLYA383 Human610-Quad v1.0

value: MALAYAN


title: Male SAKILLI South Asia  SAKD64 Human610-Quad v1.0


title: Female NORTH KANNADI South Asia  KNTK388 Human610-Quad v1.0


title: Male Armenians Caucasus  arm10 Human610-Quad v1.0


title: Male Turks Near East  tur236 Human610-Quad v1.0

value: Turks

value: Near East


title: Female Lezgins Caucasus  lez7 Human610-Quad v1.0

value: Caucasus


title: Male Turks Near East  tur2 Human610-Quad v1.0


title: Male Turks Near East  tur222 Human610-Quad v1.0


title: Female Turks Near East  tur170 Human610-Quad v1.0


title: Male Turks Near East  tur197 Human610-Quad v1.0


title: Male Turks Near East  tur20 Human610-Quad v1.0


title: Male Turks Near East  tur37 Human610-Quad v1.0


title: Male Turks Near East  tur262 Human610-Quad v1.0


title: Male Turks Near East  tur306 Human610-Quad v1.0


title: Male Turks Near East  tur277 Human610-Quad v1.0


title: Male Turks Near East  tur182 Human610-Quad v1.0


title: Male Armenians Caucasus  arm8 Human610-Quad v1.0


title: Female Turks Near East  tur154 Human610-Quad v1.0


title: Male Turks Near East  tur52 Human610-Quad v1.0


title: Male Uzbeks Central Asia  usb72 Human610-Quad v1.0

value: Uzbeks

value: Central Asia


title: Male Turks Near East  tur110 Human610-Quad v1.0


title: Male Turks Near East  tur84 Human610-Quad v1.0


title: Male Turks Near East  tur124 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb32 Human610-Quad v1.0

value: Female


title: Male NORTH KANNADI South Asia  KNTK385 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb64 Human610-Quad v1.0


title: Male Uzbeks Central Asia  usb40 Human610-Quad v1.0


title: Male Turks Near East  tur67 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb16 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb35 Human610-Quad v1.0


title: Female Turks Near East  tur139 Human610-Quad v1.0


title: Male Uzbeks Central Asia  usb83 Human610-Quad v1.0


title: Male Uzbeks Central Asia  usb13 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb8 Human610-Quad v1.0


title: Male Uzbeks Central Asia  usb24 Human610-Quad v1.0


title: Male Uzbeks Central Asia  usb78 Human610-Quad v1.0


title: Male Turks Near East  tur210 Human610-Quad v1.0


title: Male Uzbeks Central Asia  usb25 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb6 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb1 Human610-Quad v1.0


title: Male North Kannadi South Asia  KNTK397 Human610-Quad v1.0

value: North Kannadi


title: Female North Kannadi South Asia  KNTK400 Human610-Quad v1.0


title: Female North Kannadi South Asia  KNTK408 Human610-Quad v1.0


title: Male Iranians Central Asia  iran17 Human610-Quad v1.0

value: Iranians


title: Female North Kannadi South Asia  KNTK394 Human610-Quad v1.0


title: Male Iranians Central Asia  iran19 Human610-Quad v1.0

value: Male


title: Male Iranians Central Asia  iran18 Human610-Quad v1.0


title: Male Iranians Central Asia  iran20 Human610-Quad v1.0


title: Female North Kannadi South Asia  KNTK390 Human610-Quad v1.0


title: Male Iranians Central Asia  iran12 Human610-Quad v1.0


title: Male Iranians Central Asia  iran8 Human610-Quad v1.0


title: Male Iranians Central Asia  iran13 Human610-Quad v1.0


title: Male Iranians Central Asia  iran16 Human610-Quad v1.0


title: Male Iranians Central Asia  iran11 Human610-Quad v1.0


title: Male Iranians Central Asia  iran14 Human610-Quad v1.0


title: Female Uzbeks Central Asia  usb2 Human610-Quad v1.0


title: Male Iranians Central Asia  iran3 Human610-Quad v1.0


title: Female North Kannadi South Asia  KNTK392 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash17 Human610-Quad v1.0

value: Chuvashs

value: Europe


title: Male Iranians Central Asia  iran10 Human610-Quad v1.0


title: Male Iranians Central Asia  iran7 Human610-Quad v1.0


title: Male Iranians Central Asia  iran5 Human610-Quad v1.0


title: Male Iranians Central Asia  iran2 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash9 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash14 Human610-Quad v1.0


title: Male Iranians Central Asia  iran1 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash13 Human610-Quad v1.0


title: Male Iranians Central Asia  iran9 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash10 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash12 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash11 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash6 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash8 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash16 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash7 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash5 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash3 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash15 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash4 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash1 Human610-Quad v1.0


title: Male Syrians Near East  syria8 Human610-Quad v1.0

value: Syrians


title: Male Iranians Central Asia  iran15 Human610-Quad v1.0

value: blood


title: Male Syrians Near East  syria10 Human610-Quad v1.0


title: Male Iranians Central Asia  iran4 Human610-Quad v1.0


title: Male Chuvashs Europe  chuvash2 Human610-Quad v1.0


title: Male Iranians Central Asia  iran6 Human610-Quad v1.0


title: Male Syrians Near East  syria6 Human610-Quad v1.0


title: Male Syrians Near East  syria7 Human610-Quad v1.0


title: Male Syrians Near East  syria9 Human610-Quad v1.0


title: Male Syrians Near East  syria5 Human610-Quad v1.0


title: Male Syrians Near East  syria1 Human610-Quad v1.0


title: Male Syrians Near East  syria3 Human610-Quad v1.0


title: Male Syrians Near East  syria4 Human610-Quad v1.0


title: Male Iraq Jews Near East  iraq_jew10 Human610-Quad v1.0

value: Iraq Jews


title: Female Iraq Jews Near East  iraq_jew7 Human610-Quad v1.0


title: Male Iraq Jews Near East  iraq_jew8 Human610-Quad v1.0


title: Female Iraq Jews Near East  iraq_jew4 Human610-Quad v1.0


title: Male Iraq Jews Near East  iraq_jew9 Human610-Quad v1.0


title: Female Iraq Jews Near East  iraq_jew1 Human610-Quad v1.0


title: Male Belorussian Europe  belorus10 Human610-Quad v1.0

value: Belorussian


title: Male Syrians Near East  syria2 Human610-Quad v1.0


title: Female Iraq Jews Near East  iraq_jew2 Human610-Quad v1.0


title: Male Iranian Jews Near East  iran_jew3 Human610-Quad v1.0

value: Iranian Jews


title: Male Belorussian Europe  belorus5 Human610-Quad v1.0


title: Male Belorussian Europe  belorus4 Human610-Quad v1.0


title: Male Belorussian Europe  belorus3 Human610-Quad v1.0


title: Male Iraq Jews Near East  iraq_jew6 Human610-Quad v1.0


title: Female Iranian Jews Near East  iran_jew2 Human610-Quad v1.0


title: Male Belorussian Europe  belorus6 Human610-Quad v1.0


title: Male Iraq Jews Near East  iraq_jew11 Human610-Quad v1.0


title: Female Iranian Jews Near East  iran_jew1 Human610-Quad v1.0


title: Male Iraq Jews Near East  iraq_jew3 Human610-Quad v1.0


title: Male Belorussian Europe  belorus1 Human610-Quad v1.0


title: Male Belorussian Europe  belorus8 Human610-Quad v1.0


title: Male Belorussian Europe  belorus7 Human610-Quad v1.0


title: Female Ashkenazy Jews Europe  ashkenazy9e Human610-Quad v1.0

value: Ashkenazy Jews


title: Female Iraq Jews Near East  iraq_jew5 Human610-Quad v1.0


title: Female Ashkenazy Jews Europe  ashkenazy8e Human610-Quad v1.0


title: Male Belorussian Europe  belorus2 Human610-Quad v1.0


title: Female Ashkenazy Jews Europe  ashkenazy7e Human610-Quad v1.0


title: Male Ashkenazy Jews Europe  ashkenazy2e Human610-Quad v1.0


title: Female Iranian Jews Near East  iran_jew4 Human610-Quad v1.0


title: Male Ashkenazy Jews Europe  ashkenazy5e Human610-Quad v1.0


title: Male Ashkenazy Jews Europe  ashkenazy10e Human610-Quad v1.0


title: Male Ashkenazy Jews Europe  ashkenazy4e Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-16 day old (replication)

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

institute: PICB

description: Gene expression data from post-mortem superior frontal gyrus of a 16 days old rhesus macaque individual

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. We processed the human and rhesus macaque datasets separately. For the macaque dataset, to identify array probes that contain mismatches to the rhesus macaque genome, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the macaque (rheMac2) genome using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included 275398 probes that matched the genome perfectly and at a single location. For the human dataset, we applied the same procedure by mapping probes to the human genome (hg18), which yielded 740689 probes uniquely and perfectly matching the human genome. Intensities of probes that passed these masks were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. 12,397 transcripts were detected in the human dataset and 9,629 transcripts were detected in the rhesus macaque dataset.

organism: Macaca mulatta

source_name: Dissected rhesus macaque post-mortem superior frontal gyrus

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cortical region approximately corresponding to Brodmann area 9 of the prefrontal cortex (the superior frontal gyrus). We aimed to make dissections that contain 2:1 grey:white matter (60-70% grey matter).

value: male

value: 16 days

value: superior frontal gyrus of the brain

tag: batch

value: macaque batch 2


title: Male Ashkenazy Jews Europe  ashkenazy10w Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-28 year old (replication)

description: Gene expression data from post-mortem superior frontal gyrus of a 28 years  old rhesus macaque individual

value: female


title: Male Ashkenazy Jews Europe  ashkenazy9w Human610-Quad v1.0


title: Male Ashkenazy Jews Europe  ashkenazy7w Human610-Quad v1.0


title: Male Ashkenazy Jews Europe  ashkenazy6w Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-25 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 25 years  old rhesus macaque individual

value: 9125 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-25 year 166 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 25 years 166 days old rhesus macaque individual

value: 9291 days


title: Male Ashkenazy Jews Europe  ashkenazy1e Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-21 year 8 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 21 years 8 days old rhesus macaque individual

value: 7673 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-8 year 16 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 8 years 16 days old rhesus macaque individual

value: 2936 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-15 year 3 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 15 years 3 days old rhesus macaque individual

value: 5478 days


title: Male Ashkenazy Jews Europe  ashkenazy4w Human610-Quad v1.0

value: Male

value: Europe


title: Female Ethiopian Jews Africa  eth_jew7 Human610-Quad v1.0

value: Female

value: Ethiopian Jews

value: Africa

value: blood


title: Male Ashkenazy Jews Europe  ashkenazy3w Human610-Quad v1.0

value: Ashkenazy Jews


title: Affymetrix: Rhesus macaque-superior frontal gyrus-3 year 40 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 3 years 40 days old rhesus macaque individual

value: male

value: 1135 days


title: Male Ashkenazy Jews Europe  ashkenazy3e Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-1 year 242 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 1 years 242 days old rhesus macaque individual

value: 607 days

value: superior frontal gyrus of the brain


title: Male Ashkenazy Jews Europe  ashkenazy2w Human610-Quad v1.0


title: Female Ashkenazy Jews Europe  ashkenazy1w Human610-Quad v1.0


title: Male Ashkenazy Jews Europe  ashkenazy8w Human610-Quad v1.0


title: Female Ethiopian Jews Africa  eth_jew3 Human610-Quad v1.0


title: Female Ethiopian Jews Africa  eth_jew5 Human610-Quad v1.0


title: Female Ethiopian Jews Africa  eth_jew8 Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-1 year 84 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 1 years 84 days old rhesus macaque individual

value: 449 days

value: macaque batch 2


title: Affymetrix: Rhesus macaque-superior frontal gyrus-237 day old

description: Gene expression data from post-mortem superior frontal gyrus of a 237 days old rhesus macaque individual

value: 237 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-179 day old

description: Gene expression data from post-mortem superior frontal gyrus of a 179 days old rhesus macaque individual

value: 179 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-151 day old

description: Gene expression data from post-mortem superior frontal gyrus of a 151 days old rhesus macaque individual

value: 151 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-22 day old

description: Gene expression data from post-mortem superior frontal gyrus of a 22 days old rhesus macaque individual

value: 22 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-28 years old

value: female

value: macaque batch 1


title: Female Ethiopian Jews Africa  eth_jew4 Human610-Quad v1.0

value: Female


title: Affymetrix: Rhesus macaque-superior frontal gyrus-26 years 28 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 26 years 28 days old rhesus macaque individual


title: Affymetrix: Rhesus macaque-superior frontal gyrus-22 year 47 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 22 years 47 days old rhesus macaque individual

value: 8104 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-9 year 104 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 9 years 104 days old rhesus macaque individual

value: 3389 days


title: Female Ethiopian Jews Africa  eth_jew6 Human610-Quad v1.0

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

value: Ethiopian Jews

value: Africa

value: blood


title: Female Ethiopian Jews Africa  eth_jew11 Human610-Quad v1.0


title: Female Ethiopian Jews Africa  eth_jew1 Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-20 year 91 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 20 years 91 days old rhesus macaque individual

value: male

value: 7391 days


title: Female Ethiopian Jews Africa  eth_jew2 Human610-Quad v1.0


title: Female Ethiopian Jews Africa  eth_jew10 Human610-Quad v1.0


title: Female Ethiopian Jews Africa  eth_jew14 Human610-Quad v1.0


title: Female Ethiopian Jews Africa  eth_jew13 Human610-Quad v1.0


title: Affymetrix: Rhesus macaque-superior frontal gyrus-310 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 310 days  old rhesus macaque individual

value: 310 days

value: superior frontal gyrus of the brain


title: Affymetrix: Rhesus macaque-superior frontal gyrus-207 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 207 days  old rhesus macaque individual

value: 207 days


title: Male Sephardic Jews Europe  sephardic19bul Human610-Quad v1.0

value: Male

value: Sephardic Jews

value: Europe


title: Affymetrix: Rhesus macaque-superior frontal gyrus-153 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 153 days  old rhesus macaque individual

value: 153 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-20 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 20 days old rhesus macaque individual

value: 20 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-4 year 27 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 4 years 27 days old rhesus macaque individual

value: 1487 days

value: macaque batch 1


title: Affymetrix: Rhesus macaque-superior frontal gyrus-2 year 9 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 2 years 9 days old rhesus macaque individual

value: 739 days


title: Female Sephardic Jews Europe  sephardic14bul Human610-Quad v1.0

value: Female


title: Male Sephardic Jews Europe  sephardic18bul Human610-Quad v1.0


title: Female Sephardic Jews Europe  sephardic16bul Human610-Quad v1.0


title: Female Sephardic Jews Europe  sephardic13bul Human610-Quad v1.0


title: Male Sephardic Jews Europe  sephardic15bul Human610-Quad v1.0


title: Affymetrix: Human-superior frontal gyrus-98 years old (replication)

description: Gene expression data from post-mortem superior frontal gyrus of a 98 years old human individual

source_name: Dissected human post-mortem superior frontal gyrus

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland).

value: human batch 2


title: Affymetrix: Human-superior frontal gyrus-78 years 222 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 78 years old human individual

value: female


title: Affymetrix: Human-superior frontal gyrus-90 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 90 years old human individual


title: Female Ethiopian Jews Africa  eth_jew12 Human610-Quad v1.0

value: Ethiopian Jews

value: Africa

value: blood


title: Affymetrix: Human-superior frontal gyrus-39 years 74 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 39 years 74 days old human individual

value: male


title: Male Sephardic Jews Near East  sephardic9tur Human610-Quad v1.0

value: Near East


title: Female Sephardic Jews Europe  sephardic12bul Human610-Quad v1.0


title: Female Sephardic Jews Europe  sephardic17bul Human610-Quad v1.0


title: Affymetrix: Human-superior frontal gyrus-58 years 34 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 58 years 34 days old human individual

value: superior frontal gyrus of the brain


title: Affymetrix: Human-superior frontal gyrus-16 years 271 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 16 years 271 days old human individual

value: 6111 days


title: Affymetrix: Rhesus macaque-superior frontal gyrus-16 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 16 day old rhesus macaque individual

value: 16 days


title: Affymetrix: Human-superior frontal gyrus-4 years 170 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 4 years 170 days old human individual

value: 1630 days


title: Affymetrix: Human-superior frontal gyrus-22 years 334 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 22 years 334 days old human individual

value: 8364 days


title: Male Sephardic Jews Europe  sephardic11bel Human610-Quad v1.0

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

value: Male

value: Sephardic Jews

value: Europe


title: Male Sephardic Jews Near East  sephardic7tur Human610-Quad v1.0


title: Affymetrix: Human-superior frontal gyrus-1 year 78 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 1 year 78 days old human individual

value: 443 days


title: Affymetrix: Human-superior frontal gyrus-2 years 57 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 2 years 57 days old human individual

value: 787 days


title: Affymetrix: Human-superior frontal gyrus-94 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 94 day old human individual

value: 94 days

value: human batch 2


title: Male Sephardic Jews Near East  sephardic10tur Human610-Quad v1.0


title: Male Sephardic Jews Near East  sephardic8tur Human610-Quad v1.0


title: Affymetrix: Human-superior frontal gyrus-19 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 19 day old human individual

value: female

value: 19 days


title: Male Sephardic Jews Near East  sephardic6tur Human610-Quad v1.0

value: blood


title: Male Sephardic Jews Near East  sephardic2tur Human610-Quad v1.0


title: Affymetrix: Human-superior frontal gyrus-2 day old (replication)

description: Gene expression data from post-mortem superior frontal gyrus of a 2 day  old human individual

value: male

value: 2 day


title: Affymetrix: Human-superior frontal gyrus-98 years old

value: superior frontal gyrus of the brain

value: human batch 1


title: Male Sephardic Jews Near East  sephardic5tur Human610-Quad v1.0

value: Near East


title: Affymetrix: Human-superior frontal gyrus-88 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 88 years old human individual


title: Male Sephardic Jews Near East  sephardic3tur Human610-Quad v1.0


title: Male Lithuanians Europe  lithuania7 Human610-Quad v1.0

value: Lithuanians


title: Affymetrix: Human-superior frontal gyrus-66 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 66 years old human individual


title: Affymetrix: Human-superior frontal gyrus-80 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 80 years old human individual


title: Male Sephardic Jews Near East  sephardic1tur Human610-Quad v1.0


title: Male Lithuanians Europe  lithuania9 Human610-Quad v1.0


title: Female Lithuanians Europe  lithuania6 Human610-Quad v1.0

value: Female


title: Male Lithuanians Europe  lithuania10 Human610-Quad v1.0

value: Male


title: Affymetrix: Human-superior frontal gyrus-53 years 112 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 53 years 112 days old human individual


title: Affymetrix: Human-superior frontal gyrus-13 years 360 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 13 years 360 day old human individual

value: 5105 days


title: Affymetrix: Human-superior frontal gyrus-25 years 152 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 25 years 152 days old human individual

value: 9277 days


title: Affymetrix: Human-superior frontal gyrus-204 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 204 years old human individual

value: 204 days


title: Male Lithuanians Europe  lithuania8 Human610-Quad v1.0

value: Europe


title: Male Sephardic Jews Near East  sephardic4tur Human610-Quad v1.0

value: Sephardic Jews


title: Affymetrix: Human-superior frontal gyrus-34 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 34 days old human individual

value: 34 days


title: Male Hungarians Europe  hungary18 Human610-Quad v1.0

value: Hungarians


title: Affymetrix: Human-superior frontal gyrus-8 years 2 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 8 years 2 day old human individual

value: 2922 days


title: Affymetrix: Human-superior frontal gyrus-2 day old

description: Gene expression data from post-mortem superior frontal gyrus of a 2 day old human individual


title: Male Hungarians Europe  hungary20 Human610-Quad v1.0

value: blood


title: Male Lithuanians Europe  lithuania3 Human610-Quad v1.0


title: Male Hungarians Europe  hungary15 Human610-Quad v1.0


title: Male Hungarians Europe  hungary19 Human610-Quad v1.0


title: Male Hungarians Europe  hungary11 Human610-Quad v1.0


title: Male Hungarians Europe  hungary17 Human610-Quad v1.0


title: Male Hungarians Europe  hungary14 Human610-Quad v1.0


title: Male Hungarians Europe  hungary13 Human610-Quad v1.0


title: Affymetrix: Human-superior frontal gyrus-4 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 4 days old human individual

value: male

value: 4 days


title: Male Lithuanians Europe  lithuania1 Human610-Quad v1.0

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).


title: Male Hungarians Europe  hungary7 Human610-Quad v1.0


title: Tumor_9970_CGH

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

hyb_protocol: Hybridization probes were denatured, preannealed, and cohybridized to arrays pretreated with the Universal Microarray Hybridization Kit. Following hybridization, slides were washed at room temperature and dried by centrifugation.

scan_protocol: Images and raw signal intensities were acquired using an Agilent G2505B DNA microarray scanner and GenePix Pro 6.0.1.22 image analysis software

data_processing: Pin-based LOWESS normalized, spot intensities representing the tumor (cy3) and reference (cy5) channels were background-corrected by subtracting the median background from the median foreground signal intensities. BASE database used.

source_name: Human breast tumor

label_protocol: Tumor and reference genomic DNA were differentially labeled using a random labeling kit with Cy3-dCTP and Cy5-dCTP, respectively

extract_protocol: Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification

value: Human breast tumor

source_name: Normal female genomic DNA

tag: reference

value: Normal female genomic DNA


title: Tumor_9873_CGH


title: Male Lithuanians Europe  lithuania2 Human610-Quad v1.0


title: Male Hungarians Europe  hungary2 Human610-Quad v1.0


title: Male Hungarians Europe  hungary3 Human610-Quad v1.0


title: Female Lithuanians Europe  lithuania4 Human610-Quad v1.0


title: Male Hungarians Europe  hungary12 Human610-Quad v1.0


title: Tumor_9822_CGH


title: Male Cypriots Europe  Cyprus11 Human610-Quad v1.0

value: Cypriots


title: Tumor_9806_CGH


title: Male Cypriots Europe  Cyprus12 Human610-Quad v1.0


title: Male Hungarians Europe  hungary6 Human610-Quad v1.0


title: Male Hungarians Europe  hungary4 Human610-Quad v1.0


title: Male Lithuanians Europe  lithuania5 Human610-Quad v1.0

value: Lithuanians


title: Male Hungarians Europe  hungary5 Human610-Quad v1.0


title: Tumor_9747_CGH


title: Female Russian Europe evo_2 HumanHap650Y v3.0

description: Genomic DNA extracted from blood was genotyped using HumanHap650Y v3.0 Genotyping BeadChips (Illumina).

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium HumanHap650Y v3.0 Genotyping BeadChips (Illumina).
Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

value: Female

value: Russian


title: Tumor_9735_CGH


title: Male Hungarians Europe  hungary9 Human610-Quad v1.0

value: Male


title: Tumor_9612_CGH


title: Male PANIYA South Asia D36 HumanHap650Y v3.0

value: PANIYA

value: South Asia


title: Male Cypriots Europe  Cyprus10 Human610-Quad v1.0

value: Europe


title: Tumor_9637_CGH


title: Tumor_9798_CGH


title: Tumor_9493_CGH


title: Male Cypriots Europe  Cyprus8 Human610-Quad v1.0


title: Tumor_9422_CGH


title: Male Cypriots Europe  Cyprus7 Human610-Quad v1.0


title: Male Cypriots Europe  Cyprus9 Human610-Quad v1.0


title: Tumor_9716_CGH


title: Tumor_9180_CGH


title: Male Hungarians Europe  hungary1 Human610-Quad v1.0


title: Tumor_9474_CGH


title: Male Hungarians Europe  hungary16 Human610-Quad v1.0


title: Male MALAYAN South Asia A382 HumanHap650Y v3.0

value: MALAYAN


title: Male Russian Europe evo_1 HumanHap650Y v3.0


title: Male Hungarians Europe  hungary8 Human610-Quad v1.0


title: Tumor_9376_CGH


title: Tumor_9056_CGH


title: Tumor_9086_CGH


title: Tumor_9042_CGH


title: Tumor_8977_CGH


title: Tumor_8951_CGH


title: Tumor_8952_CGH


title: Tumor_8933_CGH


title: Tumor_9089_CGH


title: Male Cypriots Europe  Cyprus4 Human610-Quad v1.0


title: Tumor_8855_CGH


title: Tumor_8813_CGH


title: Male Cypriots Europe  Cyprus5 Human610-Quad v1.0


title: Tumor_8803_CGH


title: Male Cypriots Europe  Cyprus3 Human610-Quad v1.0


title: Male Romanians Europe  Romania16 Human610-Quad v1.0

value: Romanians


title: Tumor_8667_CGH


title: Male Cypriots Europe  Cyprus6 Human610-Quad v1.0


title: Male Hungarians Europe  hungary10 Human610-Quad v1.0

value: Hungarians


title: Male Cypriots Europe  Cyprus1 Human610-Quad v1.0


title: Tumor_8626_CGH


title: Tumor_8518_CGH


title: Male Cypriots Europe  Cyprus2 Human610-Quad v1.0


title: Male Romanians Europe  Romania13 Human610-Quad v1.0


title: 786-VHL

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data was obtained from human kidney tumor cell lines.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with standard Affymetrix CDF files. The data was processed and normalized with R version 2.10 and Bioconductor version 2.6.

source_name: Homo Sapiens

label_protocol: 10 ug of Qiagen-purified total RNA, R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

tag: cell line


title: 786-O


title: Male Romanians Europe  Romania15 Human610-Quad v1.0


title: Tumor_8511_CGH


title: Male Romanians Europe  Romania10 Human610-Quad v1.0


title: Tumor_8467_CGH


title: Male Romanians Europe  Romania9 Human610-Quad v1.0


title: Male Romanians Europe  Romania8 Human610-Quad v1.0


title: PB34_iPS2_1

city: Boston

first: Hu

last: Li

state: MA

address: 3 Blackfan Circle

institute: Wyss Institute

description: Gene expression data obtained from PB CD34+ blood iPS

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA (Bioconductor Affy and RMA Packages).

source_name: iPS

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

tag: cell type

value: iPS cells

tag: iPS derived from

value: PB CD34+ blood


title: Tumor_8485_CGH

tag: disease state


title: Male Romanians Europe  Romania5 Human610-Quad v1.0

value: blood


title: PB34_iPS2_2


title: PB34_iPS1_2


title: Male Romanians Europe  Romania12 Human610-Quad v1.0


title: Male Romanians Europe  Romania3 Human610-Quad v1.0


title: Male Romanians Europe  Romania4 Human610-Quad v1.0


title: Tumor_8418_CGH


title: Male Romanians Europe  Romania11 Human610-Quad v1.0


title: Tumor_8444_CGH


title: Tumor_8376_CGH


title: Male Spaniards Europe  Spain13 Human610-Quad v1.0

value: Spaniards


title: Male Romanians Europe  Romania14 Human610-Quad v1.0


title: Male Romanians Europe  Romania1 Human610-Quad v1.0


title: PB_CD34+_1

description: Gene expression data obtained from PB CD34+ blood

source_name: human  peripheral blood derived CD34+ cells

growth_protocol: Normal peripheral blood CD34+ (PB CD34+) and mononuclear cells (PBMCs) were either maintained in medium described previously (Loh et al. 2009) or grown in dendritic cell medium supplemented with SCF and GM-CSF

value: peripheral blood derived CD34+ cells (PB_CD34+)


title: Male Spaniards Europe  Spain11 Human610-Quad v1.0


title: Tumor_8395_CGH

value: Human breast tumor

value: Normal female genomic DNA


title: Male Romanians Europe  Romania2 Human610-Quad v1.0


title: PBMCs_2

description: Gene expression data obtained from PBMCs blood

source_name: human peripheral blood derived mononuclear cells (PBMCs)


title: Tumor_8491_CGH


title: stomach_N0_3

city: Kiel

first: Eva

last: Simon

state: Schleswig-Holstein

address: Arnold-Heller-Straße 3, Haus 14

department: Institute of Pathology

country: Germany

institute: Christian-Albrechts-University

description: Gene expression data from tumourous tissue of the corpus.

hyb_protocol: The biotin-labelled cRNA was fragmented and subsequently 15 µg of each sample was hybridized for 16 hours at 45°C to an Affymetrix (Human Genome) GeneChip® Human Genome U133 Plus 2.0 Array. After hybridization, the chips underwent an automated washing and staining protocol with streptavidin-phycoerythrin as recommended by Affymetrix.

scan_protocol: GeneChip arrays were scanned using the GeneChip Scanner 3000.

data_processing: Raw data were analyzed with the Affymetrix GeneChip Operating Software (GCOS 1.4). To enable the comparison between chips the data were scaled to a global intensity of 500. The Data Mining Tool 3.0 (Affymetrix) and GeneSpring software package 7.2 (Silicon Genetics, Redwood City, CA) were used to average results from different samples and perform statistical analysis. The normalization consists of the three steps: first, data transformation (set measurements less than 300.0 to 300.0); second, per chip (normalize each chip to the 50th percentile of the measurements taken from that chip); and third, per gene (normalize each gene to the median of the measurements for that gene).

source_name: tumourous tissue, surgically resected from patient with intestinal type gastric cancer.

label_protocol: Biotin-labelled cRNA was generated by in vitro transcription from the DNA using the GeneChip RNA transcript labelling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated with phenol-chloroform using the mirVana™ miRNA Isolation Kit (Ambion, Austin, USA).

treatment_protocol: Tumour tissue was fragmented into smaller pieces under liquid nitrogen using a homogenizer. Around 30 mg of the sample was subjected to RNA isolation.

value: male

value: gastric cancer

tag: tumor stage

tag: nodal status


title: stomach_N1_3

tag: age


title: stomach_N0_2

value: female

tag: tissue


title: Tumor_8295_CGH


title: Tumor_8328_CGH


title: dH1F_Fibro_1

description: Gene expression data obtained from fibroblasts

source_name: human fibroblast

growth_protocol: Fibroblasts were grown in DMEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine

value: fibroblast

value: GM04981 from Coriell


title: Male Spaniards Europe  Spain10 Human610-Quad v1.0

value: Male


title: Tumor_8277_CGH


title: stomach_N1_1

tag: tumour stage


title: L2 Induced pluripotent stem cells 6

first: Yongchao

last: Ge

address: One Gustave L Levy Place #1137

department: Neurology

description:
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: Affymetrix GeneChip Exon 1.0ST array . Manufacturer's instructions were followed.

data_processing: The data are processed by Affymetrix software Exprssion Console with RMA normalization

source_name: Induced pluripotent stem cells from L2Fib

growth_protocol: Fibroblasts were mantained in DMEM 10%FBS medium, and HES2 and all the iPSC samples were grown in HES2 medium: DMEM/F12 containing 20% KSR, 5% MEF-conditioned medium, Penicillin/Streptomycin, L-glutamine, non-essential amino acids, β-mercaptoethanol and bFGF.

extract_protocol: RNA was extracted from cells using Trizol® Reagent and subsequently column-purified with RNeasy kit (Qiagen)

treatment_protocol: Cells were harvested in basal (non-treated) conditions.

tag: patient

value: Induced pluripotent stem cells


title: L1 Induced pluripotent stem cells 13

scan_protocol: Affymetrix GeneChip Exon 1.0ST array . Manufacturer's instructions were followed.

source_name: Induced pluripotent stem cells from L1Fib


title: Male Spaniards Europe  Spain8 Human610-Quad v1.0

value: Europe


title: Tumor_8120_CGH


title: Tumor_8041_CGH


title: L1 Induced pluripotent stem cells 1

label_protocol: Affymetrix GeneChip Exon 1.0ST array . Manufacturer's instructions were followed.


title: Male Spaniards Europe  Spain12 Human610-Quad v1.0


title: stomach_N0_1


title: stomach_N1_2


title: BJ Induced pluripotent stem cells

source_name: Induced pluripotent stem cells from BJFib

value: BJ


title: Tumor_8038_CGH


title: Female Spaniards Europe  Spain6 Human610-Quad v1.0

value: Female


title: HES2 embryonic stem cell

source_name: embryoic stem cells (HES2 cell line)

value: Embryonic stell cells


title: L2 Fibroblasts

source_name: skin fibroblast from Leopard sydrome patient L2 (34 years old)

value: Fiborblast cells


title: Tumor_7923_CGH


title: BJ Fibroblasts

source_name: Foreskin fibroblast from a health newborn (BJ cell line)


title: L2 Induced pluripotent stem cells 16


title: Tumor_7895_CGH


title: Tumor_9970

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with BASE

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.


title: Male Egyptans Africa  Egypt9 Human610-Quad v1.0

source_name: blood

value: Egyptans

value: Africa

value: blood


title: Tumor_9873

value: Human breast tumor


title: Male Spaniards Europe  Spain9 Human610-Quad v1.0

value: Spaniards


title: Tumor_9798


title: Tumor_7635_CGH

value: Normal female genomic DNA


title: Male Egyptans Africa  Egypt8 Human610-Quad v1.0


title: Tumor_9822


title: Male Egyptans Africa  Egypt4 Human610-Quad v1.0


title: Male Egyptans Africa  Egypt6 Human610-Quad v1.0


title: Tumor_9806


title: Male Egyptans Africa  Egypt5 Human610-Quad v1.0


title: Tumor_7571_CGH


title: Male Romanians Europe  Romania6 Human610-Quad v1.0

value: Romanians


title: Male Egyptans Africa  Egypt11 Human610-Quad v1.0


title: Tumor_9716


title: Tumor_9735


title: Tumor_7523_CGH


title: Tumor_7612_CGH


title: Tumor_8359_CGH


title: Tumor_9637


title: L1 Fibroblasts

source_name: skin fibroblast from Leopard sydrome patient L1  (25 years old)

value: female


title: Male Egyptans Africa  Egypt7 Human610-Quad v1.0


title: Male Romanians Europe  Romania7 Human610-Quad v1.0


title: Tumor_9612


title: Tumor_9422


title: Tumor_7457_CGH


title: Tumor_9474


title: Male Egyptans Africa  Egypt1 Human610-Quad v1.0


title: Tumor_9376


title: Tumor_9180


title: Tumor_9747


title: Tumor_9086


title: Male Saudis Arabia  SaudiA10 Human610-Quad v1.0

value: Saudis

value: Arabia


title: Tumor_9089


title: Male Egyptans Africa  Egypt3 Human610-Quad v1.0

value: Male


title: Male Egyptans Africa  Egypt2 Human610-Quad v1.0


title: Tumor_7083_CGH


title: Tumor_9056


title: Tumor_7011_CGH


title: Tumor_8977


title: Tumor_7047_CGH


title: Tumor_9042


title: Tumor_6811_CGH


title: Tumor_7492_CGH


title: Tumor_6865_CGH


title: Tumor_8952


title: Tumor_9493


title: Tumor_8951


title: Tumor_8813


title: Tumor_8933


title: Male Saudis Arabia  SaudiA9 Human610-Quad v1.0


title: Tumor_8855


title: Male Saudis Arabia  SaudiA7 Human610-Quad v1.0


title: Tumor_8626


title: Tumor_6611_CGH


title: Male Egyptans Africa  Egypt12 Human610-Quad v1.0


title: Tumor_6664_CGH


title: Tumor_6680_CGH


title: Tumor_8803


title: Tumor_8518


title: Tumor_8667


title: Tumor_8511


title: Tumor_6497_CGH


title: Male Saudis Arabia  SaudiA5 Human610-Quad v1.0


title: Male Saudis Arabia  SaudiA8 Human610-Quad v1.0


title: Tumor_8491


title: Male Saudis Arabia  SaudiA4 Human610-Quad v1.0


title: Male Saudis Arabia  SaudiA3 Human610-Quad v1.0


title: Male Saudis Arabia  SaudiA6 Human610-Quad v1.0


title: Tumor_8485


title: Tumor_6423_CGH


title: Tumor_8395


title: Tumor_6341_CGH


title: Male Egyptans Africa  Egypt10 Human610-Quad v1.0


title: Tumor_8418


title: Tumor_6388_CGH


title: Tumor_8328


title: Tumor_8359


title: Tumor_8467


title: Tumor_6188_CGH


title: Tumor_8376


title: Tumor_8444


title: Tumor_8295


title: Tumor_5578_CGH


title: Tumor_6095_CGH


title: Tumor_8120


title: Tumor_5576_CGH


title: Tumor_8277


title: Tumor_8041


title: Tumor_7895


title: Tumor_5551_CGH


title: Tumor_8038


title: Tumor_7923


title: Male Saudis Arabia  SaudiA1 Human610-Quad v1.0


title: Tumor_5532_CGH


title: Tumor_7635


title: Tumor_7571


title: Male Lebanese Near East  Lebanon8 Human610-Quad v1.0

value: Lebanese

value: Near East


title: Tumor_7612


title: Tumor_7523


title: Male Lebanese Near East  Lebanon5 Human610-Quad v1.0


title: Tumor_12117_CGH


title: Male Lebanese Near East  Lebanon7 Human610-Quad v1.0


title: Tumor_7011


title: Tumor_7083


title: Male Saudis Arabia  SaudiA2 Human610-Quad v1.0


title: Tumor_5531_CGH


title: Tumor_7457


title: Tumor_7492


title: Male Lebanese Near East  Lebanon6 Human610-Quad v1.0


title: Tumor_11881_CGH


title: Male Yemenese Arabia  Yemen10 Human610-Quad v1.0

value: Yemenese


title: Tumor_7047


title: Tumor_6811


title: Male Lebanese Near East  Lebanon2 Human610-Quad v1.0


title: Tumor_11742_CGH


title: Male Lebanese Near East  Lebanon4 Human610-Quad v1.0


title: Male Yemenese Arabia  Yemen9 Human610-Quad v1.0


title: Tumor_11097_CGH


title: Male Lebanese Near East  Lebanon3 Human610-Quad v1.0


title: Tumor_11146_CGH


title: Male Yemenese Arabia  Yemen8 Human610-Quad v1.0


title: Tumor_6680


title: Tumor_6865


title: Tumor_6664


title: Tumor_10904_CGH


title: Tumor_6388


title: Tumor_6423


title: Tumor_6095


title: Male Yemenese Arabia  Yemen6 Human610-Quad v1.0


title: Tumor_10982_CGH


title: Male Yemenese Arabia  Yemen4 Human610-Quad v1.0


title: Tumor_6188


title: Male Yemenese Arabia  Yemen7 Human610-Quad v1.0


title: Tumor_10737_CGH


title: Tumor_10754_CGH


title: Tumor_5576


title: Tumor_10762_CGH


title: Tumor_10692_CGH


title: Female Spaniards Europe  Spain5 Human610-Quad v1.0

value: Female

value: Europe


title: Male Yemenese Arabia  Yemen2 Human610-Quad v1.0


title: Tumor_6341


title: Male Yemenese Arabia  Yemen3 Human610-Quad v1.0


title: Tumor_5578


title: Male Yemenese Arabia  Yemen1 Human610-Quad v1.0


title: Tumor_10664_CGH


title: Tumor_10655_CGH


title: Male Yemenese Arabia  Yemen5 Human610-Quad v1.0


title: Tumor_5532


title: Tumor_5551


title: Tumor_10690_CGH


title: Tumor_10635_CGH


title: Tumor_11881


title: Tumor_10569_CGH


title: Tumor_5531


title: Tumor_12117


title: Female Spaniards Europe  Spain3 Human610-Quad v1.0


title: Tumor_11097


title: Tumor_10982


title: Tumor_10515_CGH


title: Tumor_10521_CGH


title: Female Spaniards Europe  Spain2 Human610-Quad v1.0


title: Tumor_10551_CGH


title: Tumor_11146


title: Tumor_11742


title: Female Spaniards Europe  Spain4 Human610-Quad v1.0


title: Tumor_10762


title: Tumor_10457_CGH


title: Tumor_10377_CGH


title: Tumor_10904


title: Female Yemen Jews Arabia  Yemen_Jew_14 Human610-Quad v1.0

value: Yemen Jews


title: Tumor_10737


title: Tumor_10414_CGH


title: Tumor_10754


title: Tumor_10692


title: Female Spaniards Europe  Spain1 Human610-Quad v1.0


title: Female Yemen Jews Arabia  Yemen_Jew_13 Human610-Quad v1.0


title: Tumor_10363_CGH


title: Male Yemen Jews Arabia  Yemen_Jew_12 Human610-Quad v1.0


title: Tumor_10316_CGH


title: Tumor_10690


title: Tumor_10035_CGH


title: Female Yemen Jews Arabia  Yemen_Jew_7 Human610-Quad v1.0


title: Female Yemen Jews Arabia  Yemen_Jew_15 Human610-Quad v1.0


title: Tumor_10192_CGH


title: Female Yemen Jews Arabia  Yemen_Jew_10 Human610-Quad v1.0


title: Tumor_10664


title: Tumor_10655


title: HNSCC_N+_62_555

city: Sao Paulo

first: Anna

last: Coló

address: Rua Professor Antonio Prudente, 211

country: Brazil

institute: Hospital A.C. Camargo

description: recurrent HNSCC

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 2 ug Cot1 DNA; 5X Denhardts ; 10 ug Salmon sperm, Deyonized formamide 50% / Temperature:42oC / Time:12-24h / Touch Down: 70, 55, 50, 42 Washing - Round 1 - Solution: 2X SSC 0,1% SDS / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 SSC 0,1% SSC / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 3 - Solution: 0,1X SSC / Temperature:42 / Time:enxaguar / Washing Number: 3 Washing - Round 4 - Solution: 0,1X SSC / Temperature:42 / Time:4 min / Washing Number: 4 Washing - Round 5 - Solution: 0,1X SSC / Temperature:42 / Time:enxaguar lâm por lâm / Washing Number: 5

scan_protocol: Hardware: Perkinelmer / Software: ScanArray Express Microarray Scanner, Image quantification: Scan Array Express version 3.0

data_processing: Normalization: Lowess, software R version 2.9.2 (2009-08-24)

label: Alexa 555

source_name: HNSCC, N+, 62

label_protocol: After NaOAc/ethanol precipitation, cDNA was with indirectly labeled with Alexa Dye 555 or 647 (Invitrogen, Carlsbad, CA) and purified using QIAquick PCR purification kit (Qiagen, Germany).

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) and amplified by a T7-based protocol. Briefly, 3 ug of total RNA and 0,5 ug of oligo-dT(24)-T7 (Integrated DNA Technologies IDT, Coralville, IA) were denaturated at 70oC for 10 min and snap cooled on ice for 1 min. Reverse transcription was performed by adding 6 mM MgCl2, 1mM dNTP (Eppendorf, Germany), 1X First Strand Buffer, 20 units of RNasin and 1 ul of Improm II (Promega, Madison, WI) at 42oC for 2 hours. Second-strand synthesis was made by adding 0,2 mM dNTP (Eppendorf, Germany), 1X Second Strand Buffer, 0,6 units of RNase H (USB Corporation, Cleveland, OH), units of Ligase (New England Biolabs, Ipswich, MA) and 10 units of DNA Pol I (Invitrogen, Carlsbad, CA) at 16oC for 2 hours. Double-strand DNA was completed by adding 5 units of T4 DNA Pol (Invitrogen, Carlsbad, CA) and incubating at 16oC for 10 min. After phenol/chloroform extraction, in vitro transcription was carried out with RiboMax kit (Promega, Madison, WI) by adding 7,5mM rNTP, 1X Reaction buffer and 0.1 volume of Enzyme mix. Amplified RNA (aRNA) was extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 ug of aRNA and 10 ug of Random Hexamers (Amersham Biosciences, Piscataway, NJ) were denaturated at 70oC for 10 min and snap cooled on ice for 1 min. Reverse transcription was performed by adding 6 mM MgCl2, 0,5mM dNTP mix (Eppendorf, Germany) with Aminoallyl dUTP (Sigma-Aldrich, St. Louis, MO), 1X First Strand Buffer, 20 units of RNasin and 1 ul of Improm II (Promega, Madison, WI) at 42oC for 2 hours. aRNA was degradated with 0,42 M NaOH and 14 mM EDTA at 70oC for 10 min.

tag: sample type

value: primary untreated SCC of the larynx pN+

label: Alexa 647

source_name: Reference RNA

value: 15 human cell lines (Daudi, DLD-1, DU145, FaDu, GM637, H146, H1080, HB4α, HEK293, Jurkat, Saos-2, SK-BR-3, SK-MEL-28, T24, T98G)


title: Female Yemen Jews Arabia  Yemen_Jew_11 Human610-Quad v1.0

value: blood


title: Female Yemen Jews Arabia  Yemen_Jew_4 Human610-Quad v1.0


title: HNSCC_N+_62_647

description: recurrent HNSCC


title: Tumor_10569

source_name: Human breast tumor

value: Human breast tumor


title: HNSCC_N+_55_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 55


title: Tumor_10635


title: HNSCC_N+_55_555

description: non-recurrent HNSCC


title: Male Yemen Jews Arabia  Yemen_Jew_6 Human610-Quad v1.0


title: Tumor_10551


title: HNSCC_N+_31_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 31


title: Female Yemen Jews Arabia  Yemen_Jew_5 Human610-Quad v1.0


title: HNSCC_N+_31_555

description: non-recurrent HNSCC


title: Female Morocco Jews Africa  Morocco_Jew_14 Human610-Quad v1.0

value: Morocco Jews

value: Africa


title: Tumor_10515


title: HNSCC_N+_25_555

description: recurrent HNSCC

source_name: HNSCC, N+, 25


title: Tumor_10457


title: Female Yemen Jews Arabia  Yemen_Jew_2 Human610-Quad v1.0


title: Female Morocco Jews Africa  Morocco_Jew_15 Human610-Quad v1.0


title: Female Yemen Jews Arabia  Yemen_Jew_8 Human610-Quad v1.0


title: Female Yemen Jews Arabia  Yemen_Jew_3 Human610-Quad v1.0


title: Tumor_10521


title: HNSCC_N+_181_647

description: recurrent HNSCC

source_name: HNSCC, N+, 181

value: primary untreated SCC of the hypopharynx pN+


title: Tumor_10377


title: Male Morocco Jews Africa  Morocco_Jew_13 Human610-Quad v1.0


title: HNSCC_N+_25_647

description: recurrent HNSCC


title: HNSCC_N+_197_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 197


title: Tumor_10363


title: HNSCC_N+_197_647

description: non-recurrent HNSCC


title: Male Yemen Jews Arabia  Yemen_Jew_1 Human610-Quad v1.0


title: Tumor_10316


title: Tumor_10414


title: smc3(K112N/K113N)-3Pk chromatin-binding pattern

city: London

first: Lidia

last: Lopez-Serra

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: London Research Institute/Cancer research UK

description:
smc3 K112N/K113N chromatin-binding pattern.

Y3985_Pk_B_191109 and M31.SupA.

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes before being hybridized to the arrays for 16 hours at 42ºC in an Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: The washing and scanning protocol (FlexMidi_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450 (Affymetrix). Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Primary analysis of tiling chip data was performed using the Affymetrix GeneChip Operating Software (GCOS ver 1.4). Signal intensities between the ChIP and supernatant samples were adjusted across all probe sets using median normalization. Changes and change p-values were called as detailed in the Affymetrix Statistical Algorithms Reference Guide (http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf). Probe sets and changes were averaged within adjacent 100 bp windows for graphical depiction.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: ChIP DNA from yeast Saccharomyces cerevisiae cells, K112N/K113N Smc3

label_protocol: 10 ng of amplified DNA was digested with DNase I and end-labeled using biotin-N6-ddATP using terminal transferase TdT (Roche, 400 U/µl) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: Cells were grown in YP + 2% glucose to an OD600 of 0.5.

extract_protocol: Chromatin immunoprecipitation, followed by hybridization to a high-density oligonucleotide microarray (ChIp on chip), were performed as previously described (Katou et al. 2003; Lengronne et al. 2004; Lengronne et al. 2006). Briefly, cross-linked cells were disrupted using a Multi-Beads Shocker, and whole cell extracts were sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with anti-PK monoclonal antibody (clone SV5-Pk1, Serotec, cat. no. MCA1360) coupled to protein A Dynabeads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse the cross-link. An aliquot of the supernatant fraction of the immunoprecipitation was treated in parallel to provide a whole genome DNA sample for comparison.  The ChIP and supernatant samples were then incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming.

treatment_protocol: Log phase cycling cells were cross-linked with 1% formaldehyde for 30 minutes at room temperature. The reaction was stopped with 0.125 M glycine for 5 minutes.

tag: genotype

value: MATalpha/Mat a diploid, Smc3K112N/113N::TRP-3PK::HIS/Smc3+

tag: strain

tag: antibody

value: anti-PK monoclonal

tag: antibody vendor

value: Serotec

tag: antibody catalog number

tag: antibody clone

source_name: Input DNA from yeast Saccharomyces cerevisiae cells

extract_protocol: Chromatin immunoprecipitation, followed by hybridization to a high-density oligonucleotide microarray (ChIp on chip), were performed as previously described (Katou et al. 2003; Lengronne et al. 2004; Lengronne et al. 2006). Briefly, cross-linked cells were disrupted using a Multi-Beads Shocker, and whole cell extracts were sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with anti-PK monoclonal antibody (clone SV5-Pk1, Serotec) coupled to protein A Dynabeads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse the cross-link. An aliquot of the supernatant fraction of the immunoprecipitation was treated in parallel to provide a whole genome DNA sample for comparison.  The ChIP and supernatant samples were then incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming.

value: Mat a

value: supernatant


title: Male Yemen Jews Arabia  Yemen_Jew_9 Human610-Quad v1.0

tag: gender

value: Male

tag: population

tag: region

value: Arabia


title: Smc3-3Pk chromatin-binding pattern

description:
Smc3 chromatin-binding pattern.

Y3977_Pk_B_191109 and M31.SupA.

source_name: ChIP DNA from yeast Saccharomyces cerevisiae cells, wild type Smc3

value: MATalpha/Mat a diploid, Smc3K112N/113N::TRP/Smc3-3PK::HIS


title: HNSCC_N+_116_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 116


title: HNSCC_N+_181_555

description: recurrent HNSCC


title: Male Morocco Jews Africa  Morocco_Jew_10 Human610-Quad v1.0


title: HNSCC_N+_116_647

description: non-recurrent HNSCC


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with pyruvate, replicate 3

city: Nagaoka

first: Toju

last: Iino

state: Niigata

address: 1603-1 Kamitomioka

department: Dept. Bioengineering

country: Japan

institute: Nagaoka University of Technology

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 48 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions: 2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C. Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

scan_protocol: Microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments) and spot intensities were quantified using Imagene 6.1 (BioDiscovery, Inc.).

data_processing: Expression ratios were normalized using GeneSpring version 7.3.1 (Silicon Genetics) by the intensity-dependent Lowess method, with 20% of the data used for smoothing. Replicate spots of the same type were combined to yield a single normalized ratio, which is output for the first ID_REF number representing that spot type.

organism: Rhodococcus jostii RHA1

source_name: Rhodocuccus jostii RHA1 was grown in the sterilized soil with pyruvate at 2 day

label_protocol: Cy-labelled cDNA was prepared by indirect labelling. the Cy3/Cy5 dyes were reversed to control for dye bias.

growth_protocol: Rhodococcus jostii RHA1 was grown in the sterilized soil with 20 mM pyruvate at 30°C

extract_protocol: Cell pellets were vortexed with glass beads, hot phenol, and SDS at final concentrations of 14.3% and 0.9% (vol/vol) respectively. Debris was precipitated with acetate followed by the addition of 4.0 mL phenol-chloroform (1:1, vol/vol). Nucleic acids were precipitated with acetate plus isopropanol, treated with DNase, and purified with an RNeasy mini column (Qiagen).

value: Rhodocuccus jostii RHA1

tag: growth conditions

source_name: Rhodococcus jostii RHA1 was grown in W minimal liquid medium with pyruvate

growth_protocol: mid-exponential phase, Rhodococcus jostii RHA1 was grown in W minimal liquid medium with 20 mM pyruvate at 30°C and 120 rpm

value: Rhodococcus jostii RHA1


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with pyruvate, replicate 4

value: grown in the sterilized soil with pyruvate at 2 day

value: grown in W minimal liquid medium with pyruvate


title: Tumor_10035

tag: disease state


title: Rat liver_1000ng PCB126_52 week_ rep3

city: Buffalo

first: Corie

last: Ellison

address: 102 Farber hall

department: Pharmacology and Toxicology

institute: University at Buffalo

hyb_protocol: cRNA was hybridized to RGU34A GeneChips (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned with the Affymetrix 428 scanner.

data_processing: Probe-level data from cell intensity files were background subtracted and normalized by the gc-Robust Multiarray Analysis method using ArrayAssist.

source_name: sprague dawley rat liver (52wks)

label_protocol: High quality RNA was transformed into biotinylated cRNA by the Roswell Park Cancer Institute Gene Expression Facility (Buffalo, NY)

extract_protocol: Total RNA was isolated with the Qiagen RNeasy kit following the manufacture's instructions.

value: sprague dawley

value: liver

tag: agent


title: Rat liver_1000ng PCB126_52 week_ rep2


title: Female Morocco Jews Africa  Morocco_Jew_11 Human610-Quad v1.0

source_name: blood

value: Female

value: Morocco Jews

value: blood


title: Male Morocco Jews Africa  Morocco_Jew_9 Human610-Quad v1.0

value: Africa


title: Tumor_10192

value: Human breast tumor


title: Rat liver_1000ng PCB126_52 week_ rep1


title: Rat liver_300ng PCB126_52 week_ rep3


title: Rat liver_300ng PCB126_52 week_ rep2


title: Male Morocco Jews Africa  Morocco_Jew_12 Human610-Quad v1.0


title: Rat liver_300ng PCB126_52 week_ rep1


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with biphenyl, replicate 4

source_name: Rhodocuccus jostii RHA1 was grown in the sterilized soil with biphenyl at 3 day

growth_protocol: Rhodococcus jostii RHA1 was grown in the sterilized soil with 10 mM biphenyl at 30°C

source_name: Rhodococcus jostii RHA1 was grown in W minimal liquid medium with biphenyl

growth_protocol: mid-exponential phase, Rhodococcus jostii RHA1 was grown in W minimal liquid medium with 10 mM biphenyl at 30°C and 120 rpm


title: Rat liver_30ng PCB126_52 week_ rep3

value: 30ng PCB126


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with pyruvate, replicate 1


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with biphenyl, replicate 3

value: grown in the sterilized soil with biphenyl at 3 day

value: grown in W minimal liquid medium with biphenyl


title: Rat liver_30ng PCB126_52 week_ rep2


title: Rat liver_30ng PCB126_52 week_ rep1


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with biphenyl, replicate 2


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with pyruvate, replicate 2


title: Female Morocco Jews Africa  Morocco_Jew_2 Human610-Quad v1.0


title: Female Morocco Jews Africa  Morocco_Jew_3 Human610-Quad v1.0


title: Female Morocco Jews Africa  Morocco_Jew_5 Human610-Quad v1.0


title: Female Morocco Jews Africa  Morocco_Jew_8 Human610-Quad v1.0


title: GLC8

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description: Genomic DNA extracted from tumor cell line was interrogated for copy number against normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.

hyb_protocol: Standard Nimblegen protocol.

scan_protocol: Standard Nimblegen protocol.

data_processing: NimbleScan protocol, q-spline normalization.

source_name: Genomic DNA from GLC8 cell line.

label_protocol: Standard Nimblegen protocol.

extract_protocol: Cells were lysed in Jeffrey’s solution added with 1% SDS, treated with RNase A and proteinase K and genomic DNA was purified with two round of NaCl/water/ethanol precipitation.

tag: cell line

tag: tumor

value: small cell lung carcinoma

source_name: NimbleGen human reference DNA

extract_protocol: purchased from NimbleGen

value: Reference human DNA


title: GLC14

source_name: Genomic DNA from GLC14 cell line.


title: Rat liver TCDD_52 week_rep2

tag: tissue

value: 100ng TCDD


title: SK-N-BE

source_name: Genomic DNA from SK-N-BE cell line.

value: SK-N-BE

value: neuroblastoma


title: Rat liver TCDD_52 week_rep3


title: Rat liver TCDD_52 week_rep1


title: Female Morocco Jews Africa  Morocco_Jew_4 Human610-Quad v1.0