title: Pol2Genome_ath

city: Charlottesville

first: xin

last: zhao

state: VA

address: Department of Biology, 229 Gilmer Hall

department: Biology

institute: University of Virginia

description: Pol 2 ChIP Biological Rep 1-4

hyb_protocol: DNA was hybridized according to Affymetrix’ Chromatin Immunoprecipitation Assay Protocol Rev.3.

scan_protocol: Whole Genome Tiling array were scanned on Affymetrix scanner G7

data_processing:
Data was quantile normalized and analyzed with CisGenome (previously TileMap). Log2(IP/Input) fold changes (fc) and CisGenome moving average (ma) statistics were reported in BAR files.
fc.bar and ma.bar are generated by CisGenome software (previously TileMap). fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe.

source_name: Arabidopsis thaliana ecotype Col-0

label_protocol: DNA was labeled according to Affymetrix’ Chromatin Immunoprecipitation Assay Protocol Rev.3.

growth_protocol: Arabidopsis seedlings were grown on 1× Murashige and Skoog medium (Sigma-Aldrich) agar plates containing 1% sucrose. Unless stated otherwise, the seedlings were incubated at 4°C for 2 to 4 d, after which they were exposed to continuous light conditions at 22°C for 4 d. The white light intensity was 170 μ mol m−2 s−1.

extract_protocol: Chromatin isolation was performed with 10 g of whole seedlings tissue according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor (Diagenode, Sparta, NJ) set at high intensity for 10 min (30 sec on, 30 sec off intervals). The DNA was sheared to approximatively 0.3-0.8 kb fragments.

treatment_protocol: Whole seedlings grown were harvested and fixed in 1% formaldehyde for 15 min in a vacuum. The reaction was terminated by adding Glycine to a final concentration of 0.125 m and incubated in a vacuum for another 5 min.

tag: ecotype

value: seedling

tag: antibody

value: anti-RNA polymerase II

tag: antibody catalog#

tag: antibody vendor

value: Santa Cruz

source_name: Input DNA from ath


title: st10minrep2

status: Public on Feb 10 2012

type: RNA

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

country: Japan

institute: Japan Aerospace Exploration agency

description: Gene profile during rearrangement of actin stress fiber in HUVEC

hyb_protocol: Performed as described in One-Color Processing Protocol (Agilent, Version 5.0.1, September 2006).

data_processing:
Data were analyzed with GeneSpring GX 7.3.1. The parameters for normalization are as follows:
Data transformation: Set measurement less than 0.01 to 0.01
Per chip: Normalize to 50th percentile

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC Cyclic stretch

growth_protocol:
Cells were passaged and meintained in EGM-2 medium (Lonza)
4th passaged cells were used.

extract_protocol: Total RNA was isolated with RNeasy

treatment_protocol: 20% Cyclic stretch exposed to HUVEC on silicon membrane

tag: cyclic stretch

value: 10 min

tag: cell type

value: Pooled HUVECs

tag: replicate


title: st20minrep2

scan_protocol: Performed as described in One-Color Processing Protocol (Agilent, Version 5.0.1, September 2006).

value: 20 min


title: st90minrep3

description: Identification of molecules and pathway during rearrangement of actin stress fiber in HUVECs with cyclic stretch

source_name: Cyclic stretched HUVECs

label_protocol: Performed as described in One-Color Processing Protocol (Agilent, Version 5.0.1, September 2006).

growth_protocol:
Cells were passaged and maintained in EGM-2 medium (Lonza)
4th passaged cells were used.

extract_protocol: Total RNA was isolated with RNeasy (Qiagen)

treatment_protocol: HUVECs was exposed to 20% cyclic stretch on silicon membrane

value: 90 min

tag: number of replicate


title: st20minrep3


title: ASO transgenic 6m pooled6

status: Public on Feb 11 2012

city: Los Angeles

first: Yofre

last: Cabeza-Arvelaiz

state: California

address: 650 Charles E. Young Drive South

department: Pathology and Environmental Health Sciences

country: USA

institute: University of California, Los Angeles

hyb_protocol: cRNA probes were hybridized to mouse MOE-430A GeneChip arrays (Affymetrix) following the manufacturer’s protocol at the UCLA microarray core facility.

scan_protocol: GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.

data_processing: Significant differential gene expression between pooled tg and wt samples was ascertained by estimation of signal log2 ratios (or fold changes in expression values), after quality control checks, data normalization and estimating expression values using the Affymetrix Microarray Suite 5.0 Software (MAS 5.0) by using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Mus musculus

source_name: Mouse striatum from 6 six-month old transgenic animals overexpressing alpha synuclein

label_protocol: After synthesis, using Superscript (Invitrogen), labeling was p\erformed by using the ENZO labeling kit (Affymetrix Inc., Santa Clara, CA)

growth_protocol: Animal care was conducted in accordance with the U. S. Public Health Service Guide for the Care and Use of Laboratory Animals and procedures were approved by the University of California, Los Angeles (UCLA), I.A.C.U. Committee.  Only male mice were used in the study.  Animals were maintained on a 12 hr light/dark cycle with free access to water and food. Six-month old male Thy1-aSyn and wt littermates were sacrificed by decapitation.

extract_protocol: whole striata from each hemisphere were immediately dissected and pooled for each brain. Tissue was permeated in RNAlater (Qiagen, Valencia, CA), frozen in liquid nitrogen, and stored at - 80 C until used for RNA preparation. Total RNA was extracted from striata of Thy1-aSyn and wt littermates (all males) with Trizol (Invitrogen, Carlsbad, CA), followed by a clean-up step with RNeasy columns (Qiagen) and RNA integrity check using a Bioanalyzer  (Agilent Tech., Foster city, CA). RNA samples were pooled, one pool representing the six control wt mice and the other representing the six SNCA overexpressing animals.

treatment_protocol: Transgenic (tg) mice overexpressing human wt SNCA under the Thy-1 promoter (Thy1-aSyn) created in a mixed C57BL/6-DBA background were kept in this background by breeding mutant females with wt males.

tag: tissue

value: Striatum

tag: genotype

value: Transgenic (tg) mice overexpressing human wt SNCA under the Thy-1 promoter  in C57BL/6-DBA background

tag: age

value: 6 month

tag: gender

value: Male

tag: genetic background


title: st0minrep2

value: 0 min


title: st30minrep1

value: 30 min


title: st60minrep1

value: 60 min


title: WT grown without adenine vs. WT grown with adenine

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

description: Technical replicate 1 of 2.

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scanning

scan_protocol: Scanned on a GenePix 4000B scanner (Axon). Scanning software: GenePix Pro 6.1

data_processing:
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
GenePix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalization method.

organism: Saccharomyces cerevisiae

source_name: WT grown without adenine

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

growth_protocol: Strains were grown in SD medium containing glucose (2%), adenine (300 mM), arginine (115 mM), histidine (130 mM), isoleucine (230 mM), leucine (1,2 mM), lysine (660 mM), tryptophan (150 mM), uracil (300 mM) and valine (1,3 mM) at 30°C and diluted 1:200 in 10 ml of the same medium containing adenine (300 mM) or no adenine, to reach a concentration of 107 cells/ml the day after (A600=1). The cultures were then diluted again in the same media to grow for 3-4 generations and harvested at a concentration of 107 cells/ml

extract_protocol: Hot phenol extract procedure followed by RNeasy Mini Kit purification step (Qiagen).

value: Mat alpha his3delta1 leu2delta0 lys2delta0 ura3delta0

tag: growth condition

value: growth medium lacking adenine

source_name: WT grown with adenine

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

value: growth medium containing adenine


title: st90minrep1


title: Genetic interactions control of SIRT2 Biological Replicate 1

type: genomic

city: Taipei

first: Yu-yi

last: Lin

address: R809, No.1 Jen-Ai Road Section 1

country: Taiwan

institute: National Taiwan University College of Medicine

hyb_protocol: A hybridization mixture for each sub-array was prepared as below. Equal amount (500 ng) of Cy5- and Cy3-labeled, gel-purified half-hairpin probes were mixed together with 16.5 nmol of blocking oligo (blocking oligo sequence: 5’-GTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATA-3’). The mixture was denatured by heating to 95°C for 5 min and transferred on ice for 5 min. Hybridization solution was added to the mixture containing a final concentration of 1 x hybridization buffer (1 M NaCl, 100 mM Tris-HCl, pH 7.5, 0.5% Triton X-100) in a final volume of 110 μL; 100 μL of this was loaded to each sub-array and hybridized at 44°C in the hybridization oven (Agilent) for 16~20 hours. The microarray was washed once in wash buffer I (6X SSPE: 0.9 M NaCl, 60 mM NaH2PO4, 6 mM EDTA, 0.05% Triton X-100), once in wash buffer II (1X SSPE: 150 mM NaCl, 10 mM NaH2PO4, 1 mM EDTA ).

scan_protocol: Images were acquired with a G2565CA microarray scanner (Agilent).

data_processing: Microarray images were processed using Agilent Feature Extraction Software 10.7 (Agilent), and further statistical analysis was performed using customized software written in R. The resultant feature signal intensity datasets were normalized using a combination of linear and loess model to calculate log2(Cy5/Cy3) for the shRNA probes within each experiment, which represent the relative abundance changes of each shRNA construct between the initial and end time points. For each shRNA construct, median and robust variances (mad) of log2(Cy5/Cy3) were computed, and a robust Z-score was obtained for each measurement by subtracting the mean and dividing by the mad of that shRNA. For each shRNA the Z-score of the query sample was used to subtract the Z-score of the control sample, and an arbitrary cut-off value of the Z-score difference larger than 1.5 or less than -1.5 was used to define a candidate synthetic lethal interaction or synthetic rescue interaction, respectively.

molecule: genomic DNA

source_name: Cells selected for the query shRNA

label_protocol: The shRNA full hairpin coding sequence containing 5’ end of puromycin resistance marker gene was PCR amplified with 15 cycles from genomic DNA (PCR primer sequence, forward: 5’-TTCACCGAGGGCCTATTTCCCATG-3’, reverse: 5’-CGTGAGGAAGAGTTCTTGCAGCTC-3’) and purified using a MinElute PCR Purification kit (Qiagen). For each screen, the shRNA coding regions of the benchmark and end-point samples were further amplified and labeled with Cy5 and Cy3 dyes (PCR primer sequence, forward: 5’-[Cy5/Cy3]- AATGGACTATCATATGCTTACCGTAACTTGAA-3’, reverse: 5’-TGTGGATGAATACTGCCATTTGTCTCGAGGTC-3’), respectively, from the puromycin marker-enriched amplicon. Amplified full-hairpin DNA was further digested overnight into half-hairpins using XhoI, and the resultant half-hairpin probes were gel purified using a QIAquick Gel Purification kit (Qiagen).

growth_protocol: 7.5 x 107 HCT116 cells (1000X coverage) for each experiment were resuspended in 24 ml of DMEM containing 0.8 mg/mL geneticin and 8 μg/mL polybrene. The genome-wide lentivirus pool was added in an appropriate volume to achieve a multiplicity of infection (MOI) of 0.3 assuming the titer of transducing virus reported by the provider. This cell-virus mixture was then evenly split across one 12-well tissue culture plates for a spin transduction (centrifugation at 930 x g for 2 h at 30 °C). After spin transduction, the supernatants were aspirated and replaced by 2 mL fresh medium containing geneticin. The transduced cells were cultured overnight, and then cells of the entire plate were trypsinized and pooled together, resuspended in 30 ml of fresh medium containing geneticin and transferred in one T225 flask. At day 3 post transduction, three quarters of cells were taken from each flask as an initial “benchmark” sample. The rest of the population was selected with puromycin to remove untransduced cells and propagated for an additional 18 doublings before the end-point sample was taken.

extract_protocol: QIAamp Blood Maxi Kit protocol (Qiagen)

tag: cell line

value: HCT116 colon cancer cell line

tag: query shrna

source_name: A matched aliquot of cells collected prior to selection for the query shRNA


title: Genetic interactions control of SIRT3 Biological Replicate 1


title: st20minrep1


title: Genetic interactions control of HDAC8 Biological Replicate 2


title: st0minrep1


title: Genetic interactions control of HDAC9 Biological Replicate 2


title: Genetic interactions control of SIRT1 Biological Replicate 1


title: st10minrep1


title: Genetic interactions control of SIRT2 Biological Replicate 2


title: Genetic interactions control of SIRT5 Biological Replicate 1


title: Genetic interactions control of SIRT1 Biological Replicate 2


title: Genetic interactions control of SIRT3 Biological Replicate 2


title: Genetic interactions control of HDAC7 Biological Replicate 2


title: Genetic interactions control of SIRT5 Biological Replicate 2


title: Genetic interactions control of HDAC6 Biological Replicate 2


title: Genetic interactions control of HDAC8 Biological Replicate 1


title: Genetic interactions control of HDAC7 Biological Replicate 1


title: Genetic interactions control of HDAC3 Biological Replicate 1


title: Genetic interactions control of HDAC1 Biological Replicate 1


title: Genetic interactions control of neutral shLuciferase

value: shLuciferase


title: Genetic interactions control of HDAC4 Biological Replicate 1


title: Genetic interactions control of HDAC3 Biological Replicate 2


title: Genetic interactions control of HDAC9 Biological Replicate 1


title: Genetic interactions control of HDAC1 Biological Replicate 2


title: Genetic interactions control of HDAC2 Biological Replicate 2


title: Genetic interactions control of HDAC2 Biological Replicate 1


title: Genetic interactions control of HDAC6 Biological Replicate 1


title: Genetic interactions control of HDAC4 Biological Replicate 2


title: Gastric primary non-malignant sample 990474N SNP6

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

description: Hybridized to SNP6 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Analysis of raw cel files was performed by Affymetrix Genotyping Console 4.0 software. A reference Model File was created based on 98 non-malignant samples (included as Gastric Normal.REF in the submission). Gastric non-malignant samples and tumors samples were then processed separately using this referenece file by median normalization and GC correlation to obtain the CHP files.

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.

value: Gastric primary non-malignant tissue


title: Gastric primary non-malignant sample 990475N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990172N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990203N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990097N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990071N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990300N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990119N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990069N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990170N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990205N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990098N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990111N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990228N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990073N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990060N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990412N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990195N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990089N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990396N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990247N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990424N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990108N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990355N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990090N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990413N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990339N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990070N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990515N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990129N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990005N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980390N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990041N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990010N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990024N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980442N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980251N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980418N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980386N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990044N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990046N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 970017N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 990015N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980029N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980344N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 970005N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980011N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980021N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 91595276N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980035N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980327N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 87622942N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980156N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980369N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 96141474N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 61669256N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 58947266N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 73291145N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 65256293N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 57689477N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 57701999N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 20263644N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 46404174N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 47492137N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000303N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 66811693N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000441N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000479N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000242N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000434N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 32226415N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000238N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000346N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000403N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000175N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000088N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000286N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 38877042N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000201N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000433N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000178N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000040N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000068N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000159N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000362N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 2000114N SNP6

description: Hybridized to SNP6 array


title: Gastric primary tumor sample 990475T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990475T

value: Gastric primary tumor tissue


title: Gastric primary tumor sample 990339T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990339T


title: Gastric primary tumor sample 990247T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990247T


title: Gastric primary tumor sample 990203T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990203T


title: Gastric primary tumor sample 990396T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990396T


title: Gastric primary tumor sample 990412T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990412T


title: Gastric primary non-malignant sample 2000169N SNP6

description: Hybridized to SNP6 array


title: Gastric primary tumor sample 990413T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990413T


title: Gastric primary tumor sample 990044T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990044T


title: Gastric primary tumor sample 990069T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990069T


title: Gastric primary tumor sample 990119T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990119T


title: Gastric primary tumor sample 990070T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990070T


title: Gastric primary tumor sample 990424T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990424T


title: Gastric primary tumor sample 990111T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990111T


title: Gastric primary tumor sample 990011T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990011T


title: Gastric primary tumor sample 990024T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990024T


title: Gastric primary tumor sample 990515T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990515T


title: Gastric primary tumor sample 990005T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990005T


title: Gastric primary tumor sample 990172T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990172T


title: Gastric primary tumor sample 98748381T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 98748381T


title: Gastric primary tumor sample 990090T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990090T


title: Gastric primary tumor sample 990010T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990010T


title: Gastric primary tumor sample 990015T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990015T


title: Gastric primary tumor sample 990089T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990089T


title: Gastric primary tumor sample 990355T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990355T


title: Gastric primary tumor sample 990300T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990300T


title: Gastric primary tumor sample 980418T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980418T


title: Gastric primary tumor sample 990046T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990046T


title: Gastric primary tumor sample 990170T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990170T


title: Gastric primary tumor sample 980369T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980369T


title: Gastric primary tumor sample 980307T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980307T


title: Gastric primary tumor sample 980442T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980442T


title: Gastric primary tumor sample 990041T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990041T


title: Gastric primary tumor sample 980386T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980386T


title: Gastric primary tumor sample 980305T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980305T


title: Gastric primary tumor sample 980148T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980148T


title: Gastric primary tumor sample 980161T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980161T


title: Gastric primary tumor sample 980156T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980156T


title: Gastric primary tumor sample 980252T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980252T


title: Gastric primary tumor sample 980184T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980184T


title: Gastric primary tumor sample 980251T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980251T


title: Gastric primary tumor sample 980028T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980028T


title: Gastric primary tumor sample 980035T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980035T


title: Gastric primary tumor sample 980048T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980048T


title: Gastric primary tumor sample 980095T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980095T


title: Gastric primary tumor sample 980025T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980025T


title: Gastric primary tumor sample 980255T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980255T


title: Gastric primary tumor sample 980021T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980021T


title: Gastric primary tumor sample 980056T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980056T


title: Gastric primary tumor sample 980029T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980029T


title: Gastric primary tumor sample 980211T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980211T


title: Gastric primary tumor sample 980001T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980001T


title: Gastric primary tumor sample 980269T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980269T


title: Gastric primary tumor sample 970024T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 970024T


title: Gastric primary tumor sample 970032T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 970032T


title: Gastric primary tumor sample 980002T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980002T


title: Gastric primary tumor sample 980011T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980011T


title: Gastric primary tumor sample 970010T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 970010T


title: Gastric primary tumor sample 970017T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 970017T


title: Gastric primary tumor sample 9432729T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 9432729T


title: Gastric primary tumor sample 970005T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 970005T


title: Gastric primary tumor sample 970001T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 970001T


title: Gastric primary tumor sample 91515473T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 91515473T


title: Gastric primary tumor sample 77263387T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 77263387T


title: Gastric primary tumor sample 78373410T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 78373410T


title: Gastric primary tumor sample 87622942T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 87622942T


title: Gastric primary tumor sample 83507354T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 83507354T


title: Gastric primary tumor sample 82973565T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 82973565T


title: Gastric primary tumor sample 75554796T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 75554796T


title: Gastric primary tumor sample 73813499T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 73813499T


title: Gastric primary tumor sample 7847924T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 7847924T


title: Gastric primary tumor sample 980327T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980327T


title: Gastric primary tumor sample 74765340T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 74765340T


title: Gastric primary tumor sample 65256293T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 65256293T


title: Gastric primary tumor sample 73291145T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 73291145T


title: Gastric primary tumor sample 69245824T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 69245824T


title: Gastric primary tumor sample 63540193T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 63540193T


title: Gastric primary tumor sample 6412929T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 6412929T


title: Gastric primary tumor sample 57701999T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 57701999T


title: Gastric primary tumor sample 5218170T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 5218170T


title: Gastric primary tumor sample 66811693T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 66811693T


title: Gastric primary tumor sample 57689477T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 57689477T


title: Gastric primary tumor sample 61669256T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 61669256T


title: Gastric primary tumor sample 48982424T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 48982424T


title: Gastric primary tumor sample 46404174T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 46404174T


title: Gastric primary tumor sample 68334421T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 68334421T


title: Gastric primary tumor sample 96141474T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 96141474T


title: Gastric primary tumor sample 47149013T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 47149013T


title: Gastric primary tumor sample 47492137T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 47492137T


title: Gastric primary tumor sample 58947266T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 58947266T


title: Gastric primary tumor sample 32226415T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 32226415T


title: Gastric primary tumor sample 38877042T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 38877042T


title: Gastric primary tumor sample 31231321T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 31231321T


title: Gastric primary tumor sample 20020999T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20020999T


title: Gastric primary tumor sample 26109694T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 26109694T


title: Gastric primary tumor sample 31661621T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 31661621T


title: Gastric primary tumor sample 20263644T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20263644T


title: Gastric primary tumor sample 20020455T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20020455T


title: Gastric primary tumor sample 21080055T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 21080055T


title: Gastric primary tumor sample 29806547T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 29806547T


title: Gastric primary tumor sample 2001190T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2001190T


title: Gastric primary tumor sample 20020361T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20020361T


title: Gastric primary tumor sample 20020846T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20020846T


title: Gastric primary tumor sample 20020195T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20020195T


title: Gastric primary tumor sample 2001135T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2001135T


title: Gastric primary tumor sample 2001123T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2001123T


title: Gastric primary tumor sample 2001120T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2001120T


title: Gastric primary tumor sample 49375233T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 49375233T


title: Gastric primary tumor sample 20020032T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20020032T


title: Gastric primary tumor sample 2001086T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2001086T


title: Gastric primary tumor sample 2000887T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000887T


title: Gastric primary tumor sample 2000778T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000778T


title: Gastric primary tumor sample 2000752T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000752T


title: Gastric primary tumor sample 2000676T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000676T


title: Gastric primary tumor sample 2000696T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000696T


title: Gastric primary tumor sample 2000708T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000708T


title: Gastric primary tumor sample 2000732T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000732T


title: Gastric primary tumor sample 2000472T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000472T


title: Gastric primary tumor sample 2000479T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000479T


title: Gastric primary tumor sample 2000521T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000521T


title: Gastric primary tumor sample 2000734T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000734T


title: Gastric primary tumor sample 2000963T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000963T


title: Gastric primary tumor sample 2000616T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000616T


title: Gastric primary tumor sample 2000346T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000346T


title: Gastric primary tumor sample 2000441T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000441T


title: Gastric primary tumor sample 2000618T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000618T


title: Gastric primary tumor sample 2000362T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000362T


title: Gastric primary tumor sample 2000303T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000303T


title: Gastric primary tumor sample 2000169T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000169T


title: Gastric primary tumor sample 2000256T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000256T


title: Gastric primary tumor sample 2000178T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000178T


title: Gastric primary tumor sample 2000238T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000238T


title: Gastric primary tumor sample 2000433T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000433T


title: Gastric primary tumor sample 2000403T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000403T


title: Gastric primary tumor sample 2000286T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000286T


title: Gastric primary tumor sample 2000175T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000175T


title: Gastric primary tumor sample 2000159T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000159T


title: Gastric primary tumor sample 2000529T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000529T


title: Gastric primary tumor sample 2000201T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000201T


title: Gastric primary tumor sample 2000068T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000068T


title: Gastric primary tumor sample 10390127T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 10390127T


title: S1Cs-A3_gDNA

city: Boston

first: Alexander

last: Gimelbrant

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
D10
Hybridized to 150K_Nsp

hyb_protocol: DNA or ds-cDNA was hybridized to each array according to the manufacturer's instructions. Ds-cDNA was used at a concentration of 100 ng/ul.

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip Scanner 3000.

data_processing: CEL files were processed by Affymetrix GTYPE 4.0 using the DM algorithm and the PM/MM model. Further analysis was performed using the allele-specific expression calling algorithm described in Gimelbrant et al., 2007 Science 318:1136-40 (PMID 18006746).

label: biotin

source_name: monoclonal lymphoblasts (Abelson cells), genomic DNA

label_protocol: DNA or ds-cDNA was restriction digested, PCR amplified, fragmented, and labeled as per the manufacturer (Affymetrix).

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Nuclei were prepared from 50-100M cells. Genomic DNA was prepared using the Qiagen DNA Blood Mini Kit. Total nuclear RNA was prepared using the Trizol protocol; after DNase treatment, double-stranded cDNA was synthesized. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: None.

tag: strain

value: 129S1/SvImJ x CAST/EiJ

value: male

tag: clonality

value: monoclonal

value: lymphoblasts (Abelson cells)


title: Gastric primary tumor sample 15295992T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 15295992T


title: S1Cs-A3_cDNA_rep1

description:
D11
ds-cDNA
Hybridized to 150K_Nsp

source_name: monoclonal lymphoblasts (Abelson cells), ds-cDNA


title: Gastric primary tumor sample 2000242T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000242T


title: S1Cs-A3_cDNA_rep2

description:
D12
ds-cDNA
Hybridized to 150K_Nsp


title: BcB6-A13_gDNA

description:
D07
Hybridized to 150K_Nsp

value: Balb/cByJ x C57BL/6J

value: female


title: BcB6-A13_cDNA_rep2

description:
D09
ds-cDNA
Hybridized to 150K_Nsp


title: BcB6-A13_cDNA_rep1

description:
D08
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 2000619T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000619T


title: Gastric primary tumor sample 069LYK SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 069LYK


title: BcB6-A12_cDNA_rep2

description:
D06
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 2000040T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000040T


title: Gastric primary tumor sample 2000484T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000484T


title: Gastric primary tumor sample 2000114T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000114T


title: BcB6-A14_cDNA_rep1

description:
D02
ds-cDNA
Hybridized to 150K_Nsp

source_name: nonclonal lymphoblasts (Abelson cells), ds-cDNA

value: nonclonal


title: Gastric primary tumor sample 052GC SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 052GC


title: Gastric primary tumor sample 055KYF SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 055KYF


title: Gastric primary tumor sample 040TLK SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 040TLK


title: Gastric primary tumor sample 050IY SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 050IY


title: Gastric primary tumor sample 074TWC SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 074TWC


title: BcB6-A14_cDNA_rep2

description:
D03
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 047WPK SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 047WPK


title: Gastric primary tumor sample 068QKW SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 068QKW


title: Gastric primary tumor sample 047LAK SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 047LAK


title: B6Bc-A10_gDNA

description:
C10
Hybridized to 150K_Nsp

source_name: monoclonal lymphoblasts (Abelson cells), genomic DNA

value: C57BL/6J x Balb/cByJ


title: B6Bc-A10_cDNA_rep1

description:
C11
ds-cDNA
Hybridized to 150K_Nsp

source_name: monoclonal lymphoblasts (Abelson cells), ds-cDNA


title: BcB6-A12_cDNA_rep1

description:
D05
ds-cDNA
Hybridized to 150K_Nsp


title: BcB6-A14_gDNA

description:
D01
Hybridized to 150K_Nsp

source_name: nonclonal lymphoblasts (Abelson cells), genomic DNA


title: B6Bc-A9_cDNA_rep2

description:
C09
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 043WKF SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 043WKF


title: Gastric primary tumor sample 045TSL SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 045TSL


title: BcB6-A12_gDNA

description:
D04
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 042KS SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 042KS


title: B6Bc-A9_cDNA_rep1

description:
C08
ds-cDNA
Hybridized to 150K_Nsp


title: B6Bc-A11_cDNA_rep2

description:
C06
ds-cDNA
Hybridized to 150K_Nsp


title: B6Bc-A10_cDNA_rep2

description:
C12
ds-cDNA
Hybridized to 150K_Nsp


title: B6Bc-A9_gDNA

description:
C07
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 039TSC SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 039TSC


title: B6Bc-A11_cDNA_rep1

description:
C05
ds-cDNA
Hybridized to 150K_Nsp


title: B6Bc-A11_gDNA

description:
C04
Hybridized to 150K_Nsp


title: S1Cs-F2_cDNA_rep1

description:
C02
ds-cDNA
Hybridized to 150K_Nsp

source_name: monoclonal fibroblasts, ds-cDNA

value: fibroblasts


title: S1Cs-F2_cDNA_rep2

description:
C03
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 2000088T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000088T(R)


title: S1Cs-F2_gDNA

description:
C01
Hybridized to 150K_Nsp

source_name: monoclonal fibroblasts, genomic DNA


title: Gastric primary tumor sample 068JW SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 068JW


title: S1Cs-F1_gDNA

description:
B10
Hybridized to 150K_Nsp


title: S1Cs-A8_cDNA_rep2

description:
B09
ds-cDNA
Hybridized to 150K_Nsp

source_name: nonclonal lymphoblasts (Abelson cells), ds-cDNA


title: S1Cs-F1_cDNA_rep2

description:
B12
ds-cDNA
Hybridized to 150K_Nsp


title: S1CS-F1_cDNA_rep1

description:
B11
ds-cDNA
Hybridized to 150K_Nsp


title: S1Cs-A4_cDNA_rep1

description:
B05
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 038LYC SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 038LYC


title: Gastric primary tumor sample 035PCC SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 035PCC


title: S1Cs-A8_cDNA_rep1

description:
B08
ds-cDNA
Hybridized to 150K_Nsp


title: S1Cs-A8_gDNA

description:
B07
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 046CBP SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 046CBP


title: Gastric primary tumor sample 031KCW SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 031KCW


title: Gastric primary tumor sample 032TKK SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 032TKK


title: S1Cs-A4_cDNA_rep2

description:
B06
ds-cDNA
Hybridized to 150K_Nsp


title: S1Cs-A2_cDNA_rep2

description:
B03
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 033KHK SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 033KHK


title: S1Cs-A4_gDNA

description:
B04
Hybridized to 150K_Nsp

source_name: monoclonal lymphoblasts (Abelson cells), genomic DNA


title: S1Cs-A7_cDNA_rep2

description:
A09
ds-cDNA
Hybridized to 150K_Nsp

source_name: monoclonal lymphoblasts (Abelson cells), ds-cDNA


title: S1Cs-F3_cDNA_rep2

description:
A12
ds-cDNA
Hybridized to 150K_Nsp

source_name: nonclonal fibroblasts, ds-cDNA


title: S1Cs-A2_gDNA

description:
B01
Hybridized to 150K_Nsp


title: S1Cs-F3_cDNA_rep1

description:
A11
ds-cDNA
Hybridized to 150K_Nsp


title: S1Cs-A2_cDNA_rep1

description:
B02
ds-cDNA
Hybridized to 150K_Nsp


title: S1Cs-A6_cDNA_rep2

description:
A06
ds-cDNA
Hybridized to 150K_Nsp


title: S1Cs-A7_cDNA_rep1

description:
A08
ds-cDNA
Hybridized to 150K_Nsp


title: S1Cs-F3_gDNA

description:
A10
Hybridized to 150K_Nsp

source_name: nonclonal fibroblasts, genomic DNA


title: Gastric primary tumor sample 028LGL SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 028LGL


title: S1Cs-A6_cDNA_rep1

description:
A05
ds-cDNA
Hybridized to 150K_Nsp


title: Heart 2_2

city: Basel

first: Morgane

last: RAVON

address: Grenzacherstrasse 124

country: Switzerland

institute: Hoffmann-La Roche

description: Replicate 2

hyb_protocol: Hybridization was performed according to the whole-genome gene expression direct hybridization protocol from Illumina.

scan_protocol: Beadchips were scanned using Illumina iScan, standard protocol.

data_processing: The data were log2 transformed and normalised using  quantile normalization with Partek Genomics Suite software, version 6.5 (Partek, Inc., St. Louis, MO).

source_name: Commercial total RNAs from biopsies, Heart 2

label_protocol: Total RNA samples were converted to Cy3 labeled-cDNA using TotalPrep RNA amplification kit from Ambion.

extract_protocol: Total RNA was isolated from cell samples using TRIZol reagent according to the manufacturer's protocol.

value: Commercial total RNAs from biopsies


title: S1Cs-A6_gDNA

description:
A04
Hybridized to 150K_Nsp


title: S1Cs-A5_cDNA_rep1

description:
A02
ds-cDNA
Hybridized to 150K_Nsp


title: Heart 2_3

description: Replicate 3


title: Gastric primary tumor sample 024SWM SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 024SWM


title: Control_2

city: Cambridge

first: Tali

last: Mazor

state: MA

address: 77 Massachusetts Ave

institute: MIT

description: maturation was induced by adding 50 nM (final concentration) 12-O- tetradecanoylphorbol-13-acetate (TPA) to the medium for 3 days

hyb_protocol: hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays (MOE430v2) following standard techniques.

scan_protocol: Scanned with GeneChIP scanner 300 7G using the standard protocol.

data_processing: Expression data were analyzed using R and Bioconductor (http://www.bioconductor.org/).

source_name: Control

label_protocol: 5 microgram RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

growth_protocol: Cells were grown in 38.5% IMDM + 38.5% RPMI + 20% FCS + %2 Pen/strep + 1% L-Glutamine,

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, catalogue no. 74134).

treatment_protocol: 48 hrs after lenti-viral infection, 2 microgram/microliter puromycin was added to culture medium for selecting infected cells, and cells were harvested for RNA 72 hrs after puromycin selection. 50 nM TPA was added at the same time with puromycin to induced maturation of the cells.

value: megakaryocytic cells

tag: genotype/variation

value: empty vector control


title: Control_3


title: S1Cs-A5_cDNA_rep2

description:
A03
ds-cDNA
Hybridized to 150K_Nsp


title: Gastric primary tumor sample 025PHW SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 025PHW


title: peripheral blood cell(PBC)_neonate_Control_rep6

city: Shanghai

first: Chong

last: Li

address: Bldg.1,No.250 Bi Bo Rd.,Shanghai

country: China

institute: Chineses National Human Genome Center at Shanghai

hyb_protocol: Approximately 5.5 mg of biotin-labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45℃ for 16 hr following manufacturer’s protocol (Affymetrix).

scan_protocol: Affymetrix GCS3000 Scanner

data_processing:
Expression Console software (Affymetrix) was used to quantile-normalize the probe fluorescence intensities over all 37 samples with PM-GCBG backgroud correction. An iterative probe logarithmic intensity error(IterPlier) model was used to summarize the meta-probe set (representing gene expression) intensities. To stabilize variance, a constant of 16 was added to all probe set intensities, and then the signal values were log2 transformed. Removing the transcript clusters without any RefSeq-supported annotation, we generated the expression signals of 17,626 transcript clusters with core sets.
probe group fil: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Control, PBC, neonate

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

extract_protocol: From the 22 child samples (C group), PBMCs were isolated from peripheral blood using Lymphocyte ®-H (CEDARLANE), and total RNA was extracted using the mirVana™ miRNA Isolation Kit (Applied Biosystems) according to the manufacturer’s protocol. The remaining 12 neonate samples (N group) had limited blood volume; therefore, total RNA was extracted from PBCs. RNA concentration and purity was tested using a Nanodrop 2000c spectrophotometer (Thermo Scientific). RNA quality was further assessed with the Agilent 2100 Bioanalyzer using RNA 6000 Nanochips (Agilent Technologies). None of the 37 RNA samples had DNA contamination or RNA degradation. RNA samples were stored at -80℃ for hybridization.

value: 38 days

value: peripheral blood cell

value: Female

tag: disease

value: Control


title: S1Cs-A5_gDNA

description:
A01
Hybridized to 150K_Nsp


title: peripheral blood cell(PBC)_neonate_Control_rep7

value: 23 days


title: peripheral blood cell(PBC)_neonate_Control_rep5

value: 28 days

value: Male


title: S1Cs-A7_gDNA

description:
A07
Hybridized to 150K_Nsp

value: 129S1/SvImJ x CAST/EiJ

value: monoclonal


title: Heart diseased_3

description: Replicate 3

source_name: Commercial total RNAs from biopsies, Heart diseased


title: Control_1


title: peripheral blood cell(PBC)_neonate_Control_rep3

value: 30 days


title: Heart diseased_2

description: Replicate 2


title: Heart 2_1

description: Replicate 1


title: Ring1b_KD_3

value: shRNA-mediated Ring1b knockdown


title: peripheral blood cell(PBC)_neonate_Control_rep2

value: 7 days


title: Left ventricule_2

description: Replicate 2

source_name: Commercial total RNAs from biopsies, Left ventricule


title: Heart diseased_1

description: Replicate 1


title: Ring1b_KD_1


title: Left ventricule_3

description: Replicate 3


title: CBFb_KD_3

value: shRNA-mediated CBFb knockdown


title: peripheral blood cell(PBC)_neonate_Control_rep1

value: 3 days


title: CBFb_KD_2


title: Gastric primary tumor sample 017TPC SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 017TPC

value: Gastric primary tumor tissue


title: Gastric primary tumor sample 022CKH SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 022CKH


title: Gastric primary tumor sample 007LKB SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 007LKB


title: peripheral blood cell(PBC)_neonate_Control_rep4


title: Gastric primary tumor sample 014CKC SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 014CKC


title: Gastric primary tumor sample 021LAH SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 021LAH


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep15

source_name: Control, PBMC, child

value: 2 years

value: peripheral blood mononuclear cell


title: Left ventricule_1

description: Replicate 1

value: Commercial total RNAs from biopsies


title: Gastric primary tumor sample 006LTE SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 006LTE


title: Heart 1_3

description: Replicate 3

source_name: Commercial total RNAs from biopsies, Heart 1


title: CBFb_KD_1

value: megakaryocytic cells


title: Ring1b_KD_2


title: Heart 1_1

description: Replicate 1


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep14

value: 2.5 years


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep12

value: 3 years

value: Female

value: Control


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep13


title: Heart 1_2

description: Replicate 2


title: Fetal heart_6

description: Replicate 6

source_name: Commercial total RNAs from biopsies, Fetal heart


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep11

value: 5 years

value: Male


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep10


title: Gastric primary tumor sample 005KD SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 005KD


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep9

value: 4 years


title: Gastric primary tumor sample 011LGE SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 011LGE


title: Fetal heart_3

description: Replicate 3


title: Fetal heart_4

description: Replicate 4


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep8

value: 8 years


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep7

value: 9 years


title: 11.5dpc PCM vs 12.5dpc MC (Dye Combination 1)

city: Parkville

first: Trevor

middle: L

last: Cameron

address: Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

hyb_protocol: All aRNA samples were hybridized to 44K mouse whole genome microarrays (Agilent Technologies), in two color hybridizations including dye swaps, and in strict accordance with the manufacturer’s specifications.

scan_protocol: All microarrays were scanned at 10um resolution on an Axon 4000B scanner

data_processing: The microarray features were acquired using GenePix Pro 4.1 software, and the raw data was processed using a print tip loess method of normalization with limmaGUI, which is an implemented package of R used to fit linear models to microarray data.

source_name: Pre-condensed mesenchyme, 11.5dpc hind limb

label_protocol: Amplified RNA samples (2ug) were labelled with Cy3 or Cy5 (Amersham), according to the manufacturer’s specifications.  Fluorophore incorporation and yield were determined by spectrophotometry using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

growth_protocol: Pregnant Swiss white mice were sacrificed in accordance with institutional ethical guidelines at the appropriate stage of gestation. Embryos were then harvested and culled, and hind limb buds were dissected.

extract_protocol: Microdissected tissues were collected in TRIzol reagent (Invitrogen) for RNA extraction and purification, which was performed following the manufacturer’s specifications.  All total RNA samples were subjected to two rounds of linear amplification using the MessageAmp II aRNA Amplification Kit (Ambion), following the manufacturer’s protocol.  100-150ng of first-round amplified aRNA was used as template for each second round amplification.  Following total RNA extraction and amplification, the yield, purity, and integrity of all RNA samples were validated by capillary electrophoresis with a Bioanalyzer 2100 (Agilent Technologies), using a Series II RNA 6000 Pico Kit (Agilent Technologies), according to the manufacturer’s specifications.

treatment_protocol: Dissected limb buds were embedded in Tissue-Tek OCT (Sakura Fine Technical), snap-frozen in isopentane, and stored at -80° C.  6um cryosections were prepared using a cryostat (Leica CM1850), mounted on RNAse-free SuperFrost Plus slides (Biolab Scientific), and processed immediately by being fixed in 70% ethanol, rinsed in RNAse-free water, and dehydrated in 70%, 95%, and 100% ethanol for 30 seconds each.  They were then stored in 100% ethanol at -80° C.  Immediately prior to microdissection, sections were air-dried and the tissue of interest was microdissected using an ophthalmic scalpel (Feather) fixed to the scanning xy-object guide.  Light microscopy was performed using an Eclipse 80i light microscope (Nikon).

value: Pre-condensed mesenchyme hind limb

value: Swiss white

source_name: Mesenchymal condensation, 12.5dpc hind limb

value: Mesenchymal condensation hind limb


title: 11.5dpc PCM vs 13.5dpc CA (Dye Combination 1)

source_name: Cartilage anlagen, 13.5dpc hind limb

value: Cartilage anlagen hind limb


title: 12.5dpc MC vs 11.5dpc PCM (Dye Combination 2)


title: Fetal heart_5

description: Replicate 5


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep5

value: 12 years


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep6

value: peripheral blood mononuclear cell


title: Fetal heart_2

description: Replicate 2

value: Commercial total RNAs from biopsies


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep4


title: Promocell p5_2

description: Replicate 2

source_name: Primary cardiomyocytes, Passage 5

value: Primary cardiomyocytes


title: Promocell p5_3

description: Replicate 3


title: 13.5dpc CA vs 11.5dpc PCM (Dye Combination 2)


title: 12.5dpc MC vs 13.5dpc CA (Dye Combination 1)


title: Fetal heart_1

description: Replicate 1


title: Promocell p5_1

description: Replicate 1


title: Run3_D120

description: Replicate 3

hyb_protocol: Samples were hybidized onto beadchips according to microRNA expression profiling protocol from Illumina.

source_name: iPSC-derived cardiomyocytes, Day 120

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

value: iPSC-derived cardiomyocytes


title: 13.5dpc CA vs 12.5dpc MC (Dye Combination 2)


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep3


title: mouse PPF at E16.5, rep7

first: Meaghan

middle: Kathleen

last: Russell

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description: Laser captured tissue

hyb_protocol: Labeled fragmented cDNA (2.5 µg) was applied to Affymetrix Mouse Gene 1.0_ST GeneChips and hybridized within the GeneChip® Hybridization Oven 640 (Affymetrix) at 45 °C and rotated at 60 g for 18 hrs. After the overnight hybridization step, chips were washed and stained within the GeneChip® Fluidics Station 450 (Affymetrix) using the AGCC Fluidics Control software program.

scan_protocol: GeneChips were scanned by the GeneChip® Scanner 3000 7G (Affymetrix) using the AGVV Scan Control software program.

data_processing: Preliminary quality control metrics were performed using Affymetrix Expression Console v.1.1 and data were normalized in R (version 2.9.2) using Robust Multichip Averaging [RMA; implemented in the Affymetrix package for R (http://bioconductor.org/packages/2.1/bioc/html/affy.html].

source_name: LCM primordial diaphragm tissue at E16.5

label_protocol: RNA was purified using the PicoPure Kit (Applied Biosystems), including DNAse treatment with Qiagen RNase-Free DNase Set (Qiagen, Valencia, CA). Samples were retrotranscribed by the WT-Ovation™ Pico System (NuGEN, San Carlos, CA) and purified using Agencourt RNAClean Beads (Danvers, MA). cDNA was amplified using the SPIA amplification protocol (NuGen) and the supernatant cleared using the Zymo clean-up kit (Zymo Research, Irvine, CA). The Encore™ Biotin Module (NuGEN) was used for fragmentation and labeling. All protocols were carried out according to manufacturers’ instructions.

extract_protocol: Embryos were collected from timed-pregnant C57BL/6J mice and embedded in OCT (Tissue-Tek, Torrance, CA) in an isopentane slurry. Laser capture microdissection was performed on 10 μm transverse (E11.5 and E12.5) and sagittal (E16.5) mid-thoracic cryosections on PEN membrane glass slides (LCM0522, Applied Biosystems, Carlsbad, CA). The target tissues were microdissected using the Arcturus XT instrument on CapSure HS LCM Caps (LCM0215) (Applied Biosystems, Carlsbad, CA).  Total RNA was extracted using the PicoPure® RNA extraction reagent (KIT0204) (Applied Biosystems, Carlsbad, CA) according to manufacturer’s instructions.

tag: developmental stage


title: Celprogen p4_3

description: Replicate 3

source_name: Primary cardiomyocytes, Passage 4


title: mouse PPF at E16.5, rep8

description: Laser captured tissue


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep2

value: 13 years


title: Run2_D120

description: Replicate 2


title: Run1_D120

description: Replicate 1


title: 18207patient

city: Philadelphia

first: JIANMING

last: PEI

state: PA

address: 333 Cottman Ave.

department: Population Science

institute: Fox Chase Cancer Center

description: Hybridized to Affymetrix Cytogenetics Array

hyb_protocol: DNA was whole-genome amplified, purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files generated by Affymetrix Command Console and CYCHP files generated byAffymetrix Chromosome Analysis Suite software (ChAS).  DNA copy number and allele analysis were performed using Affymetrix ChAS, which compares all hybridization intensities against a built-in reference data set.
Primary data description: copy number, allele peaks.
The allele peaks data are included in the cychp files in addition to copy number.

source_name: patient

extract_protocol: Genomic DNA was extracted from sorted cells obtained from peripheral blood using the Qiagen Puregen Kit and buccal epithelia using Oragene DNA kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: white blood cell

tag: cell source

value: patient


title: Run3_D090

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 90

tag: cell type


title: 18238fa

source_name: patient's father

value: patient's father


title: Run1_D090

description: Replicate 1


title: Run2_D090

description: Replicate 2


title: peripheral blood mononuclear cell(PBMC)_child_Control_rep1

value: 11 years

value: Female

value: Control


title: 18237mo

source_name: patient's mother

value: patient's mother


title: CSneutrophil

source_name: neutrophil

value: CSneutrophil


title: Celprogen p4_2

description: Replicate 2


title: peripheral blood cell(PBC)_neonate_Down syndrome_rep5

source_name: Down syndrome, PBC, neonate

value: 30 days

value: peripheral blood cell

value: Down syndrome


title: peripheral blood cell(PBC)_neonate_Down syndrome_rep3

value: 7 days


title: peripheral blood cell(PBC)_neonate_Down syndrome_rep2

value: 10 days


title: Celprogen p4_1

description: Replicate 1


title: Run3_D060

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 60


title: mouse PPF at E16.5, rep4

description: Laser captured tissue


title: Sciencell p12_1

description: Replicate 1

source_name: Primary cardiomyocytes, Passage 12


title: mouse PPF at E16.5, rep6

description: Laser captured tissue


title: mouse PPF at E16.5, rep5

description: Laser captured tissue


title: peripheral blood cell(PBC)_neonate_Down syndrome_rep4

value: 11 days


title: Sciencell p12_3

description: Replicate 3

value: Primary cardiomyocytes


title: Sciencell p12_2

description: Replicate 2


title: Run2_D060

description: Replicate 2

value: iPSC-derived cardiomyocytes


title: mouse PPF at E16.5, rep2

description: Laser captured tissue


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep9

source_name: Down syndrome, PBMC, child

value: 2 years

value: peripheral blood mononuclear cell

value: Male


title: Run2_D045

description: Replicate 2

source_name: iPSC-derived cardiomyocytes, Day 45


title: Run3_D045

description: Replicate 3


title: Run1_D045

description: Replicate 1


title: Run3_D120

description: Replicate 3


title: mouse PPF at E16.5, rep1

description: Laser captured tissue


title: mouse PPF at E12.5, rep7

description: Laser captured tissue

source_name: LCM primordial diaphragm tissue at E12.5


title: Run3_D090

description: Replicate 3


title: Run1_D060

description: Replicate 1


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep10

value: 1 years


title: Run3_D035

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 35


title: CSbuccal

source_name: buccal epithelia

value: CSbuccal


title: mouse PPF at E12.5, rep8

description: Laser captured tissue


title: Run1_D120

description: Replicate 1


title: CSlymphocyte

source_name: lymphocyte

value: CSlymphocyte


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep8

value: Female


title: Run2_D120

description: Replicate 2

source_name: iPSC-derived cardiomyocytes, Day 120


title: peripheral blood cell(PBC)_neonate_Down syndrome_rep1


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep7


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep6

value: 4 years


title: Run2_D090

description: Replicate 2


title: Run2_D035

description: Replicate 2


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep5

value: 5 years


title: Run1_D035

description: Replicate 1


title: Run3_D028

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 28


title: mouse PPF at E12.5, rep5

description: Laser captured tissue


title: Run2_D028

description: Replicate 2


title: Run3_D060

description: Replicate 3


title: mouse PPF at E12.5, rep3

description: Laser captured tissue


title: mouse PPF at E12.5, rep6

description: Laser captured tissue


title: mouse PPF at E16.5, rep3

description: Laser captured tissue

source_name: LCM primordial diaphragm tissue at E16.5


title: Run1_D028

description: Replicate 1


title: Run1_D090

description: Replicate 1


title: Run3_D020

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 20


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep3

value: 11 years


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep1


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep4

value: 6 years


title: Run3_D045

description: Replicate 3


title: mouse PPF at E11.5, rep8

description: Laser captured tissue

source_name: LCM primordial diaphragm tissue at E11.5


title: mouse PPF at E11.5, rep5

description: Laser captured tissue


title: Run2_D020

description: Replicate 2


title: Run1_D060

description: Replicate 1


title: Run1_D045

description: Replicate 1


title: Run2_D045

description: Replicate 2


title: mouse PPF at E11.5, rep7

description: Laser captured tissue


title: Run2_D060

description: Replicate 2


title: mouse PPF at E12.5, rep1

description: Laser captured tissue


title: Run3_D014

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 14


title: Run3_D035

description: Replicate 3


title: Run1_D020

description: Replicate 1


title: Run2_D014

description: Replicate 2


title: mouse PPF at E11.5, rep6

description: Laser captured tissue


title: mouse PPF at E12.5, rep2

description: Laser captured tissue


title: peripheral blood mononuclear cell(PBMC)_child_Down syndrome_rep2

value: Down syndrome


title: mouse PPF at E11.5, rep4

description: Laser captured tissue


title: Run3_D010

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 10


title: Run2_D010

description: Replicate 2


title: Run1_D010

description: Replicate 1


title: Run3_D007

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 7


title: Run2_D007

description: Replicate 2


title: mouse PPF at E11.5, rep3

description: Laser captured tissue


title: Run2_D035

description: Replicate 2


title: Run1_D035

description: Replicate 1


title: mouse PPF at E11.5, rep2

description: Laser captured tissue


title: Run2_D028

description: Replicate 2


title: Run1_D014

description: Replicate 1


title: Run3_D028

description: Replicate 3


title: Run1_D007

description: Replicate 1


title: Run3_D003

description: Replicate 3

source_name: iPSC-derived cardiomyocytes, Day 3


title: Run1_D028

description: Replicate 1


title: mouse PPF at E11.5, rep1

description: Laser captured tissue


title: Run3_D020

description: Replicate 3


title: Run2_D003

description: Replicate 2


title: Run1_D020

description: Replicate 1


title: Run1_D003

description: Replicate 1


title: Run2_D020

description: Replicate 2


title: Run3_D014

description: Replicate 3


title: Run2_D014

description: Replicate 2


title: Run2_D000

description: Replicate 2

source_name: iPSC-derived cardiomyocytes, Day 0


title: Run3_D000

description: Replicate 3


title: Run1_D000

description: Replicate 1


title: Run3_D010

description: Replicate 3


title: Run1_D014

description: Replicate 1


title: Run1_D010

description: Replicate 1


title: Run2_D007

description: Replicate 2


title: Run3_D007

description: Replicate 3


title: Run3_D000

description: Replicate 3


title: Run3_D003

description: Replicate 3


title: Run2_D010

description: Replicate 2


title: Run1_D003

description: Replicate 1


title: Run2_D003

description: Replicate 2


title: Run2_D000

description: Replicate 2


title: Run1_D007

description: Replicate 1


title: mouse PPF at E12.5, rep4

description: Laser captured tissue


title: Dgat1-/-, ad libitum diet rep2

status: Public on Feb 09 2012

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Mice were housed in a pathogen-free barrier-type facility (both with a 12h light/12h dark cycle), until 15-16 months of age. Female mice were used for all studies and were fed a standard chow diet (5053 PicoLab Diet; Purina, St. Louis, MO).
Gene expression data from Dgat1 null middle-aged (15-16 mo) female mouse liver fed a standard chow diet (5053 PicoLab Diet; Purina, St. Louis, MO) ad libitum.

hyb_protocol: According to manufacturer's (Affymetrix) recommendations

data_processing: The data were analyzed with RMA using default analysis settings.

source_name: Dgat1 null mouse liver, fed an ad lib diet

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

value: liver

value: C57BL/6J background

value: 15-16 months


title: Dgat1-/-, ad libitum diet rep3

scan_protocol: According to manufacturer's (Affymetrix) recommendations


title: Run1_D000

description: Replicate 1


title: Wild-type, caloric restriction diet rep2

description:
Mice were housed in a pathogen-free barrier-type facility (both with a 12h light/12h dark cycle), until 15-16 months of age. Female mice were used for all studies and were fed a standard chow diet (5053 PicoLab Diet; Purina, St. Louis, MO).
Gene expression data from wild-type middle-aged (15-16 mo) female mouse liver fed a short-term calorie restricted diet (5053 PicoLab Diet; Purina, St. Louis, MO).

source_name: Wild-type mouse liver, fed a calorie restricted diet

label_protocol: According to manufacturer's (Affymetrix) recommendations

value: Wild-type


title: Wild-type, caloric restriction diet rep3


title: Wild-type, ad libitum diet rep3

description:
Mice were housed in a pathogen-free barrier-type facility (both with a 12h light/12h dark cycle), until 15-16 months of age. Female mice were used for all studies and were fed a standard chow diet (5053 PicoLab Diet; Purina, St. Louis, MO).
Gene expression data from wild-type middle-aged (15-16 mo) female mouse liver fed a standard chow diet (5053 PicoLab Diet; Purina, St. Louis, MO) ad libitum.

source_name: Wild-type mouse liver, fed an ad lib diet


title: Wild-type, ad libitum diet rep2


title: G1/S-synchronized CL1-5 cells

first: Tse-Ming

last: Hong

address: 128 Academia Road, Section 2, Nankang

institute: Academia Sinica

description: cells were synchronized with double thymidine at G1/S phase

hyb_protocol: 0.3 μ g of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a Agilent SurePrint G3 Human GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: Scanned on an Agilent microarray scanner (Agilent Technologies, USA)

data_processing: Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: CL1-5/AS2neo G1/S

label_protocol: 0.2 μ g of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: CL1-5/AS2neo (control) and CL1-5/AS2neo-Slug stable cells were cultured in RPMI medium containing 10% FBS,  l-glutamine, and 400ug/ml G418

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

treatment_protocol: For double thymidine block and release experiments, cells were treated with 2 mM thymidine (Sigma) for 19 h and released for 9 h, followed by the second 16 h treatment before being harvested.

value: CL1-5/AS2neo (control)

source_name: CL1-5/AS2neo-Slug G1/S

value: CL1-5/AS2neo-Slug-WT stable cells


title: Dgat1-/-, ad libitum diet rep1


title: Wild-type, caloric restriction diet rep1


title: Sample 44P_ependymoma-250knsp

city: Nottingham

first: John-Paul

last: Kilday

address: Derby Road

department: CBTRC

country: United Kingdom

institute: University of Nottingham

description:
primary ependymoma, male, PF, 16.3yrs
S0398FL0008 nsp
Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labelled and hybridised to each array according to the manufacturer's instructions.

data_processing:
CEL files and CHP files (generated by Affymetrix GTYPE using the BRLMM algorithm) were processed by CNAG. Normalization was performed using the constitutional samples. Data processing was performed as described in Miller et al Neuro Oncol 2011;13(8):866-79.
Primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall;

source_name: primary ependymoma DNA sample from patient 44

extract_protocol: Genomic DNA was extracted snap frozen tumour tissue and mononuclear cell preparations  from peripheral blood, using a standard phenol/chloroform/isoamyl alcohol method. DNA quality and quantity was assessed using a Nandrop spectrophotometer and agarose gel electrophoresis.

tag: patient

tag: disease state

value: ependymoma

tag: ependymoma status

value: primary

value: male

tag: location

value: posterior fossa (PF)

tag: tumour grade

value: World Health Organisation Grade III

tag: patient outcome

value: Alive with disease progression

tag: tumour 1q gain status

value: 1q gain


title: pt #100 (Atopic Asthmatic), IL-17 (stimulated)

city: Winnipeg

first: Abdelilah

middle: S

last: Gounni

state: Manitoba

address: 750 McDermot Avenue

department: Department of Immunology

country: Canada

institute: University of Manitoba

hyb_protocol: Technical and platform specific procedures for the genome-wide, DNA-based whole transcript (WT) sense target (ST) Affymetrix HuGene v1.0 GeneChip were contracted to the University of Health Network Microarray Centre (UHNMC) Affymetrix Service.

data_processing: The quality control metrics were evaluated by the Affymetrix Expression Console software v1.1.1 and the expression data were normalized using the Robust Multichip Analysis (RMA) algorithm. Secondary analysis such as statistical filtering of expression results and the creation of gene lists was performed with the Partek Genomics Suite v6.3.

source_name: Human ASM, asthmatic, 2hr stimulation with IL-17 [10ng/ml]

growth_protocol: Human bronchial ASM cells were obtained by deep endobronchial biopsy from the right middle or lower lobe bronchi. ASM cells were grown at 37°C with 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS, 100U/ml penicillin and 100µg/ml streptomycin. For all experiments, human ASM cells were used between passages 3 and 5.

extract_protocol: Total RNA was extracted by the Qiagen RNeasy method, and RNA purity and integrity were evaluated by electrophoretic trace with the Agilent 2100 Bioanalyzer.

treatment_protocol: Confluent human bronchial ASM cells were growth-arrested by FBS-deprivation for 48h in DMEM media containing 5µg/ml of human recombinant insulin, 5µg/ml of human transferrin, 5ng/ml of selenium (ITS) and antibiotics. Cells were then stimulated in fresh FBS-free media with or without recombinant human IL-17 [10ng/ml] for 2 hours.

value: bronchial airway smooth muscle (ASM) cells

tag: treatment

tag: time point

value: 2 hrs

tag: patient identifier

tag: gender

tag: age

tag: smoker status

value: non-smoker

tag: health status

value: asthmatic

tag: therapy

value: salbutamol

tag: atopy

value: atopic

tag: allergen

value: cat, house dust mite


title: pt #100 (Atopic Asthmatic), Medium (unstimulated)

scan_protocol: Technical and platform specific procedures for the genome-wide, DNA-based whole transcript (WT) sense target (ST) Affymetrix HuGene v1.0 GeneChip were contracted to the University of Health Network Microarray Centre (UHNMC) Affymetrix Service.

source_name: Human ASM, asthmatic, 2hr unstimulated control condition

tag: cell type


title: pt #98 (Atopic Asthmatic), IL-17 (stimulated)

label_protocol: Technical and platform specific procedures for the genome-wide, DNA-based whole transcript (WT) sense target (ST) Affymetrix HuGene v1.0 GeneChip were contracted to the University of Health Network Microarray Centre (UHNMC) Affymetrix Service.

value: cat


title: Sample 44P_blood sample-250knsp

description:
blood
S0398FL0029 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 44

tag: patient

tag: disease state

value: blood


title: Sample 42P_blood sample-250knsp

description:
blood
S0398FL0026 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 42

value: Alive and no disease progression


title: Sample 45P_ependymoma-250knsp

description:
primary ependymoma, female, SP, 20.9yrs
S0398FL0020 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 45

value: ependymoma

tag: ependymoma status

value: female

tag: location

value: spinal (SP)

value: World Health Organisation Grade II

value: No 1q gain


title: pt #98 (Atopic Asthmatic), Medium (unstimulated)

value: male


title: Wild-type, ad libitum diet rep1

tag: tissue

value: liver

tag: strain

value: C57BL/6J background

tag: genotype/variation

value: Wild-type

value: 15-16 months

value: Female


title: pt #97 (Atopic Asthmatic), IL-17 (stimulated)

value: bronchial airway smooth muscle (ASM) cells

tag: treatment

tag: time point

value: 2 hrs

value: non-smoker

value: asthmatic

value: salbutamol

value: non-atopic


title: Sample 40P_blood sample-250knsp

description:
blood
S0398FL0027 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 40

value: blood

tag: gender

tag: tumour grade

tag: patient outcome

value: Alive with disease progression

tag: tumour 1q gain status


title: Sample 42P_ependymoma-250knsp

description:
primary ependymoma, male, SP, 15.3yrs
S0398FL0047 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 42

value: ependymoma

value: primary

value: spinal (SP)

tag: age

value: World Health Organisation Grade I

value: Alive and no disease progression


title: Sample 45P_blood sample-250knsp

description:
blood
S0398FL0044 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 45

value: female


title: Sample 38P_blood sample-250knsp

description:
blood
S0398FL0024 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 38

value: male


title: Sample 40P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 14.7yrs
S0398FL0005 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 40

value: posterior fossa (PF)

value: World Health Organisation Grade III

value: No 1q gain


title: pt #111 (Healthy Normal), IL-17 (stimulated)

source_name: Human ASM, healthy, 2hr stimulation with IL-17 [10ng/ml]

value: bronchial airway smooth muscle (ASM) cells

value: 2 hrs

tag: patient identifier

tag: smoker status

tag: health status

value: healthy

tag: therapy

tag: atopy


title: Sample 37P_blood sample-250knsp

description:
blood
S0398FL0040 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 37

tag: patient

tag: disease state


title: Sample 38P_ependymoma-250knsp

description:
primary ependymoma, male, SP, 14.6yrs
S0398FL0049 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 38

tag: ependymoma status

tag: location

value: World Health Organisation Grade II


title: pt #111 (Healthy Normal), Medium (unstimulated)

source_name: Human ASM, healthy, 2hr unstimulated control condition

tag: cell type

value: non-smoker

value: non-atopic

tag: allergen


title: Sample 43R1_blood sample-250knsp

description:
blood
epn061 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 43

value: blood

value: Dead of disease


title: pt #110 (Healthy Normal), IL-17 (stimulated)

tag: treatment

tag: time point


title: Sample 34P_blood sample-250knsp

description:
blood
S0398FL0039 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 34

tag: gender

tag: tumour grade


title: Sample 37P_ependymoma-250knsp

description:
primary ependymoma, female, ST, 13.8yrs
S0398FL0017 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 37

value: ependymoma

value: primary

value: supratentorial (ST)

tag: patient outcome

tag: tumour 1q gain status


title: pt #96 (Healthy Normal), IL-17 (stimulated)

tag: patient identifier

tag: age

value: ex-smoker


title: pt #97 (Atopic Asthmatic), Medium (unstimulated)

tag: smoker status

tag: health status

value: asthmatic

value: salbutamol


title: Sample 34P_ependymoma-250knsp

description:
primary ependymoma, female, ST, 12yrs
S0398FL0016 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 34

value: female


title: pt #110 (Healthy Normal), Medium (unstimulated)

value: male

tag: therapy

tag: atopy


title: Sample 41P_ependymoma-250knsp

description:
primary ependymoma, female, ST, 14.8yrs
ept152 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 41

tag: patient

tag: disease state

value: Alive and no disease progression

value: No 1q gain


title: Sample 32P_blood sample-250knsp

description:
blood
S0398FL0042 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 32


title: Sample 41P_blood sample-250knsp

description:
blood
epn152 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 41


title: Sample 36P_ependymoma-250knsp

description:
primary ependymoma, male, ST, 12.7yrs
ept134d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 36

tag: ependymoma status

tag: location

value: World Health Organisation Grade III

value: Alive with disease progression


title: pt #96 (Healthy Normal), Medium (unstimulated)

tag: cell type

value: bronchial airway smooth muscle (ASM) cells

value: 2 hrs

value: healthy

tag: allergen


title: Sample 43R1_ependymoma-250knsp

description:
recurrent ependymoma, male, ST, 15.5yrs
ept061 nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 43

value: recurrent

value: World Health Organisation Grade II

value: 1q gain


title: SCHT control 2

city: Barcelona

first: Sandra

last: Peiró

address: Aiguader 88

department: Programa de Recerca en Càncer

country: Spain

institute: IMIM-Hospital del Mar

description: Gene expression data from MDA-MB-231 cells

hyb_protocol: Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then SAM was applied to calculate significant differential expression between samples

source_name: Total RNA from MDA-MB-231 cells infected with a lentivirus shLOXL2

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

tag: knockdown

value: shControl

tag: cell line


title: SCHT control 1

source_name: Total RNA from MDA-MB-231 cells infected with a lentivirus shControl


title: Sample 32P_ependymoma-250knsp

description:
primary ependymoma, female, ST, 11.4yrs
S0398FL0018 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 32

value: ependymoma

value: primary

tag: gender

value: supratentorial (ST)

tag: tumour grade


title: Sample 31P_blood sample-250knsp

description:
blood
S0398FL0031 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 31

value: blood

tag: patient outcome

tag: tumour 1q gain status


title: SCHT control 3


title: LOXL2 2


title: Sample 35P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 12.2yrs
ept046 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 35

value: female

value: posterior fossa (PF)

tag: age


title: LOXL2 1


title: LOXL2 3


title: Sample 35R1_ependymoma-250knsp

description:
recurrent ependymoma, PF
S0296FL0023 nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 35


title: Sample 39P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 14.7yrs
ept047r nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 39

value: male

value: Alive and no disease progression


title: Sample 36P_blood sample-250knsp

description:
blood
epn134 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 36


title: Sample 33R1_ependymoma-250knsp

description:
recurrent ependymoma, female, ST, 12yrs
ept130d nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 33

value: World Health Organisation Grade III

value: No 1q gain


title: Sample 30P_blood sample-250knsp

description:
blood
S0398FL0032 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 30

value: Dead of disease


title: Sample 28P_blood sample-250knsp

description:
blood
S0398FL0028 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 28


title: Sample 31P_ependymoma-250knsp

description:
primary ependymoma, male, SP, 10.3yrs
S0398FL0010 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 31

value: spinal (SP)

value: World Health Organisation Grade I

value: Alive with disease progression


title: Sample 30P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 10yrs
S0398FL0011 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 30

value: World Health Organisation Grade II


title: Sample 29P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 10yrs
S0398FL0003 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 29


title: Sample 33R1_blood sample-250knsp

description:
blood
epn130 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 33


title: Sample 27P_blood sample-250knsp

description:
blood
S0398FL0043nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 27


title: Sample 28P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 9.8yrs
S0398FL0007 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 28


title: Sample 44P_blood sample-250ksty

description:
blood
S0398FL0029 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 44


title: Sample 45P_blood sample-250ksty

description:
blood
S0398FL0044 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 45


title: Sample 44P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 16.3yrs
S0398FL0008 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 44

value: 1q gain


title: Sample 45P_ependymoma-250ksty

description:
primary ependymoma, female, SP, 20.9yrs
S0398FL0020 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 45


title: Sample 42P_blood sample-250ksty

description:
blood
S0398FL0026 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 42