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Sample GSM510569 Query DataSets for GSM510569
Status Public on Feb 17, 2010
Title HCM-DS12592
Sample type RNA
Source name Human Cardiac Myocytes
Organism Homo sapiens
Characteristics cell type: Human Cardiac Myocytes
Biomaterial provider ScienCell;6200
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymterix Gene Chip Scanner 3000
Description Human Cardiac Myocytes
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
Submission date Feb 17, 2010
Last update date Apr 23, 2013
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platform ID GPL5188
Series (1)
GSE19090 Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Data table header descriptions
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
2315101 93.34138
2315102 30.74948
2315104 99.17622
2315105 45.10628
2315107 187.9716
2315114 64.2426
2315126 14.10288
2315132 2.102501
2315133 85.17484
2315134 7.325768
2315138 79.18551
2315140 48.71525
2315142 12.94868
2315144 7.721826
2315146 37.86769
2315148 147.1471
2315149 214.0738
2315150 58.75962
2315151 18.06858
2315153 35.64798

Total number of rows: 1384231

Table truncated, full table size 22727 Kbytes.

Supplementary file Size Download File type/resource
GSM510569_X_Hs_HCM_E_091214_04_DS12592_W.CEL.gz 23.8 Mb (ftp)(http) CEL
GSM510569_wgEncodeUwAffyExonArrayHcmSimpleSignalRep2.broadPeak.gz 21.1 Mb (ftp)(http) BROADPEAK
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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