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Sample GSM510509 Query DataSets for GSM510509
Status Public on Feb 17, 2010
Title SKMC-DS11949
Sample type RNA
Source name Human skeletal muscle cells
Organism Homo sapiens
Characteristics cell type: Human skeletal muscle cells
term: BTO:0001801
Biomaterial provider Lonza;CC-2561
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 skeletal muscle cells
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 33.89538
2315102 41.30247
2315104 46.81337
2315105 11.88327
2315107 39.75831
2315114 20.02763
2315126 13.51578
2315132 0.0001375491
2315133 34.07731
2315134 3.544724
2315138 36.81305
2315140 25.14629
2315142 8.898912E-05
2315144 5.332354
2315146 9.71174
2315148 88.02171
2315149 55.59808
2315150 44.99301
2315151 12.88638
2315153 13.51042

Total number of rows: 1384231

Table truncated, full table size 22889 Kbytes.

Supplementary file Size Download File type/resource
GSM510509_X_Hs_SKMC_E_091028_05_DS11949_W.CEL.gz 21.6 Mb (ftp)(http) CEL
GSM510509_wgEncodeUwAffyExonArraySkmcSimpleSignalRep1.broadPeak.gz 21.0 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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