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Sample GSM824861 Query DataSets for GSM824861
Status Public on Nov 01, 2011
Title HSMMtube-DS15538
Sample type RNA
 
Source name Normal Human Skeletal Muscle Myoblasts
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HSMMtube
cell organism: human
cell description: skeletal muscle myotubes differentiated from the HSMM cell line
cell karyotype: normal
cell lineage: mesoderm
cell sex: U
labexpid: RS17572
replicate: 2
Biomaterial provider Lonza;CC-2580
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 http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwAffyExonArray
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
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
 
Submission date Oct 31, 2011
Last update date Apr 23, 2013
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
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
ID_REF
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
ID_REF VALUE
2315101 83.48087
2315102 219.1993
2315104 178.1578
2315105 38.15271
2315107 130.7704
2315112 68.86523
2315114 27.5068
2315116 23.96576
2315118 728.0997
2315120 322.2471
2315126 10.01025
2315132 5.400025
2315138 62.24412
2315140 43.31441
2315142 3.346546
2315144 8.840546
2315146 43.09455
2315148 84.98428
2315149 88.88186
2315150 92.35979

Total number of rows: 1384231

Table truncated, full table size 22753 Kbytes.




Supplementary file Size Download File type/resource
GSM824861_X_Hs_HSMM_E_101230_08_RS17572_W.CEL.gz 23.0 Mb (ftp)(http) CEL
GSM824861_hg19_wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep2.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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