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Sample GSM472927 Query DataSets for GSM472927
Status Public on Nov 19, 2009
Title K562-DS11525
Sample type RNA
 
Source name chronic myeloid leukemia
Organism Homo sapiens
Characteristics cell type: chronic myeloid leukemia
term: BTO:0000664
Biomaterial provider ATCC;CCL-243
Treatment protocol not applicable
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 X_Hs_K562_E_090716_06_DS11525_W.CEL
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 Nov 18, 2009
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 116.4993
2315102 163.4553
2315104 211.9711
2315105 53.66581
2315107 316.0149
2315114 150.7008
2315126 15.02938
2315132 21.54066
2315133 90.52112
2315134 7.760967
2315138 52.83387
2315140 36.27748
2315142 22.07042
2315144 15.71262
2315146 177.883
2315148 156.4399
2315149 116.5959
2315150 66.13355
2315151 0.0007656456
2315153 38.83596

Total number of rows: 1384231

Table truncated, full table size 22792 Kbytes.




Supplementary file Size Download File type/resource
GSM472927_X_Hs_K562_E_090716_06_DS11525_W.CEL.gz 39.3 Mb (ftp)(http) CEL
GSM472927_wgEncodeUwAffyExonArrayK562SimpleSignalRep2.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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