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Sample GSM510513 Query DataSets for GSM510513
Status Public on Feb 17, 2010
Title NB4-DS12538
Sample type RNA
Source name acute promyelocytic leukemia cell line
Organism Homo sapiens
Characteristics cell type: acute promyelocytic leukemia cell line
term: BTO:0002489
Biomaterial provider DMSZ;NB4
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 acute promyelocytic leukemia cell line
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 120.1301
2315102 202.0652
2315104 186.1071
2315105 28.08311
2315107 156.7828
2315114 109.4553
2315126 24.93936
2315132 15.85672
2315133 115.7374
2315134 8.104296
2315138 61.77879
2315140 29.59621
2315142 13.40215
2315144 12.53101
2315146 46.62153
2315148 165.7693
2315149 148.8763
2315150 57.23231
2315151 15.38273
2315153 35.13228

Total number of rows: 1384231

Table truncated, full table size 22736 Kbytes.

Supplementary file Size Download File type/resource
GSM510513_X_Hs_NB4_E_091214_02_DS12538_W.CEL.gz 23.8 Mb (ftp)(http) CEL
GSM510513_wgEncodeUwAffyExonArrayNb4SimpleSignalRep2.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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