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Sample GSM510583 Query DataSets for GSM510583
Status Public on Feb 17, 2010
Title CMK-DS12393
Sample type RNA
Source name Human Acute Megakaryocytic Leukemia Cells
Organism Homo sapiens
Characteristics cell type: Human Acute Megakaryocytic Leukemia Cells
Biomaterial provider DSMZ;ACC-392
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 Acute Megakaryocytic Leukemia 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 85.25213
2315102 73.87242
2315104 64.5511
2315105 9.764589
2315107 42.19318
2315114 42.52189
2315126 26.20979
2315132 0.0005461704
2315133 26.67793
2315134 6.257375
2315138 38.95055
2315140 4.642241
2315142 13.91095
2315144 7.466884
2315146 33.68026
2315148 86.85564
2315149 71.92522
2315150 42.96101
2315151 23.03214
2315153 18.42102

Total number of rows: 1384231

Table truncated, full table size 22791 Kbytes.

Supplementary file Size Download File type/resource
GSM510583_X_Hs_CMK_E_091118_04_DS12393_W.CEL.gz 21.8 Mb (ftp)(http) CEL
GSM510583_wgEncodeUwAffyExonArrayCmkSimpleSignalRep1.broadPeak.gz 20.9 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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