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Sample GSM472942 Query DataSets for GSM472942
Status Public on Nov 19, 2009
Title HL-60-DS11733
Sample type RNA
Source name human promyelocytic leukemia cells
Organism Homo sapiens
Characteristics cell type: human promyelocytic leukemia cells
term: BTO:0000738
Biomaterial provider ATCC;CCL-240
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_HL60_E_091007_03_DS11733_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
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 78.51128
2315102 71.79176
2315104 64.67355
2315105 37.37754
2315107 192.8635
2315114 96.54028
2315126 12.02171
2315132 8.075378E-05
2315133 51.25281
2315134 8.945785
2315138 51.41387
2315140 21.10416
2315142 3.051503
2315144 24.66374
2315146 44.91217
2315148 93.25365
2315149 88.50983
2315150 45.47782
2315151 12.68741
2315153 19.16928

Total number of rows: 1384231

Table truncated, full table size 22817 Kbytes.

Supplementary file Size Download File type/resource
GSM472942_X_Hs_HL60_E_091007_03_DS11733_W.CEL.gz 22.7 Mb (ftp)(http) CEL
GSM472942_wgEncodeUwAffyExonArrayHl60SimpleSignalRep2.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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