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Sample GSM580040 Query DataSets for GSM580040
Status Public on Aug 16, 2010
Title HCT-116-DS13547
Sample type RNA
Source name colorectal carcinoma
Organism Homo sapiens
Characteristics cell type: colorectal carcinoma
term: BTO:0002254
Biomaterial provider ATCC;CCL-247
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_HCT116_E_100603_32_DS13547_W_2.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 Aug 16, 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 60.01581
2315102 110.4904
2315104 136.9836
2315105 56.22241
2315107 259.7656
2315112 55.07088
2315114 36.31298
2315116 24.26717
2315118 430.1759
2315120 141.8901
2315126 15.1404
2315132 2.085225
2315138 95.95039
2315140 19.60486
2315142 10.60922
2315144 4.116009
2315146 26.14355
2315148 110.6785
2315149 27.87863
2315150 37.82621

Total number of rows: 1384231

Table truncated, full table size 22798 Kbytes.

Supplementary file Size Download File type/resource
GSM580040_X_Hs_HCT116_E_100603_32_DS13547_W_2.CEL.gz 22.0 Mb (ftp)(http) CEL
GSM580040_wgEncodeUwAffyExonArrayHct116SimpleSignalRep2.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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