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Sample GSM472933 Query DataSets for GSM472933
Status Public on Nov 19, 2009
Title Caco-2-DS11539
Sample type RNA
Source name colorectal adenocarcinoma
Organism Homo sapiens
Characteristics cell type: colorectal adenocarcinoma
term: BTO:0000195
Biomaterial provider ATCC;HTB-37
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_CACO2_E_090723_06_DS11539_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 75.02592
2315102 50.99583
2315104 52.90764
2315105 24.73364
2315107 244.7712
2315114 85.23631
2315126 13.1474
2315132 2.073043
2315133 69.41128
2315134 2.825036
2315138 27.53923
2315140 19.99128
2315142 6.973084
2315144 15.19901
2315146 20.14789
2315148 131.7986
2315149 104.6331
2315150 63.99902
2315151 14.00731
2315153 30.92804

Total number of rows: 1384231

Table truncated, full table size 22774 Kbytes.

Supplementary file Size Download File type/resource
GSM472933_X_Hs_CACO2_E_090723_06_DS11539_W.CEL.gz 38.9 Mb (ftp)(http) CEL
GSM472933_wgEncodeUwAffyExonArrayCaco2SimpleSignalRep2.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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