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Sample GSM472914 Query DataSets for GSM472914
Status Public on Nov 19, 2009
Title Th1-DS7840
Sample type RNA
Source name primary human Th1 T cells
Organism Homo sapiens
Characteristics cell type: primary human Th1 T cells
term: BTO:0001678
Biomaterial provider None;(primary)
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_tH1_E_080131_05_DS7840_D.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 57.57796
2315102 39.27086
2315104 88.34881
2315105 48.65627
2315107 226.9741
2315114 88.56041
2315126 6.586935
2315132 0.0001024308
2315133 33.93043
2315134 3.335548
2315138 9.303139
2315140 19.679
2315142 2.714755
2315144 8.485552
2315146 14.2926
2315148 38.38991
2315149 38.51852
2315150 38.43829
2315151 2.472394
2315153 24.11831

Total number of rows: 1384231

Table truncated, full table size 22925 Kbytes.

Supplementary file Size Download File type/resource
GSM472914_X_Hs_tH1_E_080131_05_DS7840_D.CEL.gz 37.9 Mb (ftp)(http) CEL
GSM472914_wgEncodeUwAffyExonArrayTh1SimpleSignalRep1.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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