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Sample GSM510525 Query DataSets for GSM510525
Status Public on Feb 17, 2010
Title AG09309-DS12357
Sample type RNA
Source name Adult human toe fibroblast
Organism Homo sapiens
Characteristics cell type: Adult human toe fibroblast
Biomaterial provider Coriell;AG09309
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 Adult human toe fibroblast
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 87.48103
2315102 126.7854
2315104 141.7072
2315105 62.71575
2315107 181.561
2315114 97.48502
2315126 42.6579
2315132 4.404825
2315133 107.253
2315134 3.408474
2315138 66.98732
2315140 33.02355
2315142 16.73958
2315144 14.07819
2315146 41.12859
2315148 167.4758
2315149 185.8801
2315150 113.2458
2315151 19.1684
2315153 74.91529

Total number of rows: 1384231

Table truncated, full table size 22729 Kbytes.

Supplementary file Size Download File type/resource
GSM510525_X_Hs_AG09309_E_091211_01_DS12357_W.CEL.gz 24.1 Mb (ftp)(http) CEL
GSM510525_wgEncodeUwAffyExonArrayAg09309SimpleSignalRep2.broadPeak.gz 21.1 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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