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Sample GSM510530 Query DataSets for GSM510530
Status Public on Feb 17, 2010
Title AG04449-DS12329
Sample type RNA
Source name Fetal buttock/thigh fibroblast
Organism Homo sapiens
Characteristics cell type: Fetal buttock/thigh fibroblast
Biomaterial provider Coriell;AG04449
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 Fetal buttock/thigh 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 98.95575
2315102 121.4684
2315104 92.02502
2315105 46.47482
2315107 120.335
2315114 59.61532
2315126 26.71661
2315132 3.54262
2315133 137.1672
2315134 6.536006
2315138 89.48887
2315140 57.85175
2315142 8.90646
2315144 11.08624
2315146 35.38794
2315148 272.2738
2315149 329.1805
2315150 142.1514
2315151 20.12703
2315153 42.46655

Total number of rows: 1384231

Table truncated, full table size 22743 Kbytes.

Supplementary file Size Download File type/resource
GSM510530_X_Hs_AG04449_E_091208_05_DS12329_W.CEL.gz 23.9 Mb (ftp)(http) CEL
GSM510530_wgEncodeUwAffyExonArrayAg04449SimpleSignalRep2.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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