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Sample GSM580018 Query DataSets for GSM580018
Status Public on Aug 16, 2010
Title NHDF-Ad-DS12855
Sample type RNA
Source name Adult Normal Human Dermal Fibroblasts
Organism Homo sapiens
Characteristics cell type: Adult Normal Human Dermal Fibroblasts
Biomaterial provider Lonza;CC-2511,CC-2511T225
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_NHDFAd_E_100603_05_DS12855_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 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 92.022
2315102 269.969
2315104 344.3116
2315105 38.20655
2315107 409.9679
2315112 79.04745
2315114 70.34035
2315116 40.46089
2315118 1063.712
2315120 308.8369
2315126 24.45568
2315132 3.340734
2315138 46.04179
2315140 47.88472
2315142 23.90318
2315144 12.04399
2315146 53.27163
2315148 90.06583
2315149 130.1739
2315150 179.3068

Total number of rows: 1384231

Table truncated, full table size 22746 Kbytes.

Supplementary file Size Download File type/resource
GSM580018_X_Hs_NHDFAd_E_100603_05_DS12855_W.CEL.gz 23.4 Mb (ftp)(http) CEL
GSM580018_wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep2.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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