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Sample GSM580042 Query DataSets for GSM580042
Status Public on Aug 16, 2010
Title HMF-DS13368
Sample type RNA
Source name Human Mammary Fibroblast
Organism Homo sapiens
Characteristics cell type: Human Mammary Fibroblast
Biomaterial provider ScienCell;7630
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_HMF_E_100603_21_DS13368_W_2.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 87.27184
2315102 98.75276
2315104 185.2058
2315105 28.74385
2315107 193.4077
2315112 52.85558
2315114 34.05513
2315116 25.32927
2315118 1064.164
2315120 282.3876
2315126 6.885297
2315132 4.310304
2315138 54.20642
2315140 33.17619
2315142 15.36055
2315144 14.83731
2315146 33.27098
2315148 96.59677
2315149 102.5899
2315150 104.4575

Total number of rows: 1384231

Table truncated, full table size 22752 Kbytes.

Supplementary file Size Download File type/resource
GSM580042_X_Hs_HMF_E_100603_21_DS13368_W_2.CEL.gz 22.9 Mb (ftp)(http) CEL
GSM580042_wgEncodeUwAffyExonArrayHmfSimpleSignalRep2.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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