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Sample GSM580006 Query DataSets for GSM580006
Status Public on Aug 16, 2010
Title HMEC-DS13921
Sample type RNA
Source name Human Mammary Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Human Mammary Epithelial Cells
term: BTO:0002178
Biomaterial provider Lonza;CC-3150
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_HMEC_E_100603_43_DS13921_W_3.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 53.30755
2315102 140.231
2315104 167.4354
2315105 46.35967
2315107 184.9908
2315112 34.27635
2315114 24.46107
2315116 25.51875
2315118 619.9135
2315120 143.5922
2315126 3.376242
2315132 0.0001917545
2315138 58.62709
2315140 13.63349
2315142 8.913064
2315144 9.836282
2315146 17.64657
2315148 61.60229
2315149 81.99025
2315150 73.0978

Total number of rows: 1384231

Table truncated, full table size 22773 Kbytes.

Supplementary file Size Download File type/resource
GSM580006_X_Hs_HMEC_E_100603_43_DS13921_W_3.CEL.gz 21.9 Mb (ftp)(http) CEL
GSM580006_wgEncodeUwAffyExonArrayHmecSimpleSignalRep2.broadPeak.gz 20.9 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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