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Sample GSM510510 Query DataSets for GSM510510
Status Public on Feb 17, 2010
Title MCF-7-DS12619
Sample type RNA
Source name mammary gland, adenocarcinoma
Organism Homo sapiens
Characteristics cell type: mammary gland, adenocarcinoma
term: BTO:0000093
Biomaterial provider ATCC;HTB-22
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 mammary gland, adenocarcinoma
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 109.0936
2315102 149.5801
2315104 123.0135
2315105 64.90694
2315107 155.1022
2315114 136.2269
2315126 32.19906
2315132 6.526488
2315133 98.55251
2315134 3.548559
2315138 95.4708
2315140 10.58527
2315142 13.13455
2315144 12.6772
2315146 34.29626
2315148 230.0184
2315149 270.2616
2315150 100.9641
2315151 16.5384
2315153 18.02046

Total number of rows: 1384231

Table truncated, full table size 22719 Kbytes.

Supplementary file Size Download File type/resource
GSM510510_X_Hs_MCF7_E_091214_06_DS12619_W.CEL.gz 24.3 Mb (ftp)(http) CEL
GSM510510_wgEncodeUwAffyExonArrayMcf7SimpleSignalRep2.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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