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Sample GSM510551 Query DataSets for GSM510551
Status Public on Feb 17, 2010
Title HCPEpiC-DS12457
Sample type RNA
Source name Human Choroid Plexus Epithelial Cells
Organism Homo sapiens
Characteristics cell type: Human Choroid Plexus Epithelial Cells
Biomaterial provider ScienCell;1310
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 Human Choroid Plexus Epithelial Cells
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 114.223
2315102 115.2162
2315104 123.7408
2315105 54.52443
2315107 97.55746
2315114 30.99763
2315126 31.14977
2315132 5.969199
2315133 80.10986
2315134 2.312391
2315138 94.21674
2315140 45.75661
2315142 14.7583
2315144 20.71135
2315146 34.94601
2315148 177.7871
2315149 103.8986
2315150 108.455
2315151 11.33062
2315153 34.11383

Total number of rows: 1384231

Table truncated, full table size 22720 Kbytes.

Supplementary file Size Download File type/resource
GSM510551_X_Hs_HCPEpiC_E_091208_07_DS12457_W.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM510551_wgEncodeUwAffyExonArrayHcpeSimpleSignalRep2.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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