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Sample GSM824859 Query DataSets for GSM824859
Status Public on Nov 01, 2011
Title HBVP-DS14834
Sample type RNA
 
Source name Human Brain Vascular Pericytes
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HBVP
cell organism: human
cell description: brain vascular pericytes
cell karyotype: normal
cell lineage: mesoderm
cell sex: U
labexpid: RS18997
replicate: 1
Biomaterial provider ScienCell;1200
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 http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwAffyExonArray
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
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
 
Submission date Oct 31, 2011
Last update date Apr 23, 2013
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
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
ID_REF
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
ID_REF VALUE
2315101 136.4194
2315102 38.80589
2315104 106.2893
2315105 28.34595
2315107 144.2052
2315112 82.82185
2315114 63.77589
2315116 91.77427
2315118 848.0351
2315120 545.1051
2315126 5.973821
2315132 2.390782
2315138 136.5007
2315140 76.0876
2315142 14.29293
2315144 8.083328
2315146 26.3964
2315148 122.8704
2315149 129.3207
2315150 107.7027

Total number of rows: 1384231

Table truncated, full table size 22735 Kbytes.




Supplementary file Size Download File type/resource
GSM824859_X_Hs_HBVP_E_110517_01_RS18997_W.CEL.gz 23.8 Mb (ftp)(http) CEL
GSM824859_hg19_wgEncodeUwAffyExonArrayHbvpSimpleSignalRep1.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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