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Sample GSM824860 Query DataSets for GSM824860
Status Public on Nov 01, 2011
Title HPAEC-DS12916
Sample type RNA
 
Source name Human Pulmonary Artery Endothelial Cells
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HPAEC
cell organism: human
cell description: pulmonary artery endothelial cells.
cell karyotype: normal
cell lineage: mesoderm
cell sex: F
labexpid: RS19002
replicate: 1
Biomaterial provider Lonza;CC-2530,CC-3162
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 95.73815
2315102 51.59027
2315104 103.581
2315105 35.49611
2315107 106.2069
2315112 115.0312
2315114 45.82335
2315116 49.0575
2315118 1341.756
2315120 518.5774
2315126 10.22534
2315132 0.0001273193
2315138 107.7953
2315140 49.71049
2315142 1.29097
2315144 3.574755
2315146 53.90919
2315148 135.157
2315149 125.5055
2315150 116.9535

Total number of rows: 1384231

Table truncated, full table size 22742 Kbytes.




Supplementary file Size Download File type/resource
GSM824860_X_Hs_HPAEC_E_110517_06_RS19002_W.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM824860_hg19_wgEncodeUwAffyExonArrayHpaecSimpleSignalRep1.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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