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Sample GSM824850 Query DataSets for GSM824850
Status Public on Nov 01, 2011
Title HBVSMC-RS18999
Sample type RNA
 
Source name Human Brain Vascular Smooth Muscle Cells
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HBVSMC
cell organism: human
cell description: brain vascular smooth muscle cells.
cell karyotype: normal
cell lineage: mesoderm
cell sex: F
labexpid: RS18999
replicate: 2
Biomaterial provider ScienCell;1100
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 92.06799
2315102 115.2292
2315104 120.7513
2315105 41.59647
2315107 83.09088
2315112 89.96616
2315114 24.84263
2315116 41.64501
2315118 1097.562
2315120 465.0859
2315126 34.7742
2315132 10.06856
2315138 91.36665
2315140 46.86072
2315142 19.48866
2315144 27.31327
2315146 38.90558
2315148 130.6205
2315149 146.0773
2315150 106.5105

Total number of rows: 1384231

Table truncated, full table size 22724 Kbytes.




Supplementary file Size Download File type/resource
GSM824850_X_Hs_HBVSMC_E_110517_03_RS18999_W.CEL.gz 23.7 Mb (ftp)(http) CEL
GSM824850_hg19_wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep2.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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