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Sample GSM824863 Query DataSets for GSM824863
Status Public on Nov 01, 2011
Title HA-h-DS15202
Sample type RNA
 
Source name Human Astrocytes-hippocampal
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HA-h
cell organism: human
cell description: astrocytes-hippocampal
cell karyotype: normal
cell lineage: ectoderm
cell sex: U
labexpid: RS17566
replicate: 2
Biomaterial provider ScienCell;1830
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 62.19462
2315102 54.7296
2315104 96.86781
2315105 35.37219
2315107 123.6997
2315112 55.60234
2315114 66.43954
2315116 55.17419
2315118 885.8661
2315120 260.4601
2315126 20.20743
2315132 3.22352
2315138 51.17496
2315140 35.84675
2315142 0.0005685489
2315144 5.807542
2315146 30.5732
2315148 47.87553
2315149 54.6741
2315150 149.4593

Total number of rows: 1384231

Table truncated, full table size 22780 Kbytes.




Supplementary file Size Download File type/resource
GSM824863_X_Hs_HAh_E_101230_02_RS17566_W.CEL.gz 22.9 Mb (ftp)(http) CEL
GSM824863_hg19_wgEncodeUwAffyExonArrayHahSimpleSignalRep2.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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