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Sample GSM580044 Query DataSets for GSM580044
Status Public on Aug 16, 2010
Title NHA-DS12805
Sample type RNA
 
Source name Normal Human Astrocytes
Organism Homo sapiens
Characteristics cell type: Normal Human Astrocytes
term: BTO:0000099
Biomaterial provider Lonza;CC-2565
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 X_Hs_NHA_E_100603_04_DS12805_W.CEL
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 Aug 16, 2010
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 84.16302
2315102 45.24306
2315104 62.92223
2315105 43.05798
2315107 234.5383
2315112 72.96291
2315114 18.87269
2315116 23.4535
2315118 726.6164
2315120 322.8129
2315126 23.62103
2315132 25.06822
2315138 66.16048
2315140 57.36051
2315142 9.811643
2315144 5.672628
2315146 35.42242
2315148 131.3528
2315149 148.5692
2315150 191.8776

Total number of rows: 1384231

Table truncated, full table size 22761 Kbytes.




Supplementary file Size Download File type/resource
GSM580044_X_Hs_NHA_E_100603_04_DS12805_W.CEL.gz 23.0 Mb (ftp)(http) CEL
GSM580044_wgEncodeUwAffyExonArrayNhaSimpleSignalRep2.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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