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Sample GSM824856 Query DataSets for GSM824856
Status Public on Nov 01, 2011
Title NTERA-2cl.D1-DS14575
Sample type RNA
 
Source name Malignant pluripotent embryonal carcinoma, NTERA-2 cl.D1 (PMID: 6694356)
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: NT2-D1
cell organism: human
cell description: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356)
cell karyotype: cancer
cell lineage: inner cell mass
cell sex: M
labexpid: RS19006
replicate: 2
Biomaterial provider ATCC;CRL-1973
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 182.162
2315102 425.641
2315104 303.9181
2315105 62.73753
2315107 316.5981
2315112 90.93594
2315114 60.12361
2315116 117.7853
2315118 1241.439
2315120 543.9142
2315126 26.19274
2315132 11.66264
2315138 131.7886
2315140 56.36021
2315142 10.28861
2315144 25.71021
2315146 51.13822
2315148 157.3652
2315149 169.5553
2315150 91.30434

Total number of rows: 1384231

Table truncated, full table size 22710 Kbytes.




Supplementary file Size Download File type/resource
GSM824856_X_Hs_Ntera2_E_110517_10_RS19006_W.CEL.gz 24.3 Mb (ftp)(http) CEL
GSM824856_hg19_wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep2.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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