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Sample GSM472913 Query DataSets for GSM472913
Status Public on Nov 19, 2009
Title SK-N-SH_RA-DS8482
Sample type RNA
Source name neuroblastoma cell line differentiated w/ retinoic acid
Organism Homo sapiens
Characteristics cell type: neuroblastoma cell line differentiated w/ retinoic acid
term: BTO:0002372
Biomaterial provider ATCC;HTB-11
Treatment protocol not applicable
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_SKNS_E_080325_02_DS8482_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 Nov 18, 2009
Last update date Apr 23, 2013
Contact name ENCODE DCC
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
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
2315101 93.51455
2315102 68.22485
2315104 86.60756
2315105 68.57391
2315107 148.4446
2315114 35.56039
2315126 11.99133
2315132 6.315541
2315133 67.95157
2315134 7.884666E-05
2315138 41.57906
2315140 36.20554
2315142 21.62263
2315144 5.910578
2315146 23.48158
2315148 125.0296
2315149 79.93572
2315150 34.32179
2315151 5.08703
2315153 6.533514

Total number of rows: 1384231

Table truncated, full table size 22811 Kbytes.

Supplementary file Size Download File type/resource
GSM472913_X_Hs_SKNS_E_080325_02_DS8482_W.CEL.gz 39.2 Mb (ftp)(http) CEL
GSM472913_wgEncodeUwAffyExonArraySknshraSimpleSignalRep1.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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