NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM472932 Query DataSets for GSM472932
Status Public on Nov 19, 2009
Title HeLa-S3-DS11528
Sample type RNA
 
Source name cervical carcinoma
Organism Homo sapiens
Characteristics cell type: cervical carcinoma
term: BTO:0000568
Biomaterial provider ATCC;CCL-2.2
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_HELA_E_090723_05_DS11528_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
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 66.14257
2315102 62.96996
2315104 104.8163
2315105 40.98331
2315107 281.3573
2315114 161.9484
2315126 15.91146
2315132 3.737775
2315133 38.94946
2315134 7.593826
2315138 24.76925
2315140 17.63898
2315142 2.657854
2315144 10.59583
2315146 21.58861
2315148 264.9146
2315149 93.30891
2315150 44.03267
2315151 0.0004669919
2315153 11.60507

Total number of rows: 1384231

Table truncated, full table size 22802 Kbytes.




Supplementary file Size Download File type/resource
GSM472932_X_Hs_HELA_E_090723_05_DS11528_W.CEL.gz 39.0 Mb (ftp)(http) CEL
GSM472932_wgEncodeUwAffyExonArrayHelas3SimpleSignalRep2.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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap