GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM472937 Query DataSets for GSM472937
Status Public on Nov 19, 2009
Title NHEK-DS11474
Sample type RNA
Source name adult normal human epidermal keratinocytes
Organism Homo sapiens
Characteristics cell type: adult normal human epidermal keratinocytes
term: BTO:0000375
Biomaterial provider Lonza;CC-2501
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_NHEK_E_090904_06_DS11474_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 65.52843
2315102 105.993
2315104 88.94043
2315105 33.03221
2315107 111.0071
2315114 33.52438
2315126 10.67006
2315132 6.194337
2315133 36.19806
2315134 6.511759
2315138 22.07668
2315140 20.77744
2315142 9.069321
2315144 9.221787
2315146 27.86
2315148 124.2562
2315149 125.9167
2315150 51.89223
2315151 18.47481
2315153 8.331298

Total number of rows: 1384231

Table truncated, full table size 22800 Kbytes.

Supplementary file Size Download File type/resource
GSM472937_X_Hs_NHEK_E_090904_06_DS11474_W.CEL.gz 22.2 Mb (ftp)(http) CEL
GSM472937_wgEncodeUwAffyExonArrayNhekSimpleSignalRep1.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