NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM472919 Query DataSets for GSM472919
Status Public on Nov 19, 2009
Title HRE-DS10641
Sample type RNA
 
Source name human renal epithelial cells
Organism Homo sapiens
Characteristics cell type: human renal epithelial cells
term: BTO:0000059
Biomaterial provider Lonza;CC-2556
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_HRE_E_090616_04_DS10641_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 70.50901
2315102 73.75164
2315104 56.61198
2315105 31.31637
2315107 143.1174
2315114 48.17924
2315126 26.3852
2315132 14.73733
2315133 53.12899
2315134 5.139832
2315138 64.62421
2315140 43.81044
2315142 7.43579
2315144 9.000438
2315146 17.47916
2315148 124.2852
2315149 100.8797
2315150 91.46254
2315151 6.363339
2315153 23.9982

Total number of rows: 1384231

Table truncated, full table size 22846 Kbytes.




Supplementary file Size Download File type/resource
GSM472919_X_Hs_HRE_E_090616_04_DS10641_W.CEL.gz 38.7 Mb (ftp)(http) CEL
GSM472919_wgEncodeUwAffyExonArrayHreSimpleSignalRep1.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