GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM472939 Query DataSets for GSM472939
Status Public on Nov 19, 2009
Title PANC-1-DS9955
Sample type RNA
Source name pancreatic carcinoma
Organism Homo sapiens
Characteristics cell type: pancreatic carcinoma
term: BTO:0000304
Biomaterial provider ATCC;CRL-146
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_PANC_E_090904_04_DS9955_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 40.7931
2315102 38.58757
2315104 49.46627
2315105 35.04691
2315107 80.31636
2315114 50.70929
2315126 4.606785
2315132 0.0001414525
2315133 13.32531
2315134 2.322976
2315138 24.67055
2315140 9.459569
2315142 4.883197
2315144 9.96216
2315146 19.50564
2315148 56.76915
2315149 64.82121
2315150 62.28246
2315151 8.152152E-05
2315153 9.883452

Total number of rows: 1384231

Table truncated, full table size 22851 Kbytes.

Supplementary file Size Download File type/resource
GSM472939_X_Hs_PANC_E_090904_04_DS9955_W.CEL.gz 21.6 Mb (ftp)(http) CEL
GSM472939_wgEncodeUwAffyExonArrayPanc1SimpleSignalRep1.broadPeak.gz 20.9 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