NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM580038 Query DataSets for GSM580038
Status Public on Aug 16, 2010
Title HVMF-DS13977
Sample type RNA
 
Source name Human Villous Mesenchymal Fibroblast Cells
Organism Homo sapiens
Characteristics cell type: Human Villous Mesenchymal Fibroblast Cells
Biomaterial provider ScienCell;7130
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_HVMF_E_100603_41_DS13977_W_3.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 Aug 16, 2010
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 75.53256
2315102 137.962
2315104 152.1878
2315105 35.3302
2315107 281.5361
2315112 66.99162
2315114 33.39556
2315116 15.5884
2315118 922.061
2315120 255.5036
2315126 19.67156
2315132 6.61657E-05
2315138 65.79353
2315140 15.30773
2315142 7.427053
2315144 10.08202
2315146 32.48304
2315148 140.3346
2315149 176.9716
2315150 89.70063

Total number of rows: 1384231

Table truncated, full table size 22742 Kbytes.




Supplementary file Size Download File type/resource
GSM580038_X_Hs_HVMF_E_100603_41_DS13977_W_3.CEL.gz 23.1 Mb (ftp)(http) CEL
GSM580038_wgEncodeUwAffyExonArrayHvmfSimpleSignalRep2.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