NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM824852 Query DataSets for GSM824852
Status Public on Nov 01, 2011
Title HMVEC-dAd-DS12957
Sample type RNA
 
Source name Adult Human Dermal Microvascular Endothelial Cells, Dermal-Derived.
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: HMVEC-dAd
cell organism: human
cell description: adult dermal microvascular endothelial cells.
cell karyotype: normal
cell sex: F
labexpid: RS19001
replicate: 2
Biomaterial provider Lonza;CC-2543,CC-3202
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 http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwAffyExonArray
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
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
 
Submission date Oct 31, 2011
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 73.2482
2315102 140.7678
2315104 96.47591
2315105 50.81652
2315107 91.76437
2315112 93.92982
2315114 31.41803
2315116 46.19753
2315118 993.973
2315120 361.479
2315126 18.95294
2315132 10.06756
2315138 98.82
2315140 58.07673
2315142 5.450705
2315144 5.928072
2315146 45.13161
2315148 125.1222
2315149 134.8653
2315150 102.6858

Total number of rows: 1384231

Table truncated, full table size 22731 Kbytes.




Supplementary file Size Download File type/resource
GSM824852_X_Hs_HMVECdAd_E_110517_05_RS19001_W.CEL.gz 23.2 Mb (ftp)(http) CEL
GSM824852_hg19_wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep2.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