NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM824854 Query DataSets for GSM824854
Status Public on Nov 01, 2011
Title NHBE-DS11969
Sample type RNA
 
Source name Normal Human Bronchial Epithelial Cells w/RA
Organism Homo sapiens
Characteristics lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: NHBE
cell organism: human
cell description: bronchial epithelial cells
cell karyotype: normal
cell lineage: endoderm
cell sex: F
labexpid: RS19004
replicate: 2
Biomaterial provider Lonza;CC-2540,CC3170
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 111.9141
2315102 70.88254
2315104 80.14236
2315105 28.68424
2315107 60.64774
2315112 113.0099
2315114 30.46046
2315116 38.61956
2315118 623.4068
2315120 449.9391
2315126 33.05114
2315132 10.14845
2315138 219.2896
2315140 112.6987
2315142 27.96985
2315144 6.446228
2315146 20.28467
2315148 195.6463
2315149 173.7415
2315150 100.0496

Total number of rows: 1384231

Table truncated, full table size 22754 Kbytes.




Supplementary file Size Download File type/resource
GSM824854_X_Hs_NHBE_E_110517_08_RS19004_W_3.CEL.gz 23.1 Mb (ftp)(http) CEL
GSM824854_hg19_wgEncodeUwAffyExonArrayNhbeSimpleSignalRep2.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