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Sample GSM472923 Query DataSets for GSM472923
Status Public on Nov 19, 2009
Title SAEC-DS10518
Sample type RNA
Source name small airway epithelial cells
Organism Homo sapiens
Characteristics cell type: small airway epithelial cells
term: BTO:0002022
Biomaterial provider Lonza;CC-2547
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_SAEC_E_090716_02_DS10518_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 51.23209
2315102 41.86343
2315104 58.53455
2315105 18.6753
2315107 157.1686
2315114 43.10643
2315126 15.03063
2315132 0.0002836871
2315133 51.23408
2315134 2.651422
2315138 16.66969
2315140 16.34496
2315142 4.73446
2315144 22.89664
2315146 37.26553
2315148 180.7451
2315149 135.6254
2315150 53.34412
2315151 9.2725
2315153 6.56807

Total number of rows: 1384231

Table truncated, full table size 22811 Kbytes.

Supplementary file Size Download File type/resource
GSM472923_X_Hs_SAEC_E_090716_02_DS10518_W.CEL.gz 39.3 Mb (ftp)(http) CEL
GSM472923_wgEncodeUwAffyExonArraySaecSimpleSignalRep1.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

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