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Sample GSM510579 Query DataSets for GSM510579
Status Public on Feb 17, 2010
Title NHLF-DS12829
Sample type RNA
Source name Normal Human Lung Fibroblasts
Organism Homo sapiens
Characteristics cell type: Normal Human Lung Fibroblasts
term: BTO:0000161
Biomaterial provider Lonza;CC-2512
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 Normal Human Lung Fibroblasts
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 Feb 17, 2010
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 124.2998
2315102 163.213
2315104 219.1651
2315105 50.66746
2315107 180.0386
2315114 34.60439
2315126 41.42976
2315132 6.364586
2315133 138.272
2315134 5.535929
2315138 72.76247
2315140 32.21579
2315142 8.052311
2315144 8.94355
2315146 52.14858
2315148 210.5143
2315149 214.2223
2315150 133.6822
2315151 23.80187
2315153 62.55841

Total number of rows: 1384231

Table truncated, full table size 22730 Kbytes.

Supplementary file Size Download File type/resource
GSM510579_X_Hs_NHLF_E_091214_10_DS12829_W.CEL.gz 24.1 Mb (ftp)(http) CEL
GSM510579_wgEncodeUwAffyExonArrayNhlfSimpleSignalRep2.broadPeak.gz 21.1 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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