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Sample GSM510557 Query DataSets for GSM510557
Status Public on Feb 17, 2010
Title NHDF-neo-DS11918
Sample type RNA
Source name Neonatal Human Dermal Fibroblasts
Organism Homo sapiens
Characteristics cell type: Neonatal Human Dermal Fibroblasts
Biomaterial provider Lonza;CC-2509
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 Neonatal Human Dermal 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 40.59967
2315102 52.74024
2315104 46.18861
2315105 31.37156
2315107 84.86355
2315114 99.91273
2315126 26.15345
2315132 9.431826
2315133 43.32208
2315134 1.208137
2315138 17.90356
2315140 13.56629
2315142 1.297075
2315144 6.373137
2315146 12.94342
2315148 92.44625
2315149 90.37112
2315150 58.99733
2315151 25.2881
2315153 20.71238

Total number of rows: 1384231

Table truncated, full table size 22842 Kbytes.

Supplementary file Size Download File type/resource
GSM510557_X_Hs_NHDFneo_E_091028_03_DS11918_W.CEL.gz 21.7 Mb (ftp)(http) CEL
GSM510557_wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep2.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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