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Sample GSM651564 Query DataSets for GSM651564
Status Public on Jan 07, 2011
Title HBMEC-DS13806
Sample type RNA
Source name Human Brain Microvascular Endothelial Cells
Organism Homo sapiens
Characteristics cell type: Human Brain Microvascular Endothelial Cells
Biomaterial provider ScienCell;1000
Treatment protocol For WI-38 cell type, Tamoxifen treated replicates only: induce senescence, cells at 50-80% confluency are treated for 72 hours with 20nM 4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol). At harvest, greater than 95% of DNA synthesis is inhibited and the cells have an induced fusiform/round morphology with greater than 95% showing dramatic senescence-associated heterochromatic foci
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 Human Brain Microvascular Endothelial Cells
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 Jan 07, 2011
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 97.18933
2315102 38.79258
2315104 79.40105
2315105 27.19603
2315107 252.4815
2315112 72.06009
2315114 38.23056
2315116 22.94877
2315118 598.2764
2315120 292.8134
2315126 19.67068
2315132 2.552857
2315138 68.14211
2315140 39.81461
2315142 11.56355
2315144 14.15831
2315146 24.46116
2315148 129.5381
2315149 127.5026
2315150 60.4948

Total number of rows: 1384231

Table truncated, full table size 22737 Kbytes.

Supplementary file Size Download File type/resource
GSM651564_X_Hs_HBMEC_E_100901_11_RS16427_W.CEL.gz 23.0 Mb (ftp)(http) CEL
GSM651564_wgEncodeUwAffyExonArrayHbmecSimpleSignalRep2.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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