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Sample GSM651575 Query DataSets for GSM651575
Status Public on Jan 07, 2011
Title HSMM-DS14430
Sample type RNA
Source name Normal Human Skeletal Muscle Myoblasts
Organism Homo sapiens
Characteristics cell type: Normal Human Skeletal Muscle Myoblasts
term: BTO:0000256
Biomaterial provider Lonza;CC-2580
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 Normal Human Skeletal Muscle Myoblasts
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 116.2305
2315102 170.2247
2315104 205.6744
2315105 58.2833
2315107 146.5646
2315112 86.70691
2315114 55.58508
2315116 38.17233
2315118 768.4794
2315120 318.4448
2315126 21.78977
2315132 3.359579
2315138 147.669
2315140 56.04846
2315142 12.81873
2315144 9.882079
2315146 51.98382
2315148 155.5944
2315149 171.0701
2315150 109.4366

Total number of rows: 1384231

Table truncated, full table size 22704 Kbytes.

Supplementary file Size Download File type/resource
GSM651575_X_Hs_HSMM_E_101115_09_RS17245_W.CEL.gz 23.5 Mb (ftp)(http) CEL
GSM651575_wgEncodeUwAffyExonArrayHsmmSimpleSignalRep2.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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