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Sample GSM424354 Query DataSets for GSM424354
Status Public on Sep 20, 2010
Title GM12762_RNAseq
Sample type SRA
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics coriell cell line repository identifier: GM12762
Biomaterial provider Coriell Cell Repositories
Treatment protocol None
Growth protocol Immortalized B cells were grown at a density of 5 x 105 cells/mL in RPMI 1640 with 15 % fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin.
Extracted molecule polyA RNA
Extraction protocol mRNA-Seq was performed as recommended by the manufacturer (Illumina). Briefly, poly(A) mRNA was fragmented and first strand cDNA generated using random hexamers. Following second strand cDNA synthesis, end repair, addition of a single A base, adaptor ligation, agarose gel isolation of ~200 bp cDNA and PCR amplification of the ~200 bp cDNA, the samples were sequenced using the Illumina Genome Analyzer.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
Description polyA RNA_RNAseq
Data processing For alignment of the short reads sequences to the human reference sequence (HG18) and identification of SNPs, we used the program MAQ (version 0.6.8)26. To minimize sequence errors, we used the first 40 of the 50 nucleotides in each sequence read for our analysis. For the alignment, we used the default settings of MAQ: allowing up to 2 mismatches per read and requiring that the mismatch base qualities to be less than 70. From the aligned reads with map quality scores of 30 or higher, we identified SNPs. For this analysis, we used only known SNPs in (dbSNP 129). To call a sample to be heterozygous at a SNP for our DAE analysis, we required that each allele to be represented in at least 5% of the total reads covering that locus. To determine the expression level of a gene, we calculated RPKM as per Mortazavi et al17.
Submission date Jul 01, 2009
Last update date May 15, 2019
Contact name Michael Patrick Morley
Phone 215-898-2026
Organization name Perelman School of Medicine at the University of Pennsylvania
Department Penn Cardiovascular Institute
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL9052
Series (1)
GSE16921 Polymorphic cis- and trans-regulation of human gene expression
Reanalyzed by GSE25840
SRA SRX014962
BioSample SAMN00007091

Supplementary file Size Download File type/resource 1.6 Gb (ftp)(http) MAP
GSM424354_GM12762_RPKM.txt.gz 453.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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