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Sample GSM1252248 Query DataSets for GSM1252248
Status Public on Mar 18, 2014
Title Skeletal muscle mmPCR-Seq R1
Sample type SRA
 
Source name Skeletal muscle
Organism Homo sapiens
Characteristics tissue: Skeletal muscle
Extracted molecule total RNA
Extraction protocol Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
mmPCR-Seq libraries were prepared as previously described in Zhang R, et al. (Nature Methods 2013)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description library strategy: mmPCR-Seq
Data processing Aligned samples to reference genome (hg19) with STAR (v2.1.4)
Sorted aligned files (.sam) using Samtools (v0.1.18)
Performed variant calling using Samtools mpileup command
Calculated allelic ratio for each genomic loci by dividing the number of reads mapped to the non-ref allele divided by the total reads per site
Genome_build: hg19
Supplementary_files_format_and_content: Allelic read counts for each genomic loci and corresponding gene tested by mmPCR-Seq
 
Submission date Oct 28, 2013
Last update date May 15, 2019
Contact name Stephen Montgomery
E-mail(s) smontgom@stanford.edu
Organization name Stanford University
Street address 300 Pasteur Lane
City Stanford
ZIP/Postal code 94305
Country USA
 
Platform ID GPL15520
Series (1)
GSE51769 Allele-specific expression of multiple tissues
Relations
BioSample SAMN02384956
SRA SRX368963

Supplementary file Size Download File type/resource
GSM1252248_index8.R1.ase.txt.gz 27.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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