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Sample GSM1262393 Query DataSets for GSM1262393
Status Public on May 13, 2015
Title RNA-seq_WT_hMSC_rep2
Sample type SRA
 
Source name Mesenchymal stem cell
Organism Homo sapiens
Characteristics cell type: Mesenchymal stem cell
genotype/variation: WT
Treatment protocol We sought to generate an isogenic human embryonic stem cell (hESC) line by knocking out the conserved 15th and 16th exons of WRN gene encoding for the DNA helicase domain of the WRN protein by helper-dependent adenoviral vector (HDAdV).
Growth protocol H9 hESCs (WiCell Research) and their WRN mutant derivatives were maintained on Mitomycin C treated mouse embryonic fibroblasts (MEFs) in hESC medium or on Matrigel (BD Biosciences) coated plates in mTeSR medium (STEMCELL Technology). Human bone marrow-derived MSCs were maintained in Minimum Essential Medium (MEM) Alpha Medium supplemented with 10% FBS, and 0.1 mM NEAA with or without 1ng/ml bFGF.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Total RNA extracted from cells
Data processing Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to gynab refference genome (hg19) using BWA software
Unique mapping reads were used to call peaks by MACS(v1.4) software
The abundance measurements were determined by RPKM with the fomula: RPKM=TR/(MR(million)*EL(KB)), TR is the total reads that mapped to the reference, MR is total number of the reads that mapped to one of the transcripts of the gene, EL is the length of the longest transcript of a gene.
Genome_build: hg19
Supplementary_files_format_and_content: bed files whilch include the peaks called by MACS(v1.4)
Supplementary_files_format_and_content: bedgraph files which depict the reads distribution among the genome
Supplementary_files_format_and_content: .txt files which include abundance measurements (RPKM)
 
Submission date Nov 12, 2013
Last update date May 15, 2019
Contact name Jingyi Li
E-mail(s) lijy201@gmail.com
Organization name Peking University
Street address Yiheyuan Road, No.5, Haidian District
City Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL11154
Series (1)
GSE52285 A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging
Relations
BioSample SAMN02401739
SRA SRX376714

Supplementary file Size Download File type/resource
GSM1262393_RNA-seq_WT_hMSC_rep2.txt.gz 290.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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