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Series GSE70874 Query DataSets for GSE70874
Status Public on Jan 20, 2017
Title Spontaneous single-copy loss of TP53 in human embryonic stem cells markedly increases cell proliferation and survival [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The potential safety issues related to the acquisition of common genomic aberrations in hPSC cultures are well-recognized, but these risks have not been evaluated for sporadic mutations. Here, we explore whether a sporadic mutation that spontaneously arose in a hESC culture consisting of a single-copy deletion of chr17p13.1 would confer a survival advantage to the mutant cells. Compared to wild-type cells with two normal copies of the chr17p13.1 region, the mutant cells displayed a selective advantage when exposed to stressful conditions, and retained a higher percentage of pluripotent cells after two weeks of in vitro differentiation. Knockdown of TP53, which is a gene encompassed by the deleted region, in wild-type cells mimicked the chr17p13.1 deletion phenotype. RNA sequencing analysis showed differential expression of genes in pathways related to proliferation and differentiation. Thus, phenotypic implications of sporadic mutations must be taken into consideration before using the hPSC for clinical applications.
Overall design Triplicate cDNA libraries of two mutant WA09 lines with a single-copy deletion of chr17p13.1, and two wild-type WA09 lines, for a total of 12 libraries were sequenced using Illumina HiSeq 2500. The sequence reads were mapped to hg19 reference genome and hits that passed quality filters were analyzed for differential expression.
Contributor(s) Morey RE, Amir H, Laurent LC
Citation(s) 27888558
Submission date Jul 14, 2015
Last update date May 15, 2019
Contact name Robert E Morey
Organization name UCSD
Department Pathology
Lab Parast
Street address 2880 Torrey Pines Scenic Dr
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1821002 Mutant2_1
GSM1821003 Mutant2_2
GSM1821004 Mutant2_3
This SubSeries is part of SuperSeries:
GSE70875 Spontaneous single-copy loss of TP53 in human embryonic stem cells markedly increases cell proliferation and survival
BioProject PRJNA289747
SRA SRP061037

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Supplementary file Size Download File type/resource
GSE70874_rmorey_processed_data.xlsx.gz 2.7 Mb (ftp)(http) XLSX
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Processed data are available on Series record
Raw data are available in SRA

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