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Series GSE81402 Query DataSets for GSE81402
Status Public on Jul 04, 2016
Title Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration, and utilizes already available gene expression profiles to determine chromosomal aberrations.
Overall design RNA was extracted from different cell lines and analyzed for chromosomal stability using eSNP-Karyotyping
Contributor(s) Weissbein U, Egli D, Benvenisty N
Citation(s) 27385103
Submission date May 13, 2016
Last update date May 15, 2019
Contact name Uri Weissbein
Organization name Hebrew University of Jerusalem
Department Genetics
Lab Nissim Benvenisty Lab
Street address Haalon 4
City Pardess hana
State/province Please Select
ZIP/Postal code 37023
Country Israel
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (13)
GSM2151889 CSES9
GSM2151890 CSES7
GSM2151891 CSES22
BioProject PRJNA321469
SRA SRP075000

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81402_Samples_FPKM.txt.gz 3.8 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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