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Series GSE75659 Query DataSets for GSE75659
Status Public on Sep 26, 2016
Title Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Cellular heterogeneity can emerge from the expression of only one parental allele, however it has remained unknown to what degree patterns of random monoallelic expression of autosomal genes (aRME) are mitotically inherited (clonal) or stochastic (dynamic) in somatic cells. Here, we resolved this by applying allele-sensitive single-cell RNA-seq on primary mouse fibroblasts and in vivo human T-cells to simultaneously investigate clonal and dynamic aRME. Dynamic aRME affected a considerable portion of the transcriptome, with levels dependent on the cell’s transcriptional activity, but clonal aRME was surprisingly scarce (<1% of genes) and affected mainly lowly expressed genes. Consequently, the overwhelming portion of aRME occurs transiently and is scattered throughout somatic populations rather than, as previously hypothesized, confined to spatially restricted patches of clonally related cells.
 
Overall design Cells were collected from in vitro clonal expansions, or from tissue or blood, to study the effect of relatedness and cell size on allele-specific expression
 
Contributor(s) Reinius B, Mold J, Ramsköld D, Sandberg R
Citation(s) 27668657
Submission date Dec 03, 2015
Last update date Mar 20, 2019
Contact name Daniel Ramsköld
E-mail daniel.ramskold@ki.se
Organization name Karolinska Institutet
Lab Rickard Sandberg's group (rickard.sandberg@ki.se) (2008-2014); Rheumatology unit (2014-)
Street address Nobels väg 3
City Stockholm
ZIP/Postal code 17177
Country Sweden
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (1318)
GSM1961747 fibroblast.1.cl1
GSM1961749 fibroblast.2.cl1
GSM1961752 fibroblast.3.cl1
Relations
BioProject PRJNA304993
SRA SRP066963

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75659_RAW.tar 1.2 Gb (http)(custom) TAR (of TXT)
Raw data are available in SRA
Processed data provided as supplementary file

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