HCA Data Explorer

Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq

Updated July 19, 2023

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.

Daniel RamsköldKarolinska Institutetdaniel.ramskold@ki.se
Daniel Ramsköld (Principal Investigator)1
1Karolinska Institutet
Stephenson Asgton
Nejad Parisa
Schwartz Rachel

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/ccef38d7-aa92-4010-9621-c4c7b1182647

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1.ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75659/suppl/GSE75659_RAW.tar
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Analysis Portals

None

Project Label

AllelicExpressionPatterns

Species

2 species

Sample Type

specimens

Anatomical Entity

5 anatomical entities

Organ Part

5 organ parts

Selected Cell Types

3 cell types

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

2 development stages

Library Construction Method

Smart-seq2

Nucleic Acid Source

single cell

Paired End

false, true

Analysis Protocol

MultiSampleSmartSeq2_v2.2.6, SmartSeq2SingleSample_v5.1.5

File Format

6 file formats

Cell Count Estimate

1.3k

Donor Count

10
bai1,312 file(s)bam1,312 file(s)fastq.gz2,205 file(s)loom5 file(s)tar1 file(s)xlsx1 file(s)