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Series GSE154727 Query DataSets for GSE154727
Status Public on Oct 07, 2021
Title Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law
Organisms Mus musculus; Mus spretus
Experiment type Expression profiling by high throughput sequencing
Summary We investigated the cis-regulatory divergences in alternative splicing and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid mouse. By obtaining more than 240 million read pairs on average in each sample from 5 organs and ESC as well as published data in liver, we comprehensively analyzed the allelic splicing patterns across tissues in hybrid mice. We find that tissue-dependent regulation causing large splicing differences is highly conserved and likely functional, while splicing divergence mainly affects genes under relaxed selective constraints. Although cis-divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform could tolerate more mutations, which explains the paradoxical sequence conservation pattern in their exonic versus intronic splicing site flanking regions. Finally, we demonstrated that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attributed such buffering effect to trans-regulatory splicing efficiency.
Overall design High-throughput RNA-seq data of 5 organs (cerebral cortex, heart, kidney, lung, and spleen) and ESC from Female F1 hybrid mice (female C57BL/6J x male SPRET/EiJ).
High-throughput RNA-seq data of fibroblast cells from F1 hybrid mice with and without Pladienolide B treatment.
Contributor(s) Chen W
Citation(s) 34969779
Submission date Jul 20, 2020
Last update date Jan 06, 2022
Contact name Wei Chen
Organization name Southern University of Science and Technology
Department Department of Biology
Street address China
City Shenzhen
State/province --- Select a state ---
ZIP/Postal code 518055
Country China
Platforms (3)
GPL28892 Illumina HiSeq 2500 (Mus musculus; Mus spretus)
GPL28893 Illumina HiSeq 2000 (Mus musculus; Mus spretus)
GPL28894 Illumina NovaSeq 6000 (Mus musculus; Mus spretus)
Samples (18)
GSM4677953 Cortex_F1_rep1
GSM4677954 Cortex_F1_rep2
GSM4677955 Heart_F1_rep1
BioProject PRJNA647333
SRA SRP272580

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE154727_Cortex.allelic.SE.MATS.JC.txt.gz 1.7 Mb (ftp)(http) TXT 2.1 Mb (ftp)(http) TXT
GSE154727_DMSO.allelic.SE.MATS.JC.txt.gz 1.6 Mb (ftp)(http) TXT
GSE154727_ESC.allelic.SE.MATS.JC.txt.gz 2.1 Mb (ftp)(http) TXT 2.6 Mb (ftp)(http) TXT
GSE154727_F1_total.tpm.txt.gz 3.8 Mb (ftp)(http) TXT
GSE154727_Heart.allelic.SE.MATS.JC.txt.gz 1.2 Mb (ftp)(http) TXT 1.5 Mb (ftp)(http) TXT
GSE154727_Kidney.allelic.SE.MATS.JC.txt.gz 1.6 Mb (ftp)(http) TXT 2.0 Mb (ftp)(http) TXT
GSE154727_Liver.allelic.SE.MATS.JC.txt.gz 1.0 Mb (ftp)(http) TXT 1.2 Mb (ftp)(http) TXT
GSE154727_Lung.allelic.SE.MATS.JC.txt.gz 1.5 Mb (ftp)(http) TXT 1.8 Mb (ftp)(http) TXT
GSE154727_PladB.allelic.SE.MATS.JC.txt.gz 2.3 Mb (ftp)(http) TXT 150.3 Kb (ftp)(http) TXT 3.3 Mb (ftp)(http) TXT
GSE154727_Spleen.allelic.SE.MATS.JC.txt.gz 1.5 Mb (ftp)(http) TXT 1.8 Mb (ftp)(http) TXT
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