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Series GSE262348 Query DataSets for GSE262348
Status Public on Apr 01, 2024
Title NEMO Knockout Drives Variations in Gene Expression Regenerative Trajectory and Induces Chromatin Remodeling in murine muscle satellite cells during healing from traumatic injury
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary This study investigates the impact of NEMO knockout on healing from traumatic tibial injury within a murine muscle satellite cell model. NEMO KO mice were profiled via RNA-seq at 0, 2, 4, 7 days post cold shock injury (DPI). The largest transcriptional response was observed at 2 DPI within the WT model, but NEMO knockouts exhibited delayed myogenesis and muscle regenerative defects. Furthermore, it was observed that new fiber formation is defected upon transplantation of mutant derived MuSCs. mRNA profiling further suggested that loss of NF-kB signaling in MuSC’s in response to NEMO KO alters their ECM and cytokine secretome production. Additional profiling was performed at 2DPI via ATAC-seq within WT and NEMO mouse satellite cells, with observed changes in chromatin remodeling suggesting bidirectional MuSC-transcriptional regulator communication in skeletal muscle regeneration.
 
Overall design To investigate the impact of NEMO knockout on healing from muscle injury within murine muscle satellite cells, NEMO KO mice were profiled via RNA-seq at 0, 2, 4, 7 days post tibial injury. The largest transcriptional response was observed at 2 DPI, so additional profiling was performed at 2DPI via ATAC-seq within WT and NEMO mouse satellite cells.
 
Contributor(s) Aguilar C, Yang B, Shcherbina A, Mourkioti F
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Submission date Mar 24, 2024
Last update date Apr 01, 2024
Contact name Carlos Aguilar
E-mail(s) caguilar@umich.edu
Organization name University of Michigan - Ann Arbor
Department Dept. of Biomedical Engineering & Biointerfaces Institute
Lab NANO-OMIC-BIO-ENGINEERING-LAB
Street address 300 Pasteur Dr
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (20)
GSM8163670 Day0_SatelliteCells_biol_rep1_RNA
GSM8163671 Day0_SatelliteCells_biol_rep2_RNA
GSM8163672 Day0_SatelliteCells_biol_rep3_RNA
Relations
BioProject PRJNA1091379

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

Supplementary file Size Download File type/resource
GSE262348_RAW.tar 1.9 Gb (http)(custom) TAR (of BIGWIG, NARROWPEAK, TXT)
GSE262348_RSEM.genes.expected_count.tsv.gz 1.2 Mb (ftp)(http) TSV
GSE262348_RSEM.genes.fpkm.tsv.gz 1.2 Mb (ftp)(http) TSV
GSE262348_RSEM.isoforms.expected_count.tsv.gz 3.4 Mb (ftp)(http) TSV
GSE262348_RSEM.isoforms.fpkm.tsv.gz 3.0 Mb (ftp)(http) TSV
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