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Series GSE275835 Query DataSets for GSE275835
Status Public on Aug 31, 2024
Title The alternative splicing landscape of infarcted mouse heart identifies isoform level therapeutic targets
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Alternative splicing is an important process that contributes to highly diverse transcripts and protein products, which can affect the development of disease in various organisms. Cardiovascular disease (CVD) represents one of the greatest global threats to humans, particularly acute myocardial infarction (MI) and subsequent ischemic reperfusion (IR) injury, which involve complex transcriptomic changes in heart tissues associated with metabolic reshaping and immunological response. In this study, we used a newly developed ONT full-length transcriptomic approach and performed transcript-resolved differential expression profiling in murine models of MI and IR. We built an analytical pipeline to reliably identify and quantify alternative splicing products (isoforms), expanding on the currently available catalog of isoforms described in mice. The updated alternative splicing landscape included transcripts, genes, and pathways that were differentially regulated during IR and MI. Our study establishes a pipeline to profile highly diverse isoforms using state-of-the-art long-read sequencing, builds a landscape of alternative splicing in the mouse heart during MI and IR.
 
Overall design Cardiac tissue was sampled from myocardial infarction and ischemia-reperfusion mice, and sham-operated controls were set up separately. Using different sequencing methods, novel transcripts were identified and pairs of differential transcripts and genes were investigated.

Please note that Nanopore-based long-reads data (GSM8486343-GSM8486346) were used to identify novel transcripts and genes, therefore there is no coresponding data columns in the raw_count_gene.tsv and tpm_transcript.csv files.
 
Citation(s) 39424867
Submission date Aug 27, 2024
Last update date Oct 20, 2024
Contact name Xia Binbin
E-mail(s) xiabinbin18@mails.ucas.edu.cn
Organization name The Institute of Microbiology of the Chinese Academy of Sciences
Street address NO.1 Beichen West Road, Chaoyang District
City Beijing
State/province Beijing
ZIP/Postal code 100101
Country China
 
Platforms (2)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL26624 PromethION (Mus musculus)
Samples (20)
GSM8486327 ischemic reperfusion rep1
GSM8486328 ischemic reperfusion rep2
GSM8486329 ischemic reperfusion rep3
Relations
BioProject PRJNA1153372

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
GSE275835_raw_count_gene.tsv.gz 1.2 Mb (ftp)(http) TSV
GSE275835_tpm_transcript.csv.gz 7.9 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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