NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE269522 Query DataSets for GSE269522
Status Public on Jun 14, 2024
Title Identification of Circular RNAs Regulating Cardiomyocyte Proliferation in Neonatal Pig Hearts
Organism Sus scrofa
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Little is known about the expression patterns and functions of circular RNAs (circRNAs) in the heart of large mammals. In this study, we examined the expression profiles of circRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) in neonatal pig hearts. Pig heart samples collected on postnatal days 1 (P1), 3 (P3), 7 (P7) and 28 (P28) were sent for total RNA sequencing. Our data revealed a total of 7000 circRNAs in the 24 pig hearts. Pathway enrichment analysis of hallmark gene sets demonstrated that differentially expressed circRNAs are engaged in different pathways. The most significant difference was observed between P1 and the other three groups (P3, P7 and P28) in pathways related to cell cycle and muscle development. Out of the ten circRNAs that were validated through real-time quantitative polymerase chain reaction (qRT-PCR) to confirm their expression, six exhibited significant effects on cell cycle activity in human induced pluripotent stem cells-derived cardiomyocytes (hiPSC-CMs) following small interfering RNA-mediated knockdown. The circRNA-miRNA-mRNA networks were constructed to understand the potential mechanisms of circRNAs in the heart. In conclusion, our study provided a dataset for exploring the roles of circRNAs in pig hearts. In addition, we identified several circRNAs that regulate cardiomyocyte cell cycle.
 
Overall design To provided insights into the complex regulatory processes involving circRNAs, miRNAs, and mRNAs during postnatal heart development in newborn pigs, we performed RNA sequencing of mRNAs and noncoding RNAs including circRNAs and miRNAs using samples from neonatal pig hearts at different developmental stages (P1, P3, P7, and P28).
The heart samples were sent to two different companies for sequencing. In the first batch, 12 samples from animals of different ages (3 animals at each age) were sent to Novogene Inc. for circRNA sequencing (annotated as “nv1”). A second batch of 12 more samples was sent to CD Genomocs Inc. (annotated as “cd”) for total RNA sequencing. In the third batch, new samples from the same 12 animals in the first batch were sent to Novogene Inc. (annotated as “nv2”) for total RNA sequencing.
We validated the sequencing data using real-time quantitative polymerase chain reaction (qRT-PCR).
Differential expression analysis and pathway enrichment analysis were done using different bioinformatics tools. Functional experiments in the cultured cardiomyocytes via small interfering RNA (siRNA) mediated knockdown of selected circRNA candidates.
 
Contributor(s) Zhu W, Wang J, Tang L, Nyarige V, Li P
Citation(s) 38916964
Submission date Jun 10, 2024
Last update date Sep 16, 2024
Contact name Wuqiang Zhu
E-mail(s) zhu.wuqiang@mayo.edu
Phone 3179372632
Organization name Mayo Clinic
Department Cardiovascular Medicine
Street address 13400 E shea blvd
City Scottsdale
State/province AZ
ZIP/Postal code 85258
Country USA
 
Platforms (1)
GPL22475 Illumina HiSeq 4000 (Sus scrofa)
Samples (36)
GSM8318255 Pig heart tissue, Day1, Sample 1, Sequencing by Novogene, Round1
GSM8318256 Pig heart tissue, Day1, Sample 2, Sequencing by Novogene, Round1
GSM8318257 Pig heart tissue, Day1, Sample 3, Sequencing by Novogene, Round1
Relations
BioProject PRJNA1122191

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
GSE269522_circAtlas_pig_bed_v2.0.txt.zip 1.3 Mb (ftp)(http) ZIP
GSE269522_circAtlas_pig_sequence_v2.0.txt.zip 11.3 Mb (ftp)(http) ZIP
GSE269522_circAtlas_susScr11_susScr10_v2.0.txt.zip 2.0 Mb (ftp)(http) ZIP
GSE269522_merged_gene_counts.CD.tsv.gz 340.3 Kb (ftp)(http) TSV
GSE269522_miRNA_raw_CD.tsv.gz 11.0 Kb (ftp)(http) TSV
GSE269522_rawCounts_CIRCexplorer2.CD.txt.gz 324.1 Kb (ftp)(http) TXT
GSE269522_rawCounts_CIRCexplorer2.nvb1.txt.gz 498.5 Kb (ftp)(http) TXT
GSE269522_rawCounts_CIRCexplorer2.nvb2.txt.gz 280.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap