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| Status |
Public on Jun 03, 2021 |
| Title |
Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Myofibers (primary and secondary myofiber) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibers to secondary myofibers, we conducted an integrative 3D structure of genome and transcriptomic characterization of longissimus dorsi muscle (LDM) of pig from primary myofiber formation stage [embryonic day 35 (E35)] to secondary myofiber formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains (TADs) are changed intra- domain interactions (D-scores) and 3,166 genes with differential promoter-enhancer interactions (PEIs) and (or) enhancer activation from E35 to E80. The alterations of genome architecture were found to affect expression of genes that play significant roles in neuromuscular junction (NMJ) and embryonic morphogenesis in E35, such as NEFL, BRINP1, NTNG1, and MuSK and that function on skeletal muscle development or metabolism, typically MYL1, SLN, Sox6 and Mef2D.
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| Overall design |
We designed the comparation between E35 and E80 by generating 6 in situ Hi-C libraries (3 vs 3), 6 RNA-seq libraries (3 vs 3),and 3 H3K27ac ChIP-seq data (2 vs1).
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| Contributor(s) |
Mo D, Li M, Yuan R |
| Citation(s) |
34009337 |
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| Submission date |
Feb 08, 2021 |
| Last update date |
Jun 03, 2021 |
| Contact name |
Renqiang Yuan |
| E-mail(s) |
yuanrq3@mail2.sysu.edu.cn
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| Organization name |
SUN YAT-SEN UNIVERSITY
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| Street address |
No. 135, Xingang Xi Road
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510275 |
| Country |
China |
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| Platforms (2) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA700585 |
| SRA |
SRP305313 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE166346_E35.true.whole.IS.tad.bed.gz |
22.5 Kb |
(ftp)(http) |
BED |
| GSE166346_E80.true.whole.IS.tad.bed.gz |
22.5 Kb |
(ftp)(http) |
BED |
| GSE166346_RAW.tar |
505.3 Gb |
(http)(custom) |
TAR (of BED, HIC, TXT) |
| GSE166346_quant_mRNA.tpm.txt.gz |
667.2 Kb |
(ftp)(http) |
TXT |
| GSE166346_whole.consensus.tad.Dscore.combine.txt.gz |
132.4 Kb |
(ftp)(http) |
TXT |
| GSE166346_whole.consensus.tad.merge.true.bed.gz |
20.4 Kb |
(ftp)(http) |
BED |
| GSE166346_whole.samples.20k.ABindex.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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