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Status |
Public on Oct 19, 2022 |
Title |
Chromatin structure programs between genetically matched PEF and porcine iPSCs |
Organism |
Sus scrofa |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
Somatic cells gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM), and chromatin remodeling has been proved to be involved in this process. To date, chromatin accessibility in porcine induced pluripotency stem cells (piPSCs) was less researched. Here, we explore the connection of chromatin accessibility and transcriptome between genetically matched PEF and piPSCs with high throughput sequencing (ATAC-seq and RNA-seq) approach. In addition, we acquire parent-of-origin chromatin loci and genes after blasting ATAC-seq and RNA-seq data with polymorphic SNP loci which derive from two parental genomes. As a result, we find 4,373 differentially expressed genes (DEGs), and 10,883 differential chromatin locus. Compared with PEF, the closed chromatin loci in piPSCs are tightly connected with the down-expressed genes, while the opened chromatin plays a limited role in the up-regulation of genes. Potential mechanisms of transcription factors (TF) in piPSCs reprogramming have been identified. Moreover, we find 77 parent-of-origin genes and 7 parent-of-origin chromatin loci commonly existed in PEF and piPSC; parent-of-origin chromatin accessibility is not related to the bias expression of RNA. These data reveal regulatory association between global or parent-of-origin chromatin accessibility and transcriptome, which provides new sight to research porcine iPSC reprogramming and genome imprinting.
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Overall design |
ATAC-seq were applied on PEF and piPScs,three replicates were performed for each group.
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Contributor(s) |
Jiang A, Zhang X, Liu H, Ma Y |
Citation(s) |
36233240 |
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Submission date |
Apr 25, 2021 |
Last update date |
Oct 21, 2022 |
Contact name |
Aiwen Jiang |
E-mail(s) |
2019205006@njau.edu.cn
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Phone |
+8618751969631
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Organization name |
Nanjing Agricultural University
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Street address |
Weigang
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City |
Nanjing |
State/province |
Jiangsu |
ZIP/Postal code |
210095 |
Country |
China |
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Platforms (1) |
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Samples (6)
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This SubSeries is part of SuperSeries: |
GSE173308 |
Chromatin structure and gene expression programs between genetically matched PEF and porcine iPSCs |
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Relations |
BioProject |
PRJNA725007 |
SRA |
SRP316255 |
Supplementary file |
Size |
Download |
File type/resource |
GSE173275_RAW.tar |
506.6 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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