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Series GSE173275 Query DataSets for GSE173275
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
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.
 
Overall design ATAC-seq were applied on PEF and piPScs,three replicates were performed for each group.
 
Contributor(s) Jiang A, Zhang X, Liu H, Ma Y
Citation(s) 36233240
Submission date Apr 25, 2021
Last update date Oct 21, 2022
Contact name Aiwen Jiang
E-mail(s) 2019205006@njau.edu.cn
Phone +8618751969631
Organization name Nanjing Agricultural University
Street address Weigang
City Nanjing
State/province Jiangsu
ZIP/Postal code 210095
Country China
 
Platforms (1)
GPL22918 HiSeq X Ten (Sus scrofa)
Samples (6)
GSM5264600 PEF5
GSM5264601 PEF7
GSM5264602 PEF8
This SubSeries is part of SuperSeries:
GSE173308 Chromatin structure and gene expression programs between genetically matched PEF and porcine iPSCs
Relations
BioProject PRJNA725007
SRA SRP316255

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Supplementary file Size Download File type/resource
GSE173275_RAW.tar 506.6 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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