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SRX9444985: GSM4886708: RL416: Day_13_Primed_32F; Homo sapiens; Bisulfite-Seq
4 ILLUMINA (Illumina HiSeq 1500) runs: 764.5M spots, 77.2G bases, 50.8Gb downloads

Submitted by: NCBI (GEO)
Study: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [WGBS 2]
show Abstracthide Abstract
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory. Overall design: Examination of genome-wide DNA methylation in human embryonic stem cells and different classes of induced pluripotent stem cells
Sample: RL416: Day_13_Primed_32F
SAMN16676906 • SRS7658906 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 1500
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: RANDOM
Layout: SINGLE
Construction protocol: Genomic DNA was isolated with the Qiagen Blood and Tissue Kit according to manufacturer's instructions. 0.5% (w/w) of unmethylated lambda phage DNA (Promega) was added to the sample genomic DNA for the purpose of an unmethylated control to measure the bisulfite non-conversion frequency in each sample. Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems). Single-end sequencing was performed on a HiSeq1500, NextSeq500 or NovaSeq.
Experiment attributes:
GEO Accession: GSM4886708
Links:
Runs: 4 runs, 764.5M spots, 77.2G bases, 50.8Gb
Run# of Spots# of BasesSizePublished
SRR12993492188,730,87619.1G12.5Gb2023-08-12
SRR12993493192,579,88519.5G12.8Gb2023-08-12
SRR12993494192,107,81019.4G12.8Gb2023-08-12
SRR12993495191,063,96419.3G12.8Gb2023-08-12

ID:
12341546

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