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SRX16871060: GSM6432775: OF/IWR1 cjiPSC, shallow WGBS, rep2; Callithrix jacchus; Bisulfite-Seq
2 ILLUMINA (Illumina HiSeq 2000) runs: 98.3M spots, 11.3G bases, 3.9Gb downloads

External Id: GSM6432775_r1
Submitted by: Biomedical Sciences, University of Pennsylvania
Study: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [bisulfite-seq]
show Abstracthide Abstract
Reconstitution of germ cell fate from pluripotent stem cells provide the opportunities to understand the molecular underpinning of germ cell development. Here, we established a several culture methods of induced pluripotent stem cells (iPSCs) in common marmoset (Callithrix jacchus, cj), which stably propagate in an undifferentiated state. Notably, iPSCs cultured on feeder layer in the presence of a WNT signaling inhibitor upregulate genes related to ubiquitin-dependent protein catabolic process and acquire permissive state that readily differentiate into primordial germ cell-like cells (PGCLCs) bearing immunophenotypic and transcriptomic similarities to pre-migratory cjPGCs. Induction of cjPGCLCs accompanies transient upregulation of mesodermal genes and culminate in establishing primate-specific transcriptional network similar to humans and cynomolgus monkeys. Moreover, cjPGCLCs can be expanded in monolayer while retaining cellular state. Upon co-culture with mouse testicular somatic cells, these cells acquire DDX4+ early prospermatogonia-like state. Our findings provide a framework for understanding and reconstituting germ cell development in marmoset in vitro, which serve as an comparative tool and foundation for a preclinical model for human in vitro gametogenesis. Overall design: Harvest marmoset cjiPSC on feeder with IWR1, d4 cjPGCLCs and extension culture of cjPGCLCs at day30 and make bisulfite sequencing libraries to estimate the overall DNA methylation levels.
Sample: OF/IWR1 cjiPSC, shallow WGBS, rep2
SAMN30158674 • SRS14458843 • All experiments • All runs
Library:
Name: GSM6432775
Instrument: Illumina HiSeq 2000
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: RANDOM
Layout: SINGLE
Construction protocol: Cells were collected and lysed in 50 mM Tris (pH 8.0), 10 mM EDTA, 0.5% SDS, 100µg/ml Proteinase K. Then crude DNA was used to build methylation sequencing library according to the protocol of Pico Methyl-Seq Library Prep Kit (Zymo, #D5455). Then libraries were sequenced on Illumina HiSeq 2000. Pico Methyl-Seq Library Prep Kit.
Runs: 2 runs, 98.3M spots, 11.3G bases, 3.9Gb
Run# of Spots# of BasesSizePublished
SRR2085180919,553,2592.2G756.2Mb2023-02-17
SRR2085181078,781,0869G3.2Gb2023-02-17

ID:
23637907

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