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SRX16848652: GSM6432358: FF cjiPSCs, rep2; Callithrix jacchus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 30.2M spots, 3.4G bases, 1.1Gb downloads

External Id: GSM6432358_r1
Submitted by: Biomedical Sciences, University of Pennsylvania
Study: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [bulk RNA-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: CjiPSCs cultured in the presence or absence of feeders, in the presence or absence of IWR1, were collected. Extension culture of cjPGCLCs were collected at day 30.
Sample: FF cjiPSCs, rep2
SAMN30153775 • SRS14453396 • All experiments • All runs
Library:
Name: GSM6432358
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: CjiPSCs cultured in the presence or absence of feeders, in the presence or absence of IWR1, were collected. To minimize the contamination of feeder cells, >30 colonies of cjiPSCs cultured on feeder layer colonies were randomly picked up under inverted microscope and pooled before isolation of total RNA. Total RNA was extracted by RNeasy Plus Micro Kit (#74034, QIAGEN). RNA-seq libraries were made by SMRT-Seq HT plus kit (#R400748, Takara) by following the protocol. Briefly, total RNA was quantified by Qubit and RNA integrity was checked by Tapstation. Then 1 ng RNA was used for cDNA conversion following one-step first-strand cDNA synthesis and double-stranded cDNA amplification protocol. cDNA was purified by AMPxp beads, concentration was measued by Qubit, and quality was checked by Tapstation. Next, 2 ng cDNA was used for library construction. Libraries were dual indexed and pooled by equal molecular concentration. 100-base pair reads were sequenced on Illumina Hiseq 2000.
Runs: 1 run, 30.2M spots, 3.4G bases, 1.1Gb
Run# of Spots# of BasesSizePublished
SRR2082924530,233,5963.4G1.1Gb2023-02-17

ID:
23614684

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