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SRX18286094: GSM6734718: marmoset D2 PGCLCs, scRNAseq; Callithrix jacchus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 173M spots, 20.3G bases, 6.3Gb downloads

External Id: GSM6734718_r1
Submitted by: Biomedical Sciences, University of Pennsylvania
Study: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [scRNA-Seq 2]
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 iPSC and PGCLCs aggregates, and run single cell RNA-seq
Sample: marmoset D2 PGCLCs, scRNAseq
SAMN31757326 • SRS15777872 • All experiments • All runs
Library:
Name: GSM6734718
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC SINGLE CELL
Selection: cDNA
Layout: PAIRED
Construction protocol: To minimize the contamination with feeder cells, >30 colonies of cjiPSCs cultured on feeder layer were randomly picked under an inverted microscope. Aggregates were rinsed with PBS twice and dissociated into single cells with 0.1% trypsin/EDTA treatment for 15 min at 37°C with periodic pipetting. Cells were loaded into chromium microfluidic chips with the Chromium Next GEM Single Cell 3ʼReagent Kit (v3.1 chemistry) and then used to generate single-cell gel bead emulsions (GEMs) using the Chromium Controller (10× Genomics) according to the manufacturer's protocol. GEM-RT was performed in a C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module (Bio-Rad). All subsequent cDNA amplification and library construction steps were performed according to the manufacturer's protocol. Libraries were sequenced using a 2 × 150 paired-end sequencing protocol on an Illumina HiSeq 4000 or NovaSeq 6000 instrument. 10X genomics
Runs: 1 run, 173M spots, 20.3G bases, 6.3Gb
Run# of Spots# of BasesSizePublished
SRR22312589173,020,59920.3G6.3Gb2023-02-17

ID:
25294806

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