Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA Sequencing of in vitro Day 6 mPGCLCs

ABSTRACT: Mouse Primordial Germ Cell Like Cells (mPGCLCs) are an in vitro model of the specification of mPGCs which happen around E6.25 in the developing mouse embryo. The aim of this study is the detection and profiling of mouse small RNAs via small RNA sequencing of E14-mESC-derived and Blimp1-GFP (BG5)-mESC-derived Day 6 mPGCLCs, each from diffent mouse strain backgrounds, alongside Day 6 non-PGCLC cells from E14, BG5 and Stella-GFP/Esg1-tdTomato (SGET) Embryoid Bodies. In particular, this study is aimed at the detection of small RNA length and first nucleotide biases.

ORGANISM(S): Mus musculus

PROVIDER: GSE196934 | GEO | 2022/10/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Small RNA Sequencing of GOF mPGCs and SGET mPGCLCs

Project description:Mouse Primordial Germ Cells (mPGCs) are the precursors of gametes specified around E6.25 in the developing mouse embryo. This process can be modelled in vitro using the mPGC-Like Cell (mPGCLC) differentiation protocol. The aim of this study is the detection and profiling of mouse small RNAs via small RNA sequencing of male E12.5 to E15.5 mPGCs and Day 6 SGET mPGCLCs. In particular, this study is aimed at the detection of small RNA length and first nucleotide biases, covering the time window for in vivo piRNA emergence.

2022-10-14 | GSE196851 | GEO

ATAC-seq of mESC treated with doxorubicin

Project description:E14 mESC were treated with doxorubicin

2021-05-21 | GSE168687 | GEO

scRNA-seq of in vitro differentiated D6 mPGCLCs

Project description:Germ cell specification is an elusive biological event, as it occurs in a small group of cells in the very early embryo (E6.5). In vitro differentiation of naive mouse Embryonic Stem Cells (mESCs) to mouse Primordial Germ Cell like cells (mPGCLCs) allows the mechanistic investigation of germ cell specification. The goal of this study is to profile of gene expression via single cell RNA sequencing throughout the differentiation protocol. In particular, this project aims at examining the transcriptional activation of the molecular networks that direct the epigenetic reprogramming of mPGCLCs.

2022-10-15 | GSE197335 | GEO

EZH2 and H3K27me3 ChIP-seq in E14 mouse embryonic stem cells harboring wildtype or mutant EZH2.

Project description:We report the occupancy and catalysis of wildtype and allosteric activation-decifient mutants of EZH2 in E14 mESC by ChIP-seq.

2018-03-06 | GSE111433 | GEO

Cyclosporin A and FGF signaling support the proliferation/survival of mouse primordial germ cell-like cells in vitro [bis-seq]

Project description:Primordial germ cells (PGCs) are the founding population of the germ cell lineage that undergo a multistep process to generate spermatozoa or oocytes. Establishing an appropriate culture system for PGCs is a key challenge in reproductive biology. By a chemical screening using mouse PGC-like cells (mPGCLCs), which were induced from mouse embryonic stem cells, we reported previously that forskolin and rolipram synergistically enhanced the proliferation/survival of mPGCLCs with an average expansion rate of ∼20-fold. In the present study, we evaluated other chemicals or cytokines to see whether they would improve the current mPGCLC culture system. Among the chemicals and cytokines examined, in the presence of forskolin and rolipram, cyclosporin A (CsA) and fibroblast growth factors (FGFs: FGF2 and FGF10) effectively enhanced the expansion of mPGCLCs in vitro (∼50-fold on average). During the expansion by CsA or FGFs, mPGCLCs comprehensively erased their DNA methylation to acquire a profile equivalent to that of gonadal germ cells in vivo, while maintaining their highly motile phenotype as well as their transcriptional properties as sexually uncommitted PGCs. Importantly, these mPGCLCs robustly contributed to spermatogenesis and produced fertile offspring. Furthermore, mouse PGCs (mPGCs) cultured with CsA ex vivo showed transcriptomes and DNA methylomes similar to those of cultured mPGCLCs. The improved culture system for mPGCLCs/mPGCs would be instructive for addressing key questions in PGC biology, including the mechanisms for germ cell migration, epigenetic reprogramming, and sex determination of the germline.

2021-02-16 | GSE151445 | GEO

Cyclosporin A and FGF signaling support the proliferation/survival of mouse primordial germ cell-like cells in vitro [RNA-seq]

2021-02-16 | GSE151444 | GEO

Deep transcriptome analysis of mouse embryonic fibroblast following simultaneous overexpression of Stella, Oct4 and Nanos2 (SON)

Project description:We constructed a polycistronic lentiviral vector to overexpress 3 germ cell specific genes (Stella, Oct4 and Nanos2) in mouse embryonic fibroblast (MEFs) and evaluated the transcriptome portrait in partially reprogrammed cells.We sequenced RNA samples from bulk cell population of two biological duplicates of MEF-GFP (control) and MEF-SON (overexpressed) 21 days post infection. Differential expression analysis of 50 M pair-end read per samples showed overexpression of neurogenesis, blood vessel and proliferation related genes and downregulation of chondroitin sulphate metabolic process, nitric oxide production and innate immune response genes. Examination of whole transcriptome following concurrent overexpression of Stella, Oct4 and Nanos2 in MEFs.

2016-07-30 | E-GEOD-77351 | biostudies-arrayexpress

ChIP_seq

Project description:Ctbp2 regulates exit from pluripotency via silencing of embryonic stem cell active genes during differentiation. We mapped the genome-wide occupancy of Ctbp2 by ChIP-seq in mESC (E14).

2015-06-30 | E-MTAB-2002 | biostudies-arrayexpress

Six in situ Hi-C libraries of control and mESC auxin-inducible degrons for Scc1 and Ring1b.

Project description:In this experiment, we've examined chromatin conformation differences of E14 mESC against cohesin and Ring1b degrons. We performed a modified in situ Hi-C protocol from (Rao et al., 2014) that can be found in detail at (Díaz et al., 2018). Samples were digested with MboI restriction enzyme. The aim of the experiment was to characterize the role of cohesin and polycomb on the 3D structure of mouse chromatin.

2020-01-23 | E-MTAB-7816 | biostudies-arrayexpress

RING1B calibrated ChIP-seq (cChIPseq) datasets for control mESCs and an Scc1-AID auxin-inducible degron.

Project description:We examined 3D chromatin structure in the absence of cohesin (Scc1-AID auxin-inducible degron) and a control line (E14-Tir1) and found that PRC1 core promoter component RING1B was one of the most enriched proteins. Hence, we performed calibrated ChIP-seq experiments on the control (E14-Tir1) and the Scc1-AID mESC lines with a spike in of HEK293 human cells to further study this relationship.

2020-01-23 | E-MTAB-7817 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data