Whole-transcriptome sequencing of the chicken embryonic fibroblast, EGK.X blastoderm, and primordial germ cells
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ABSTRACT:
PROVIDER: PRJNA730716 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14575409_1.fastq.gz | Fastqsanger.gz | |||
| SRR14575409_2.fastq.gz | Fastqsanger.gz | |||
| SRR14575410_1.fastq.gz | Fastqsanger.gz | |||
| SRR14575410_2.fastq.gz | Fastqsanger.gz | |||
| SRR14575411_1.fastq.gz | Fastqsanger.gz |
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Project description:Eyal-Giladi and Kochav stage X (EGK.X) blastoderm mostly consists undifferentiated progenitor (pluripotent) cells that have the potency to differentiate into all cell types. Analyzing the transcriptional programs of blastoderm is critical to understand the molecular mechanisms that underlie the developmental fate of early embryos, and practical application of blastoderm-derived pluripotent cells, including ESC. Primordial germ cells (PGC) are also undifferentiated progenitor cells that later differentiate into male and female germ cells. Analyzing the transcriptional programs of PGC is critical to understand the molecular mechanisms that underlie the developmental fate of early germ cells, and practical application of PGC in generating transgenic chickens. Therefore, we performed whole-transcriptome sequencing (WTS) in the chicken EGK.X blastoderm and PGCs together with the chicken embryonic fibroblasts (CEF, as a reference sample). CEF are differentiated and an abundant somatic cells. The generated WTS data of CEF, EGK.X blastoderm and PGC are rich resources to utilize for various focused research. As a first focused research, we utilized the generated WTS data for analyzing the expression profiling of DNA repair and apoptosis pathway genes in EGK.X blastoderm and PGC compared with CEF. DNA is the fundamental unit of inheritance and is susceptible to damage by various exogenous and endogenous sources. When the DNA is damaged, the cell sense the nature of damage through multiple surveillance mechanisms and select an appropriate DNA repair pathway to repair the damage and avoid passing the damage to a progeny of cells. When the cell fails to repair DNA damage, cell cycle progression is halted and apoptosis is initiated. Despite several genes are involved in five major DNA repair pathways and two major apoptosis pathways, a comprehensive understanding on the expression of those genes are not well-understood in chicken tissues. Through WTS analysis in CEF, stage X blastoderm and PGC, we identified that most of the DNA repair pathway genes were expressed more high in blastoderm and high in PGC than CEF. At the other hand, most of the apoptosis pathway genes were expressed low in blastoderm and PGC than CEF.
2022-01-12 | GSE174603 | GEO
Project description:As germ cell precursor, primordial germ cells (PGCs) are widely used in transgenic animal production, regenerative medicine and other fields. However, the regulation mechanism of chicken PGCs is not incomplete, which leads to the insufficient amount of chicken PGCs obtained in vitro, which seriously affects the specific application of PGCs. During PGC formation (differentiation from ESCs to PGCs), some proteins have inconsistent changes in transcription level and protein abundance. Mediating proteasome degradation is one of the most important roles of protein ubiquitination, and enrichment analysis of transcriptome and proteome also suggests an important role of ubiquitination in the process of PGCs. In order to explore the important functions and potential targets of ubiquitination, we collected chicken ESCs and PGCs cells for label free ubiquitomics analysis. This study preliminarily analyzed how ubiquitination regulates the formation of chicken PGCs, providing a theoretical basis for the subsequent research and specific application of PGCs.
2025-09-08 | PXD052543 | Pride
Project description:The present investigation was to identify the signaling and metabolic pathways of expressed genes by microarray comparison between Primordial Germ Cells (PGCs) and their somatic counterpart, chicken embryonic fibroblasts (CEFs). We identified a total of 2,605 expressed transcripts. Among these, 1,197 were predominantly expressed in PGCs, and 1,408 were predominantly expressed in CEFs.
2013-01-10 | GSE38168 | GEO
Project description:In poultry, in vitro derived primordial germ cells (PGCs) represent an important tool for management of genetic resources. However, several studies have highlighted sexual differences exhibited by PGCs through in vitro steps, which may compromise their reproductive capacities. To understand this phenomenon, we compared the proteome of pregonadal chicken male (ZZ) and female (ZW) PGCs expanded in vitro by quantitative proteomic analysis using a GeLC-MS/MS strategy. The proteins found to be differentially abundant in chicken male and female PGCs indicated their early sexual identity. Many of the proteins up-accumulated in male PGCs were encoded by genes strongly enriched in the sexual chromosome Z. This suggests that the known lack of dosage compensation of the transcription of Z-linked genes between sexes persists at protein level in PGCs, and that this may be a key factor of their autonomous sex differentiation. Male and female PGCs up-accumulated protein sets were associated with differential biological processes, and contained proteins biologically relevant for male and female germ cell development respectively. This study presents first evidence on early predetermined sex specific cell fate of chicken PGCs that will help to understand their sexual physiological specificities and enable more precise sex-specific adaptation of in vitro culture conditions.
2021-11-03 | PXD022452 | Pride
Project description:To investigate the function of Lin28A and B in primordial germ cell (PGC) , we generated chicken PGCs in which Lin28A or B has been knocked out by CRISPR/Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cell types.
2023-05-15 | GSE232032 | GEO
Project description:The comparative transcriptomic analysis of chicken stem cells defines a chicken set of pluripotency associated genes that is almost coincident with mammalian pluripotency-assocaited genes. A total of 5944 differentially expressed unique identifiers (target IDs) were defined for CEF, 5942 for BM2 cells, 4550 for cES, 5465 for PGC and 5522 for cBC. Chicken Blastodermal cells (cBC) were taken from stage IX-XII (Eyal-Giladi & Kochav, 1976) embryos,chicken embryonic stem (cES) cells were established, amplified on inactivated STO feeder cells in proliferative medium containing cytokines and growth factors as described (Pain et al., 1996, Lavial et al., 2007). Long term cultured primordial germ cells (PGCs) were derived from 48h embryonic blood and maintained as described (McDonald et al., 2010). The non-tumorigenic BM2 monocytic cell line was grown as described (Solari et al., 1996). Primary chicken Embryonic fibroblasts (CEF) were prepared from 11-12 day old embryos according to standard protocols (Gandrillon et al., 1987), maintained and homogenised for 3-4 passages before being used as a somatic cell control. RNAs were extracted using Trizol (Invitrogen) according to the manufacturer and microarray analysis performed in biological triplicate.
2014-11-01 | E-GEOD-61221 | biostudies-arrayexpress
Project description:We report the chromatin status in chicken Embryonic stem cells（ESCs）, Primordial germ cells (PGCs) and Spermatogonial stem cells (SSCs). H3K4me2 antibody was used to collect DNA sequences through CHIP experiments, and the DNA was analyzed by next-generation sequencing. We mapped the genome-wide chromatin maps of chicken ESCs, PGCs, and SSCs. We found that the entire genome of H3K4me2 in ESCs, PGCs, and SSCs was erased and then reconstructed. Most of the enriched genes were related to the cell lineage. It is mainly enriched in distal intergenic. H3K4me2 in the promoter first enriches in ESCs, then decreases in PGCs. The enrichment rebuilds in SSCs. This study provides a basis for analyzing the differences of chromatin status in ESCs, PGCs, and SSCs.
2020-03-21 | GSE147255 | GEO
Project description:The aim of this investigation was to identify differentially expressed transcripts in chicken primordial germ cells (PGCs) compared with blastoderms, chicken embryonic fibroblasts (CEFs) and gonadal stromal cells (GSCs). Based on the P values (P < 0.05) and fold-change cutoff (4.0), several transcripts were differentially expressed in PGCs. However, we restricted our analysis to identify gene-matched transcripts only. Finally, we identified 1,505 differentially expressed transcripts in PGCs compared with blastoderms, 760 differentially expressed transcripts in PGCs compared with CEFs, and 466 differentially expressed transcripts in PGCs compared with GSCs.
2026-04-30 | GSE44534 | GEO
Project description:We used the MPSS technology to uncover gene expression profiling in a greater depth in the early embryonic gonads and primordial germ cells (PGCs) in the chicken. Total numbers of sequenced signatures were 1,012,533 and 995,676 for the PGCs and gonad. Using a false discovery rate cut-off of 0.05, we found 3.05 % of all signatures in the PCGs and 1.89 % of all signatures in the gonad signatures were significantly up-regulated compared to each sample. The MPSS result was very consistent with our previous result using EST data(http://chickgce.snu.ac.kr/). Keywords: cell type comparison
2007-03-01 | GSE5909 | GEO
Project description:The present investigation was to identify the signaling and metabolic pathways of expressed genes by microarray comparison between Primordial Germ Cells (PGCs) and their somatic counterpart, chicken embryonic fibroblasts (CEFs). We identified a total of 2,605 expressed transcripts. Among these, 1,197 were predominantly expressed in PGCs, and 1,408 were predominantly expressed in CEFs. Cell culture and microarray data generation were performed in triplicate. Blood PGCs from E2.5 embryos (N=20 for each replication) and CEFs from E6.5 embryos (N=5 for each replication) were cultured in appropriate culture medium. Total RNA was extracted from cultured PGCs (1,500,000 cells for each replication) and cultured CEFs (6,000,000 cells for each replication) with a Qiagen RNeasy kit. About 5 M-BM-5g of total RNA from each replication was used for labeling. Probe synthesis from total RNA samples, hybridization, detection, and scanning were performed according to standard protocols from Affymetrix.
2013-01-10 | E-GEOD-38168 | biostudies-arrayexpress