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WGBS on prospermatogonia at E18.5

ABSTRACT: WGBS on prospermatogonia at E18.5

PROVIDER: PRJNA682750 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13202262_1.fastq.gz	Fastqsanger.gz
	SRR13202262_2.fastq.gz	Fastqsanger.gz
	SRR13202263_1.fastq.gz	Fastqsanger.gz
	SRR13202263_2.fastq.gz	Fastqsanger.gz
	SRR13202264_1.fastq.gz	Fastqsanger.gz

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WGBS on prospermatogonia at E18.5

Project description:To evaluate the impact of the Dnmt3C, Dnmt3L and Dnmt3A mutations in the methylome of male germ cells, mutant and control whole genome bisulfite sequencing experiments were conducted starting from genomic DNA obtained from FACS-sorted germ cells.

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Single-Cell Transcriptome Analysis of Rb1 Conditional Knockout Prospermatogonia

Project description:Prospermatogonia, precursors to the mature male germline, undergo a period of sustained quiescence during late fetal and early postnatal development. The purpose of this mitotic arrest is not fully understood. Therefore, utilizing conditional ablation of retinoblastoma protein 1 (Rb1) in mice which blocks entry into quiescence, we analyzed prospermatogonia at the cusp of mitotic arrest at embryonic day 14.5. Prospermatogonia from heterozygous controls or conditional knockout males were isolated via fluorescence-activated cell sorting and profiled via single-cell RNA-sequencing (scRNA-seq). Outcomes of scRNA-seq analysis revealed that a metabolic shift to oxidative phosphorylation and meiotic inhibition are disrupted in prospermatogonia that fail to initiate quiescence. Collectively, these findings and others suggest that biosensing mechanisms eliminate prospermatogonia that fail to mitotically arrest and that key layers of programming are applied during quiescence to ensure proper fate specification.

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CUT&RUN of TAF4b and H3K4me3 in E16.5 prospermatogonia

Project description:Taf4b-deficient male mice are initially sub-fertile and become infertile due to a depletion of the spermatogonial stem cell (SSC) reserve. During embryonic time points, significantly reduced numbers of germ cells have been observed in the Taf4b-deficient male gonad and previous research has shown that Taf4b mRNA expression peaks at E15.5. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates cell cycle and SSC gene programs. However, the direct targets of TAF4b have not been thoroughly explored. Therefore, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in E16.5 mouse prospermatogonia.

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e18.5 pancreas: WT vs Cyp11a1 KO

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RNA-seq from lung E18.5

Project description:RNA-seq from lung E18.5

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Prospermatogonia transcriptome changes in Taf4b-deficient male mice

Project description:Prospermatogonia transcriptome changes in Taf4b-deficient male mice

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Transcriptome of E18.5 CHD4-M195I mouse hearts

Project description:Purpose: The goal of this study is to compare the cardiac transcriptome profiling (RNA-seq) of WT and CHD4-M195I hearts at E18.5 to conclude genes affected by this CHD4 mutation. Methods: mRNA profiles of E18.5 WT and CHD4-M195I mouse hearts were generated by deep sequencing, n=4 for each genotype, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: RNA-sequencing (RNA-seq) analyses on E18.5 WT and CHD4-M195I hearts and identified 323 genes that were differentially expressed [adjusted P value <0.05, |log2(Fold Change)| > 0.5], 113 upregulated and 210 downregulated in CHD4-M195I hearts.

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Project description:RNA expression microarray analysis of prospermatogonia in 15 day post-conceptus (dpc) fetuses, a stage when they are undergoing rapid de novo DNA methylation. For comparison, we also analysed 15 dpc pachytene oogonia, 15 dpc female and male gonadal somatic cells, and adult pachytene spermatocytes.

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