Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA257422 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1536140.fastq.gz | Fastqsanger.gz | |||
| SRR1536135.fastq.gz | Fastqsanger.gz | |||
| SRR1536136.fastq.gz | Fastqsanger.gz | |||
| SRR1536137.fastq.gz | Fastqsanger.gz | |||
| SRR1536138.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We generated RRBS data to analyse the DNA methylation profiling among WT-AG-haESCs, DKO-AG-haESCs and round spermatids, we found deletion of H19 and Gtl2 DMRs do not change the methylation patterns in AG-haESCs base on all detected CpG sites.
2015-06-29 | GSE60075 | GEO
Project description:We generated RRBS data to analyse the DNA methylation profiling among WT-AG-haESCs, DKO-AG-haESCs and round spermatids, we found deletion of H19 and Gtl2 DMRs do not change the methylation patterns in AG-haESCs base on all detected CpG sites. We used round spermatids as control and analysed the DNA methylation profiles of all the cell lines were by RRBS.
2015-06-29 | E-GEOD-60075 | biostudies-arrayexpress
Project description:RNA seq result shows that WT-AG-haESCs and DKO-AG-haESCs samples are clustered together using hierarchical cluster both in the all expression genes and imprinting genes. This suggests that DKO of DMRs of H19 and Gtl2 do not change the overall gene expression patterns in AG-haESCs. We used round spermatids as control. Using RNA-seq, profile of all the expression genes and imprinting genes beteween different samples were analysed.
2015-06-29 | E-GEOD-60072 | biostudies-arrayexpress
Project description:Gene expression analysis in WT-AG-haESCs, DKO-AG-haESCs and round spermatids
| PRJNA257423 | ENA
Project description:RNA seq result shows that WT-AG-haESCs and DKO-AG-haESCs samples are clustered together using hierarchical cluster both in the all expression genes and imprinting genes. This suggests that DKO of DMRs of H19 and Gtl2 do not change the overall gene expression patterns in AG-haESCs.
2015-06-29 | GSE60072 | GEO
Project description:We found that the overall DNA methylation and hydroxymethylation in AG-haESCs are extremely low, and the downregulation of both de novo methyltransferase Dnmt3b and methylation maintenance enzyme Dnmt1was discovered responsible for this DNA hypomethylation. Further, our study discovered that the correction of DNA methylation can greatly reduce the incidence of diploidization and further improve the survival of semi-cloned mice produced from AG-haESCs.
2017-12-31 | GSE99588 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived WT and dKO round spermatids transcriptome profiling (RNA-seq) Methods: Adult WT and dKO round spermatids mRNA profiles mice were generated by deep sequencing, in dulplicate. 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. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and dKO round spermatids, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Adult wild type (WT) and dKO mouse round spermatids were generated by deep sequencing, in dulplicate, using Illumina GAIIx.
2014-07-03 | E-GEOD-59017 | biostudies-arrayexpress
Project description:The use of two inhibitors of Mek1/2 and Gsk3β (2i) promotes the generation of mouse diploid and haploid embryonic stem cells (ESCs) from the inner cell mass of biparental and uniparental blastocysts, respectively. However, a system enabling long-term maintenance of imprints in ESCs has proven challenging. Here, we report that usage of a two-step a2i (alternative two inhibitors of Src and Gsk3β, TSa2i) derivation/culture protocol results in the establishment of androgenetic haploid ESCs (AG-haESCs) with stable DNA methylation at paternal DMRs (differentially DNA methylated regions) up to passage 60 that can efficiently support generating mice upon oocyte injection. We also show coexistence of H3K9me3 marks and ZFP57 bindings with intact DMR methylations. Furthermore, we demonstrate that TSa2i-treated AG-haESCs are a heterogeneous cell population regarding paternal DMR methylation. Strikingly, AG-haESCs with late passages display increased paternal-DMR methylations and improved developmental potential compared to early-passage cells, in part through the enhanced proliferation of H19-DMR hypermethylated cells. Together, we establish AG-haESCs that can long-term maintain paternal imprints.
2022-01-26 | GSE168447 | GEO
Project description:Our lab first derived mouse androgenetic haploid embryonic stem cells (AG-haESCs) and demonstrated that AG-haESCs can be used as an “artificial spermatids” to generate gene-edited semi-cloned (SC) mice through intracytoplasmic injection (ICAHCI) into mature oocyte, even though the birth efficiency is very low. Further we proved that H19-DMR and IG-DMR were the main barrier to generate viable mice through androgenetic and parthenogenetic haESCs. More importantly, AG-haESCs mediated SC technology combined with CRISPR-Cas9 is a powerful tool to generate gene-modified mouse models and carry out genetic screening at organismal level. However, it is still not clear how the H19-DMR and IG-DMR coordinately regulate SC embryo development. Here, we found that the H19-DMR and IG-DMR regulate the development of SC embryos in spatio-temporal scales. Firstly, we found that the H19-DMR and IG-DMR are not indispensable for the development of preimplantation of SC embryos. Secondly, H19-DMR is essential for the development of SC embryos in mid-gestation and IG-DMR takes effect in late-gestation. Further, the maintenance of paternal H19-DMR methylation status and deletion of paternal H19 transcription unit play a key role in the structures and transport functions of SC embryo placenta. Importantly, AG-haESCs carrying triple deletions, including H19, H19-DMR and IG-DMR, can further improve the efficiency in generation of viable, normal-size, and fertile mice.
2019-09-17 | GSE132254 | GEO