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Mus musculus

ABSTRACT: Single cell RNA-Seq of Hira-KO and control MII oocytes [Zp3-Cre]

PROVIDER: PRJNA296829 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2508872_1.fastq.gz	Fastqsanger.gz
	SRR2508872_2.fastq.gz	Fastqsanger.gz
	SRR2508873_1.fastq.gz	Fastqsanger.gz
	SRR2508873_2.fastq.gz	Fastqsanger.gz
	SRR2508874_1.fastq.gz	Fastqsanger.gz

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Mus musculus

Project description:Single cell RNA-Seq of Hira-KO and control MII oocytes [Gdf9-Cre+]

| PRJNA278394 | ENA

Single cell RNA-Seq of Hira-KO and control MII oocytes [Zp3-Cre]

Project description:The integrity of chromatin, which provides a dynamic template for all DNA-related processes in eukaryotes, is maintained through replication-dependent and -independent assembly pathways. To address the role of replication-independent histone deposition, we deleted the histone H3.3 chaperone Hira in developing mouse oocytes. We show that chromatin of non-replicative developing oocytes is highly dynamic, and that lack of continuous H3.3/H4 deposition alters chromatin structure, resulting in increased DNase I sensitivity, the accumulation of DNA damage, and, ultimately, a severe fertility phenotype. On the molecular level, abnormal chromatin structure leads to a dramatic decrease in the dynamic range of gene expression, the appearance of spurious transcripts, and inefficient de novo DNA methylation. In contrast to the only minor transcriptional phenotype observed in mouse pluripotent cells, we unequivocally show the importance of histone replacement and chromatin homeostasis for transcriptional regulation and normal developmental progression in an in vivo context. RNA-Seq on 4 Hiraf/f and 4 Hiraf/f, Zp3-Cre single MII oocytes.

2015-11-03 | E-GEOD-73381 | biostudies-arrayexpress

Single cell RNA-Seq of Hira-KO and control MII oocytes

Project description:Single cell RNA-Seq of Hira-KO and control MII oocytes

| PRJNA296825 | ENA

Comparing the Transcriptomes of Wild Type and Zp3-Cre mediated Mtor-Oocyte-Conditional Knockout (CKO) Mouse Metaphase II oocytes by RNA-Seq Analysis

Project description:The goal of this study is to identify the differentially expressed genes in Zp3-Cre mediated Mtor oocyte-specific knockout (CKO) Metaphase II (MII) oocytes by comparing the transcriptomes of Wild-Type (WT) and CKO Mouse MII oocytes via RNA-Seq Analysis. Methods: mRNA profiles of 3 sets of super-ovulated MII oocytes collected from 24-day old WT- and Mtor CKO female mice were generated by deep sequencing using an Illumina Hiseq2500 platform with 41bp single read. All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.8b). Reads aligned to genes are counted by cufflinks (v2.1.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.

2021-05-01 | GSE98548 | GEO

Single cell RNA-Seq of Hira-KO and control MII oocytes [Gdf9-Cre+]

Project description:The integrity of chromatin, which provides a dynamic template for all DNA related processes in eukaryotes, is maintained through replication dependent and independent assembly pathways. To address the role of replication independent histone deposition, we deleted the histone H3.3 chaperone Hira in developing mouse oocytes. We show that chromatin of non-replicative developing oocytes is highly dynamic, and that lack of continuous H3.3/H4 deposition alters chromatin structure, resulting in increased DNase I sensitivity, the accumulation of DNA damage, and, ultimately, a severe fertility phenotype. On the molecular level, abnormal chromatin structure leads to a dramatic decrease in the dynamic range of gene expression, the appearance of spurious transcripts, and inefficient de novo DNA methylation. In contrast to the only minor transcriptional phenotype observed in mouse pluripotent cells, we unequivocally show the importance of histone replacement and chromatin homeostasis for transcriptional regulation and normal developmental progression in an in vivo context. RNA-Seq on 4 Hiraf/f and 4 Hiraf/f, Gdf9-Cre+ single MII oocytes

2015-11-03 | E-GEOD-66931 | biostudies-arrayexpress

Single-cell proteomics in EIF5 knockout mouse GV oocytes at PD21

Project description:Changes in GV phase oocyte proteome after specific knockout of mouse oocytes with ZP3-cre

2024-04-15 | PXD051435 |

Tracing the derivation of embryonic stem cells from the inner cell mass by single cell RNA-seq analysis

Project description:Here we modified a single cell whole transcriptome amplification method to make it capable of amplifying cDNAs as long as 3kb efficiently and unbiasedly. We combined this modified single cell cDNA amplification method with Applied Biosystems next generation sequencing SOLiD™ System to set up a single cell whole transcriptome assay. The modified amplification strategy allows us to amplify full-length cDNAs for most of the expressed genes. We show that it is feasible to get digital gene expression profiles at single cell resolution. This allows us to ask fundamental biological questions that could not be addressed previously, especially in the embyronic stem cell studues , and to understand transcriptome complexity at the resolution of a single cell. Four-cell stage embryos were recovered from MF1 females mated with MF1 male mice (Nagy et al. 2003). The zona pellucida was removed by treatment with acidic tyrode solution. The individual blastomeres were separated by gentle pipeting using a glass capillary. Mature oocytes were isolated from Dicer knockout [Dicer-/Flox, Zp3-Cre] and Ago2 knockout [Ago2-/Flox, Zp3-Cre] female mice (14,17). Cumulus cells were removed from oocytes by treatment with hyaluronidase. All the ‘mature oocytes’ mentioned in the text are ovulated mature oocytes. RNA-Seq from 13 single mouse ES cells, 9 single mouse E3.5 ICM, 3 Day3-Oct4+ outgrowth, 3 Day5-Oct4+ outgrowth, 3 Day5-Oct4- outgrowth and 3 mouse E.4.5 Epiblast

2013-06-11 | E-GEOD-20187 | biostudies-arrayexpress

Shotgun proteomics of mouse oocytes

Project description:Shotgun mass spectrometric analysis of Cre control and CNOT7&8 KO GV oocytes

2023-09-28 | PXD039816 | JPOST Repository

Tracing the derivation of embryonic stem cells from the inner cell mass by single cell RNA-seq analysis

2010-05-10 | GSE20187 | GEO

Comparing the Transcriptomes of Wild Type (WT) and Gdf9-Cre or Zp3-Cre mediated Mtor Oocyte-Conditional Knockout (referred to as MG and MZ, respectively) Mouse GV-stage fully-grown oocytes (FGO) by RNA-Seq Analysis

Project description:The goal of this study is to identify the differentially expressed genes in Gdf9-Cre and Zp3-Cre mediated Mtor oocyte-specific knockout (CKO) GV-stage fully-grown oocytes (FGO) by comparing their transcriptomes with that of the wild-type (WT) via RNA-Seq Analysis.

2018-06-01 | GSE114126 | GEO

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