RNA-seq data of Spermatogonia cells of Tet1-ko and WT
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE140014 | GEO | 2020/01/18
REPOSITORIES: GEO
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Project description:We analysed 2 samples of mouse spermatogonia cells including 3-month-old WT and 3 month-old Tet1
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Project description:RNA-seq data of Spermatogonia cells of Tet1-ko and WT
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Project description:Histone modification and DNA methylation among epigenetic modifications play a coordinated role in the regulation of spermatogonia. Tet methylcytosine dioxygenase 1 (TET1) can either act as a DNA demethylase, converting 5-methylcytosine to 5-hydroxymethylcytosine or regulate gene expression by forming a complex with other proteins. Increased levels of H3K27me3 will result in transcriptional repression and reduced or silenced protein expression. However, the mechanism by which TET1 mediates the regulation of H3K27me3 in spermatogonia and the target genes that act is not clear. The results of this study showed that the expression of self-renewal-related gene GFRA1 and proliferation-related gene PCNA were up-regulated after JMJD3 overexpression. Moreover, it was demonstrated that TET1 and JMJD3 can interact with H3K27me3 by forming a protein complex, and the CHIP-Seq sequencing results analyzed that TET1 targets and regulates the Pramel3 gene when interacting with H3K27me3, and TET1 overexpression promotes the up-regulation of Pramel3 expression. Our study identified a novel link between TET1 and H3K27me3 and established a TET1-JMJD3-H3K27me3-Pramel3 regulatory axis to regulate spermatogonia self-renewal, proliferation and differentiation. It provides a new idea to further investigate the mechanism of spermatogenesis and spermatogenic disorders from the epigenetic level.
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Project description:Loss of Tet1 expression causes global 5mC and 5hmC changes in stem and progenitor cells in mice and causes enhanced Pro-B cell self-renewal, increased DNA damage and B-lymphomageneis. In this study we performed microarray analysis of total LSK cells from WT and Tet1 KO mice. These results revealed that genes regulated byTet1 in LSKs included Histones, DNA repair enzymes and B-lineage specific factors. LSK cells were purified from the bone marrow of 6-month old WT and Tet1 KO mice . RNA was extracted using RNeasy kit (Qiagen) and hybridized on Affymetrix microarrays. Microarray profiling of LSK cells in WT and Tet1 KO mice.
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Project description:Chip-seq data of mouse Spermatogonia cells of Tet1-ko and WT
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Project description:Loss of Tet1 expression causes global 5mC and 5hmC changes in stem and progenitor cells in mice and causes enhanced Pro-B cell self-renewal, increased DNA damage and B-lymphomageneis. In this study we performed reduced representative bisulfite sequencing (RRBS) of DNA from WT and Tet1 KO LSK cells. DNA methylation sequencing was performed and analyzed using an enhanced reduced representation (ERRBS) methodology as previously described. DNA was extracted from purified LSK cells of 6-month old WT and Tet1 KO mice, Bisulphite treatment was performed using the EZ DNA Methylation Kit (Zymo Research). Libraries were amplified according to illumina protocols and sequenced on an Illumina HiSeq2500 machine DNA methylation profiling of LSK cells in WT and Tet1 KO mice.
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Project description:By analyzing the sequencing results of RNA-seq, we found that TET1 maintains self-renewal of mouse spermatogonia and promotes cellular transcription and enhances cellular activity, and we identified key differential genes that are specifically affected by TET1 and the mechanism of interaction between these key differential genes, providing a scientific basis for studying spermatogenesis, revealing the causes of spermatogenic disorders, and elucidated the mechanisms, which may contribute to the understanding of male reproductive disorders.
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Project description:This batch of data is for three independent projects. Since in this three projects, the mouse strains are all CD1/ICR, the sex are both female, and the mouse ages are all two-month-old, three projects shared control data to save expenditure legitimately. But in our hand we couldn't segregate the raw data into two parts corresponding to two projects, so we uploads all raw data. However, we also provided researcher-analyzable excel files including the expression of all phosphorylated proteins. The concise description of these three projects are as follow: Project 1: We found that in Chronic Resistant Stress (CRS)-treated mice, the fertility and oocyte quality significantly decreased, and plenty of biochemical indexes significantly changed, so we guessed that the overall physical health of CRS mice was severely impacted. As one major strategy to investigate the mechanism how CRS impact the physical health, We chose TMT-labeled quantitative ovarian phosphoproteomics service from Hangzhou PTM Bio Co. We sent two repeats of two-month-old CRS CD1/ICR mouse ovaries and two repeats of control ovaries for characterization of differentially phosphorylated proteins. Each repeat contained about 60 ovaries from 30 female mice, about 300 mg. Project 2: We found that in High Salt (HS)-treated mice, the fertility and oocyte quality significantly decreased, and plenty of biochemical indexes significantly changed, so we guessed that the overall physical health of HS mice was severely impacted. As one major strategy to investigate the mechanism how HS impact the physical health, We chose TMT-labeled Quantitative ovarian phosphoproteomics service from Hangzhou PTM Bio Co. We sent two repeats of two-month-old HS CD1/ICR mouse ovaries and two repeats of control ovaries for characterization of differentially phosphorylated proteins. Each repeat contained about 60 ovaries from 30 female mice, about 300 mg. Project 3: We found that in arecoline (Are)-treated mice, the fertility and oocyte quality significantly decreased, and plenty of biochemical indexes significantly changed, so we guessed that the overall physical health of Are mice was severely impacted. As one major strategy to investigate the mechanism how Are impact the physical health, We chose TMT-labeled Quantitative ovarian phosphoproteomics service from Hangzhou PTM Bio Co. We sent two repeats of two-month-old Are CD1/ICR mouse ovaries and two repeats of control ovaries for characterization of differentially phosphorylated proteins. Each repeat contained about 60 ovaries from 30 female mice, about 300 mg. Two repeats of control samples and data were shared among project 1, 2 and 3. Gross protein levels were also examined and used to normalize the protein phosphorylation level.
2024-05-22 | PXD028932 | Pride