Trancriptome profiling of medial frontal cortices of P28 offspring from breeding of Dnmt3l conditional knockin and Emx1-cre mice
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1119493 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The objective of the study was to examine the genomic DNA methylation changes in the medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, the strain of C57BL/6J. There were 12 samples in total- CC1rest, CC3rest, CF2rest, B-3, B-4, and B-5 were medial frontal cortices from the male and female Emx1-cre mice, respectively, which were used as the control groups (CON). CC2rest, CD5rest, CF1rest, D-1, CD6rest, and CD16rest were medial frontal cortices from the male and female Dnmt3l overexpression mice, respectively, which were used as the experimental groups (OE). The genomic DNA of each sample was extracted from the medial frontal cortices. We analyzed methylation level changes across the genome using methylation-capture followed by bisulfite sequencing. Overall, among the more than 1.7 million captured CpG sites, 16.38% had significant differences in methylation levels; the overall methylation rate of the genome was slightly increased (~5%); the methylation level distribution of all CpG sites did not change significantly. In different functional regions of the genome, most of the differentially methylated CpG sites were mildly increased (β value difference <0.2), and most of the methylation difference sites were concentrated in the intergenic and intron regions.
2024-08-31 | GSE271949 | GEO
Project description:The objective of the study was to examine the gene expression changes in the medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, strain of C57BL/6J. There were 12 samples in total- A-1, A-2, A-3, B-1, B-2, B-3, C-1, C-2, C-3, D-1, D-2, and D-3. A-1 to A-3 and B-1 to B-3 were medial frontal cortices from the male and female Emx1-cre mice respectively, which were used as the control groups (CON). C-1 to C-3 and D-1 to D-3 were medial frontal cortices from the male and female Dnmt3l overexpression mice respectively, which were used as the experimental groups (OE). The total RNA of each sample was extracted from the medial frontal cortices by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. There were two types of libraries: the circRNA, mRNA, and lncRNA were all constructed by removing rRNA (one library, three types of RNA were analyzed together), and the insert fragment was about 300bp; the small RNA was constructed and analyzed separately, mainly microRNA of about 22bp. Results: among 119414 cleaned mRNAs, 3015 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). The differential expressed genes distributed in all chromosomes. Functional annotation with GO and KEGG enrichment revealed the top functional groups including ATP binding, zinc ion binding, glutamatergic synapse, dopaminergic synapse, MAPK signaling pathway, and PI3K-Akt signaling pathway. Among 23698 lncRNAs, 658 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 10673 circRNAs, 49 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 1821 microRNAs, 101 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold).
2024-08-31 | GSE268951 | GEO
Project description:WGBS of medial frontal cortices of P28 offspring from breeding of Dnmt3l conditional knockin and Emx1-cre mice
| PRJNA1134190 | ENA
Project description:Altered DNA methylation is a crucial epigenetic event in hepatocellular carcinoma (HCC) development and progression. Through methylation-transcriptomic analysis, we identified a set of sixty potential DNA methylation-based epidriver genes. This set of genes focuses on the hypermethylation of EMX1, which is frequently observed in hepatobiliary tumors. Despite of its frequent occurrence, the function of EMX1 remains largely unknown. By utilizing bisulfite-next-generation sequencing, we have detected EMX1 DNA hypermethylation on the gene body, which is positively correlated with EMX1 mRNA expression. Further analysis revealed that EMX1 mRNA terminal exon splicing in HCC generated two protein isoforms: EMX1 full length (EMX1-FL) and alternative terminal exon splicing isoform (EMX1-X1). Cellular functional assays demonstrated that gain-of-function EMX1-FL, but not EMX1-X1, induced HCC cells migration and invasion while silencing EMX1-FL inhibited HCC cells motility. This result was further validated by in vivo tumor metastasis models. Mechanistically, EMX1-FL bound to EGFR promoter, promoting EGFR transcription and activating EGFR-ERK signaling to trigger tumor metastasis. Therefore, EGFR may be a potential therapeutic target for EMX1-high expression HCC. Our work illuminated the crucial role of gene body hypermethylation-activated EMX1-FL in promoting tumorigenesis and metastasis in HCC. These findings pave the way for targeting the EMX1-EGFR axis in HCC tumorigenicity and metastasis.
2023-11-29 | GSE245505 | GEO
Project description:Clostridioides difficile P28 Genome sequencing and assembly
| PRJNA85995 | ENA
Project description:We used RRBS to analyze DNA methylation in mESC lines deficient for maternal Dnmt3L (Dnmt3L mKO), zygotic Dnmt3L (Dnmt3L KO), and both maternal and zygotic Dnmt3L (Dnmt3L mzKO). Compared to wild-type (WT) mESCs, Dnmt3L mKO mESCs exhibit severe loss of methylation at imprinted loci but no changes in global DNA methylation, Dnmt3L KO mESCs exhibit moderate loss of methylation at many Dnmt3a target regions but do not affect methylation at imprinted loci, and Dnmt3L mzKO mESCs exhibit combined changes of mKO and KO cells, with severe loss of methylation at imprinted loci and moderate loss of methylation at Dnmt3a target regions.
2018-10-04 | GSE116489 | GEO
Project description:P28.ET0213, ET0318, ET0267 Datasets
| PRJNA998165 | ENA
Project description:Comparison of gene expression differences between Dnmt3L heterozygous and wildtype pachytene spermatocytes, and similarly between Dnmt3L heterozygous and wildtype round spermatids which were isolated from the Dnmt3L knockout mouse line. This array was conducted to address the hypothesis that Dnmt3L heterozygosity results in deregulated gene expression within spermatocytes and spermatids. Results show that Dnmt3L heterozygosity causes numerous genes to be differentially regulated on a genome-wide level, showing that DNMT3L has an important role in regulating gene expression within these male germ cells.
2011-03-01 | GSE20241 | GEO
Project description:Comparison of gene expression differences between Dnmt3L heterozygous and wildtype pachytene spermatocytes, and similarly between Dnmt3L heterozygous and wildtype round spermatids which were isolated from the Dnmt3L knockout mouse line. This array was conducted to address the hypothesis that Dnmt3L heterozygosity results in deregulated gene expression within spermatocytes and spermatids. Results show that Dnmt3L heterozygosity causes numerous genes to be differentially regulated on a genome-wide level, showing that DNMT3L has an important role in regulating gene expression within these male germ cells. Three preparations each of Dnmt3L purified wildtype spermatocytes, wildtype spermatids, heterozygous spermatids, and two preparations of heterozygous spermatocytes were isolated for a total of 11 samples. Each preparation was made up of cells isolated from 10 mice.
2011-03-01 | E-GEOD-20241 | biostudies-arrayexpress
Project description:During oogenesis, DNA methyltransferase 3-like (Dnmt3l) is required for the establishment of the maternal germline DNA methylation imprints that in the offspring, govern the parent-of-origin-specific expression of most known imprinted genes (Science 2001, 294:2536-9). Dnmt3l-deficient dams were crossed with wildtype sires to obtain Dnmt3l-/+ embryos that lack maternal methylation imprints. Gene expression was measured in Dnmt3l-/+ and wildtype embryos and is expected to differ for imprinted genes that are under the control of a maternal methylation mark. Keywords: genetic modification, DNA methylation
2008-04-14 | GSE8756 | GEO