MiRNA-seq in ovarian tissues of prenatally androgenized (PNA) mice
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA706385 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13848056_1.fastq.gz | Fastqsanger.gz | |||
| SRR13848056_2.fastq.gz | Fastqsanger.gz | |||
| SRR13848057_1.fastq.gz | Fastqsanger.gz | |||
| SRR13848057_2.fastq.gz | Fastqsanger.gz | |||
| SRR13848058_1.fastq.gz | Fastqsanger.gz |
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Project description:Ovarian tissues of prenatally androgenized (PNA) mice
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Project description:To investigate the molecular mechanism of PCOS underlying the hyperandrogenic phenotype, prenatally androgenized (PNA) mice were used to mimic this phenotype in women with PCOS. Methylated DNA binding domain sequencing (MBD-seq) and RNA-seq were performed on PNA mice (n=6) and control group (n=4) and validations were applied on ovarian samples from PNA mice (n=6) and control group (n=6) using MSP (methylation-specific PCR) and qPCR. The immunohistochemistry (IHC) and transmission electron microscope (TEM) profiling was separately conducted on tissue sections and granular cells of PNA mice (n=6) and control group (n=6). We identified 857 genes with differently methylated promoters and 3317 differently expressed genes in PNA mice and control group. We found that PCOS group had a down-regulation of Dnmt1 gene expression, accompanied by global hypomethylation compared with the control group. The promoter regions of Map3k1(mitogen-activated protein kinase kinase kinase 1) and Map1lc3ka (microtubule-associated protein1 light chain 3) were hypomethylated, accompanied by up-regulation of their mRNA expression, which may be involved in the regulation of PCOS through MAPK/p53 pathway activition and autophagy alteration.
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Project description:To investigate the molecular mechanism of PCOS underlying the hyperandrogenic phenotype, prenatally androgenized (PNA) mice were used to mimic this phenotype in women with PCOS. Methylated DNA binding domain sequencing (MBD-seq) and RNA-seq were performed on PNA mice (n=6) and control group (n=4) and validations were applied on ovarian samples from PNA mice (n=6) and control group (n=6) using MSP (methylation-specific PCR) and qPCR. The immunohistochemistry (IHC) and transmission electron microscope (TEM) profiling was separately conducted on tissue sections and granular cells of PNA mice (n=6) and control group (n=6). We identified 857 genes with differently methylated promoters and 3317 differently expressed genes in PNA mice and control group. We found that PCOS group had a down-regulation of Dnmt1 gene expression, accompanied by global hypomethylation compared with the control group. The promoter regions of Map3k1(mitogen-activated protein kinase kinase kinase 1) and Map1lc3ka (microtubule-associated protein1 light chain 3) were hypomethylated, accompanied by up-regulation of their mRNA expression, which may be involved in the regulation of PCOS through MAPK/p53 pathway activition and autophagy alteration.
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Project description:To investigate the molecular mechanisms of miRNA-mRNA expression underlying this phenotype, ovarian samples from PNA and control mice were subjected to microRNA-seq and RNA-seq. Differential expression analyses were carried out to identify differentially expressed microRNAs (DEmiRs) and differentially expressed genes (DEGs). Target genes of DEmiRs were predicted by miRTarbase and visualization by Cytoscape. Functional annotation and pathway enrichment analyses for the DEGs and target genes were performed through the DAVID database. Then, to reveal the interactions involved in the pathogenesis of PCOS, the integrated analysis of miRNA-mRNA was performed in PNA mice vs. controls and granulosa cells (GCs) of PCOS women vs. health women. Protein–protein interaction (PPI) networks were established for these negatively regulated pairs via the STRING database. The expression and correlation of potential miRNAs and targets were further validated using RT-qPCR in more PNA mice and clinical human granulosa cells.
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Project description:To investigate the etiology of the hyperandrogenic phenotype of polycystic ovary syndrome (PCOS), a prenatally androgenized (PNA) mouse model was validated and used for microarray analysis.
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Project description:Leishmania infantum is the causative agent of zoonotic visceral leishmaniasis in Mediterranean areas and also acts as an opportunistic parasite in HIV patients. Metacyclic promastigotes are transmitted during bloodmeals of the sand-fly host after development. Metacyclogenesis can be micmiked in axenic cultures and peanut lectin (PNA) agglutination followed by two-step centrifugation allows the separation of procyclic and metacyclic promastigotes in L. major. The purpose of this study is to isolate both fractions simultaneously from the same population of L. infantum in stationary phase of axenic culture and compare their expression profiles through DNA microarrays, specially focusing on metacyclic promastigotes. Whole-genome shotgun DNA microarrays were constructed and used to analyse the stationary-phase procyclic and metacyclic expression profiles. Four biological replicates of the experiment were performed and analysed, so that 322 clones with meaningful values of stage-specific regulation were selected. We found several genes dealing with primary metabolism, differentiation in procyclic promastigotes and with development of infectivity in metacyclic promastigotes. The differences we have found between the procyclic (PNA+) and metacyclic (PNA-) transcriptomes demonstrate that negative selection of metacyclic promastigotes through PNA agglutination is suitable in L. infantum and both fractions can be isolated. In addition, up-regulation of genes implied in lipophosphoglycan (LPG), proteophosphoglycan (PPG) and glycoprotein biosynthesis indicate that metacyclic promastigotes are related with infectivity. Keywords: comparative hybridization between cDNAs from procyclic PNA+ and metacyclic PNA- promastigotes of L.infantum
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Project description:Here, we determined the ability of peptide nucleic acid (PNA) oligomers, coupled to different cell-penetrating peptides (CPPs), to interfere in regulatory RNA circuits of human blood-derived leukocytes. Using RNA-seq, FACS and confocal microscopy we identified octaarginin as a CPP enabling PNA delivery and sequence-dependent RNA inhibition in blood-derived myeloid cells at nanomolar concentration. At 200 nM, an R8-PNA targeting immune-regulatory microRNA-155 was delivered into nearly 100 % of human macrophages within 24 hours without apparent cytotoxicity, and globally de-repressed microRNA-155 target-mRNAs. This was not observed when coupling the PNA inhibitor to a K3 instead of the R8 peptide. We suggest that CPP choice is a fundamental success-determining factor for therapeutic RNA-inhibition in human myeloid leukocytes.
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