RNA-Seq analysis of the pancreatic islets from 6-week-old Paupar WT and KO mice
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE121884 | GEO | 2019/10/10
REPOSITORIES: GEO
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2017-08-18 | GSE85873 | GEO
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2016-12-03 | E-MTAB-4958 | biostudies-arrayexpress
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2020-01-15 | E-MTAB-7686 | biostudies-arrayexpress
Project description:Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a vertebrate-conserved and central nervous system-expressed lncRNA transcribed from a locus upstream of the gene encoding the Pax6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neuronal differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with Pax6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. Our findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes. The genome-wide binding profile of Paupar was determined using Capture Hybridisation Analysis of RNA Targets (CHART)-Seq technique (Simon et al, Proc Natl Acad Sci U S A 108: 20497-20502, 2011) in N2A cells. Following the CHART-seq protocol, we used RNase H elution to recover genomic DNA associated with endogenous Paupar transcripts and genomic DNA associated with a control oligonucleotide (corresponding to the E.coli LacZ sequence). We identified Paupar binding sites in comparison both to DNA recovered using the control LacZ oligonucleotide and to an input DNA sample from N2A cells.
2013-11-21 | E-GEOD-52570 | biostudies-arrayexpress
Project description:Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on mRNA expression in the context of differential susceptibility Methods: Following prenatal stress and behavioural screening in adulthood, month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). Following library preparation, samples were sequenced on the illumina HiSeq2000 platform (single end, 50 bp, 30 million reads/sample). Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015). These counts were then used for the analysis of differentially expressed genes (DEGs) using the R package DeSeq2 (Love et al. 2014). Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct gene expression. As expected, the effect sizes and significances were rather subtle. Conclusion: the modulation of differential susceptibility seems to be modulated by distinct mRNA expression profiles, dependent on the serotonin transporter genotype
2024-01-27 | GSE109929 | GEO
Project description:Aim:Transcriptional analysis of the MIN6 beta cell line following control or Paupar lncRNA KD to identify genes regulated by Paupar Methods:MIN6 cells subjected to either control or Paupar KD were transfected for 48 hours before extraction of total RNA using the Qiagen Mini kit. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 30 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq2. Results: We did not observe any signficant changes in genes important for beta cell function Conclusion: Paupar does not have a signficant regulatory function in beta cells
2019-10-10 | GSE132072 | GEO
Project description:Purpose: The goals of this study are to analyze the NGS-derived transcriptome profiling (RNA-seq) between the normal, control and experimental group after extended hepatectomy. Results: All sequencing reads from RNA-seq were mapped to the mouse reference genome (GRCm38.84) using hisat2-2.10 (Kim et al., 2015). FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks v.2.2.1 (Trapnell et al., 2012) using default parameters for gene expression levels. We used htseq-count (Anders et al., 2015) to count reads on genes. Differential expression analysis was performed using DESeq2 (R package, (Love et al., 2014)). Genes were considered differentially expressed if FPKM >=1 in at least one sample and |fold change| >= 2, adjusted p-value < 0.05. The gene ontology analyses was performed using Metascape v3.5 (http://metascape.org/gp/index.html, (Zhou et al., 2019)). Principal component analysis was performed with whole genes using the R package (function: prcomp()). Conclusions: Our study represents the first detailed analysis of liver transcriptomes after extended hepatectomy, 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.
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Project description:Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a vertebrate-conserved and central nervous system-expressed lncRNA transcribed from a locus upstream of the gene encoding the Pax6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neuronal differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with Pax6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. Our findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes. N2A cells transfected with a non-targeting control vector were compared to N2A cells transfected with a Paupar knockdown construct. Three biological replicates of each condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.
2013-11-21 | E-GEOD-52569 | biostudies-arrayexpress
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2017-08-18 | GSE85874 | GEO