Single nuclei ATAC-seq (10X Genomics Chromium) of FACS enriched cortical and hippocampal interneurons from P30 mouse brains
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PROVIDER: PRJNA702792 | ENA |
REPOSITORIES: ENA
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Project description:Single nuclei RNA-seq (10X Genomics Chromium) of FACS enriched cortical and hippocampal interneurons from P30 mouse brains
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Project description:While epigenetic modifications are critical for cell state changes throughout development, a detailed characterization of chromatin accessibility during neurogenesis has not been explored. We collected single-cell chromatin accessibility profiles of ~40,000 cells from 4 distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many of which were restricted to distinct progenitor cell types or brain regions. By integrating snATAC-Seq and transcriptome data, we characterized changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance throughout neurodevelopment. Integrating our chromatin accessibility profiles from embryonic and adult interneurons with the iPSYCH2012 GWAS dataset revealed several disease-associated polymorphisms overlapped accessible regions in embryonic cells and MGE-derived mature interneurons. These findings highlight the coordination between chromatin accessibility and gene expression as neural progenitors mature during embryogenesis, and open the door for future studies to define critical enhancer-promoter interactions that direct cell fate decisions.
2021-12-31 | GSE167016 | GEO
Project description:While epigenetic modifications are critical for cell state changes throughout development, a detailed characterization of chromatin accessibility during neurogenesis has not been explored. We collected single-cell chromatin accessibility profiles of ~40,000 cells from 4 distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many of which were restricted to distinct progenitor cell types or brain regions. By integrating snATAC-Seq and transcriptome data, we characterized changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance throughout neurodevelopment. Integrating our chromatin accessibility profiles from embryonic and adult interneurons with the iPSYCH2012 GWAS dataset revealed several disease-associated polymorphisms overlapped accessible regions in embryonic cells and MGE-derived mature interneurons. These findings highlight the coordination between chromatin accessibility and gene expression as neural progenitors mature during embryogenesis, and open the door for future studies to define critical enhancer-promoter interactions that direct cell fate decisions.
2021-12-31 | GSE167048 | GEO
Project description:Unilateral Traumatic Brain Injury (TBI) causes functional disturbances of the neuronal networks spreading even to the undamaged cortical hemisphere. The phenomenon, referred to as transhemispheric diaschisis, is suggested to be mediated by an imbalance of the strength of glutamatergic, excitatory vs. GABAergic, inhibitory neurotransmission. Here we present evidence that a switch in expression of α Subunits of pore-forming L-Type voltage-gated calcium channels (VGCC), by an expression of CaV1.3 and simultaneous ablation of CaV1.2 in GABAergic interneurons could balance early cortical disturbances manifested as contralateral hyperexcitability in the early phase after TBI. The switch of the VGCC alpha Subunits in GABAergic interneurons was detected using the GAD67-GFP (Glutamate Decarboxylase 67 – Green Fluorescent Protein) Knock-in mouse line. Mice received a TBI with a Controlled Cortical Impact (CCI) to the primary motor and somatosensory cortex at postnatal day 19-21 under anesthesia in vivo. Single GFP+ interneurons located in the undamaged, contralateral cortex were isolated by Fluorescence-Activated Cell Sorting (FACS) and further analyzed by Mass Spectrometry (MS). The switch was associated with an increased excitability of Somatostatin (SST) interneurons and extracellular network activity in acute brain slices in Microelectrode Array (MEA) recordings, which could be restored in presence of isradipine (100 nM), which selectively blocks CaV1.3-containing VGCCs. These data suggest that a switch in alpha.subunits of VGCCs expressed on SST-positive interneurons stabilizes early hyperactivity of the contralateral cortical network at 72 h after TBI, thereby promoting an adaptive mechanism to counterbalance post-traumatic hyperexcitabilty that might lead to epileptogenesis.
2022-01-03 | PXD023551 | Pride
Project description:Study of expression of proteins as a response to varying chromium concentrations
2019-12-02 | PXD012993 | Pride
Project description:10x Genomics Chromium WGS of Tursiops Aduncus
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Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. In this dataset, we assess the RNA detection rates using high-throughput 10x Genomics Chromium system. We mix equal volume of Control Brain RNA (3ul; FirstChoice Total Brain RNA; #AM7962) and ERCC spikes (3ul 1:4 dilution; #4456653) to make a '2x Control RNA+ERCC' master mix. The '2x Control RNA+ERCC' master mix is diluted with equal volume nuclease-free water to make '1x Control RNA+ERCC' master mix. 3ul of '1x Control RNA+ERCC' master mix is added to Chromium single cell suspension and processed as per Chromium guidelines. The sample-data relationship format (SDRF) file for this submission contains only a high-level representation of the sample, library and run information per flow cell, and not per cell. For meta-data at the level of individual cells, please refer to the supplementary file called single_cells_list.txt, which is included as part of this ArrayExpress submission.
2017-03-08 | E-MTAB-5480 | biostudies-arrayexpress
Project description:Clostridioides difficile P30 Genome sequencing and assembly
| PRJNA85999 | ENA
Project description:Single-cell RNA sequencing (scRNA-seq) is generally used for profiling transcriptome of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data generated by these two platforms from the same samples of CD45- cells, we systematically evaluated their features using a wide spectrum of analyses. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data more. For 10X-based data, we observed higher noise for mRNAs with low expression levels. Approximately 10%-30% of all detected transcripts by both platforms were from non-coding genes, with long non-coding RNAs (lncRNAs) accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected distinct groups of differentially expressed genes between cell clusters, indicating the different characteristics of these technologies. Our study promotes better understanding of these two platforms and offers the basis for an informed choice of these widely used technologies.
| S-EPMC8602399 | biostudies-literature