Cell type-specific Chromatin Accessibility Analysis in the Mouse and Human Brain (Mouse ATAC-seq experiments)
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ABSTRACT:
PROVIDER: PRJNA645059 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12182284_1.fastq.gz | Fastqsanger.gz | |||
| SRR12182284_2.fastq.gz | Fastqsanger.gz | |||
| SRR12182285_1.fastq.gz | Fastqsanger.gz | |||
| SRR12182285_2.fastq.gz | Fastqsanger.gz | |||
| SRR12182286_1.fastq.gz | Fastqsanger.gz |
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Project description:The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming increasing popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using this assay include a small amount of material needed, relatively simple and fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. However, with increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs in both animals and humans. Here we tested three different protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescent-activated nuclei sorting (FANS) and the ATAC-seq analysis. Our study shows that the cryopreservation method impacts the number of open chromatin regions that can be identified from frozen brain tissue using the cell-type specific ATAC-seq assay. However, we show that all three protocols generate consistent and robust data and enable the identification of functional regulatory elements, promoters and enhancers, in neuronal cells. Our study also implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. In comparison to the mouse brain analysis, we reveal the additional challenges of doing chromatin analysis on postmortem human brain tissue. However, we also show that these studies are revealing important cell type-specific information about gene regulation in the human brain. Overall, the ATAC-seq coupled with FANS is a powerful method to capture cell-type specific chromatin accessibility information in the mouse and human brain. Our study provides alternative brain preservation methods that generate high quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in healthy and malfunctioning brain.
2021-03-10 | GSE154067 | GEO
Project description:Cell type-specific Chromatin Accessibility Analysis in the Mouse and Human Brain (Human ATAC-seq experiments)
| PRJNA645058 | ENA
Project description:The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming increasing popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using this assay include a small amount of material needed, relatively simple and fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. However, with increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs in both animals and humans. Here we tested three different protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescent-activated nuclei sorting (FANS) and the ATAC-seq analysis. Our study shows that the cryopreservation method impacts the number of open chromatin regions that can be identified from frozen brain tissue using the cell-type specific ATAC-seq assay. However, we show that all three protocols generate consistent and robust data and enable the identification of functional regulatory elements, promoters and enhancers, in neuronal cells. Our study also implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. In comparison to the mouse brain analysis, we reveal the additional challenges of doing chromatin analysis on postmortem human brain tissue. However, we also show that these studies are revealing important cell type-specific information about gene regulation in the human brain. Overall, the ATAC-seq coupled with FANS is a powerful method to capture cell-type specific chromatin accessibility information in the mouse and human brain. Our study provides alternative brain preservation methods that generate high quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in healthy and malfunctioning brain.
2021-03-10 | GSE154066 | GEO
Project description:We profiled accessibility by ATAC-seq of G1/S-synchronised HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.
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Project description:The majority of common genetic risk variants associated with neuropsychiatric disease are non-coding and are thought to exert their effects by disrupting the function of cis regulatory elements (CREs), including promoters and enhancers. Within each cell, chromatin is arranged in specific patterns to expose the repertoire of CREs required for optimal spatiotemporal regulation of gene expression. To further our understanding of the complex mechanisms that modulate transcription in the brain, we utilized frozen postmortem samples to generate the largest human brain and cell type-specific open chromatin dataset to date. Using the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq), we created maps of chromatin accessibility in 2 cell types (neurons and non-neurons) across 14 distinct brain regions of 5 individuals. Chromatin structure varies markedly by cell type, with neuronal chromatin displaying higher regional variability than that of non-neurons. Among our findings is an open chromatin region (OCR) specific to neurons of the striatum. When placed in the mouse, a human sequence derived from this OCR recapitulates the cell-type and regional expression pattern predicted by our ATAC-seq experiments. Furthermore, differentially accessible chromatin overlaps with the genetic architecture of neuropsychiatric traits and identifies differences in molecular pathways and biological functions. By leveraging transcription factor binding analysis, we identify protein coding and long noncoding RNAs (lncRNAs) with cell-type and brain region specificity. Our data provides a valuable resource to the research community and we provide this human brain chromatin accessibility atlas as an online database “Brain Open Chromatin Atlas (BOCA)” to facilitate interpretation.
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Project description:Characterization of chromatin accessibility in T-cell lymphoma. ATAC-seq experiments were performed in both control (CT) and HELLS knockdown (shHELLS) cells to evaluate changes in chromatin accessibility.
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Project description:Chromatin accessibility was analysed in Kasumi-1 cells after AML1-ETO knock-down and in controls by ATAC-sequencing. The experiments were done in triplicates.
2022-02-01 | E-MTAB-9021 | biostudies-arrayexpress
Project description:To describe chromatin accessibility changes associated with differentiation of mouse presomitic mesoderm (PSM) cells into somites, ATAC sequencing (paired-end) was performed using non-cultured, wild-type PSM tissues that were microdissected into tailbud, posterior PSM, anterior PSM, and somite regions. Omni-ATAC protocol was used, and each condition includes six biological replicates.�
2025-08-06 | E-MTAB-13692 | biostudies-arrayexpress
Project description:To gain insight into patterns of chromatin accessibility in distinct cell subtypes of mouse pituitary, pituitaries from two adult mice were collected and subjected to single-cell ATAC-seq analysis using 10X Genomics platform
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Project description:To study the chromatin accessibility in E9.5d mouse brains with neural tube defects or control, we performed ATAC-seq in mouse brains. NTDs mouse model: CD-1 mice (7–8 weeks old) were provided by Beijing Vital River laboratory Animal Technology Co., Ltd, China (no: 110011200105514958, 16-25g). Female CD-1 mice were fed on low folate diet for more than 8 weeks. Sexually matured individuals were mated overnight; vaginal plug was detected at 8:00 am in the following morning and was designated as E0.5 day. NTDs mouse models were induced by intraperitoneal injection with 1.5 mg/kg of MTX (Sigma-Aldrich, USA) on E7.5. On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope. All samples with NTDs clinical manifestations were collected for experiments.
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