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Assay for Transposase-Accessible Chromatin using sequencing of spleen memory CD4+ T cells

ABSTRACT: Assay for Transposase-Accessible Chromatin using sequencing of spleen memory CD4+ T cells

PROVIDER: PRJNA579595 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10349917_1.fastq.gz	Fastqsanger.gz
	SRR10349917_2.fastq.gz	Fastqsanger.gz
	SRR10349918_1.fastq.gz	Fastqsanger.gz
	SRR10349918_2.fastq.gz	Fastqsanger.gz
	SRR10349919_1.fastq.gz	Fastqsanger.gz

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Assay for Transposase-Accessible Chromatin using sequencing of spleen memory CD4+ T cells

Project description:We performed a ATAC seq analysis of 2 biological independent splenic samples from pooled mice sorted for lcmv-specific memory CD4 T cells and 2 technical replicates from one mouse sorted for naive CD4 T cells .

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Optimized protocol for assay for transposase-accessible chromatin by sequencing (ATAC-seq) from Drosophila melanogaster brain tissue

Project description:Transposase-accessible chromatin by sequencing (ATAC-seq) has emerged as an advantageous technique to assess chromatin accessibility owing to the robustness of "tagmentation" process and a relatively faster library preparation. A comprehensive ATAC-seq protocol from Drosophila brain tissue is currently unavailable. Here, we have provided a detailed protocol of ATAC-seq assay from Drosophila brain tissue. Starting from dissection and transposition to amplification of libraries has been elaborated. Furthermore, a robust ATAC-seq analysis pipeline has been presented. The protocol can be easily adapted for other soft tissues.

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Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analysis of U937 cells depleted of NSPs

Project description:Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analysis of U937 cells depleted of NSPs

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Chromatin changes in lateral organ founder cells of Arabidopsis thaliana detected by assay for transposase-accessible chromatin sequencing (ATAC-seq)

Project description:Two methods Fluorescence Activated Cell Sorting (FACS) and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) are combined to analyse the chromatin accessibility of Lateral Organ Founder Cells (LOFCs) in the peripheral zone of the apetala1 cauliflower double mutant Arabidopsis inflorescence meristem. Genome-wide we observed a striking correlation between Transposase Hypersensitive Sites (THS) detected in ATAC-seq and DNase I Hypersensitive Sites (DHS), covering mostly extended regions substructured into several individual THS that correspond to phylogenetically conserved sequence, enhancer elements and binding sites of MADS-box transcription factors. Relative to available RNA-seq data, chromatin configuration changes according to gene activation or repression, i.e. at cellular resolution chromatin regions gain or lose Tn5 transposase accessibility in direct correlation with gene expression levels. A pronounced THS priority immediately upstream of the transcription start and reduced numbers of THSs in the transcription unit are complementary to established H3K4me3 activation or H3K27me3 repressive marks. At this resolution, the FACS/ATAC-seq combination should be widely applicable to detect chromatin changes in course of cell type specification and facilitate the detection of regulatory promoter elements in plant promoters.

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Iterative assay for transposase-accessible chromatin by sequencing to home in on functionally relevant neuronal subtypes

Project description:The Drosophila brain contains tens of thousands of distinct cell types. Numerous different transgenic lines reproducibly target specific neuron subsets, yet most still express in several distinct cell types. Furthermore, most lines were developed without a priori knowledge of where the transgenes would be expressed. To aid in the development of cell type-specific tools for neuronal identification and manipulation, we used an iterative assay for transposase-accessible chromatin by sequencing (ATAC-seq) approach. Open chromatin regions (OCRs) that were enriched in neurons compared to whole bodies drove transgene expression preferentially in subsets of neurons. A second round of ATAC-seq from these specific neuron subsets revealed additional enriched OCRs that further restricted transgene expression within the chosen neuron subset. This approach allows for continued refinement of transgene expression and can be used to identify neurons relevant for sleep behavior. Furthermore, this approach is widely applicable to other cell types and to other organisms.

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Integrating RNA-seq and assay for transposase-accessible chromatin by sequencing (ATAC-seq) predicts functionally-relevant chromatin regions

Project description:Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for epigenomic investigations. Integrating epigenomic and transcriptomic data has the potential to reveal the chromatin-mediated mechanisms regulating transcription. However, integrating these two data types remains challenging. We used the insulin signaling pathway as a model to investigate chromatin regions and gene expression changes using ATAC- and RNA-seq in insulin-treated Drosophila S2 cells. We show that insulin causes widespread changes in chromatin accessibility and gene expression. Then, we attempted to integrate ATAC- and RNA-seq data to predict functionally-relevant chromatin regions that control the transcriptional response to insulin. We show that using differential chromatin accessibility can predict functionally-relevant genome regions, but that stratifying differentially-accessible chromatin regions by annotated feature type provides a better prediction of whether a chromatin region regulates gene expression. In particular, our data demonstrate a strong correlation between chromatin regions annotated to distal promoters (1-2 kb from the transcription start site). To test this prediction, we cloned candidate distal promoter regions upstream of luciferase and validated the functional relevance of these chromatin regions. Our data show that distal promoter regions selected by correlations with RNA-seq are more likely to control gene expression. Thus, correlating ATAC- and RNA-seq data can home in on functionally-relevant chromatin regions

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Chromatin changes in lateral organ founder cells of Arabidopsis thaliana detected by assay for transposase-accessible chromatin sequencing (ATAC-seq)

Project description:Chromatin changes in lateral organ founder cells of Arabidopsis thaliana detected by assay for transposase-accessible chromatin sequencing (ATAC-seq)

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Liver Transposase-Accessible Chromatin signal changes related to fat content in pigs

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