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A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues [CUT&RUN]

ABSTRACT: A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues [CUT&RUN]

PROVIDER: PRJNA868730 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21016719_1.fastq.gz	Fastqsanger.gz
	SRR21016719_2.fastq.gz	Fastqsanger.gz
	SRR21016720_1.fastq.gz	Fastqsanger.gz
	SRR21016720_2.fastq.gz	Fastqsanger.gz
	SRR21016721_1.fastq.gz	Fastqsanger.gz

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A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues [CUT&RUN]

Project description:Chromatin accessibility, histone modifications and transcription factor binding are highly dynamic during Drosophila metamorphosis and drive global changes in gene expression as larval tissues differentiate into adult structures. Unfortunately, the presence of pupa cuticle on many Drosophila tissues during metamorphosis prevents enzyme access to cells and has limited the use of enzymatic in situ methods for assessing chromatin accessibility and histone modifications. Here, we present a dissociation method for cuticle-bound pupal tissues that is optimized for use with ATAC-Seq and CUT&RUN to interrogate chromatin accessibility and histone modifications. We show this method provides comparable chromatin accessibility data to the non-enzymatic approach FAIRE-seq, with only a fraction of the amount of input tissue required. This approach is also compatible with CUT&RUN, which allows genome-wide mapping of histone modifications with less than 1/10th of the tissue input required for more conventional approaches such as Chromatin Immunoprecipitation Sequencing (ChIP-seq). Our protocol makes it possible to use newer, more sensitive enzymatic in situ approaches to interrogate gene regulatory networks during Drosophila metamorphosis.

2022-08-14 | GSE211043 | GEO

A tissue dissociation method optimized for ATAC-Seq and CUT&RUN in Drosophila pupal tissues [ATAC-Seq]

2022-08-15 | GSE211152 | GEO

A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues

Project description:A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues

| PRJNA869702 | ENA

A tissue dissociation method optimized for ATAC-Seq and CUT&RUN in Drosophila pupal tissues [ATAC-Seq]

Project description:A tissue dissociation method optimized for ATAC-Seq and CUT&RUN in Drosophila pupal tissues [ATAC-Seq]

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A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-08-15 | GSE211269 | GEO

A tissue dissociation method for ATAC-seq and CUT&RUN in <i>Drosophila</i> pupal tissues.

Project description:Chromatin accessibility, histone modifications, and transcription factor binding are highly dynamic during Drosophila metamorphosis and drive global changes in gene expression as larval tissues differentiate into adult structures. Unfortunately, the presence of pupa cuticle on many Drosophila tissues during metamorphosis prevents enzyme access to cells and has limited the use of enzymatic in situ methods for assessing chromatin accessibility and histone modifications. Here, we present a dissociation method for cuticle-bound pupal tissues that is compatible for use with ATAC-Seq and CUT&RUN to interrogate chromatin accessibility and histone modifications. We show this method provides comparable chromatin accessibility data to the non-enzymatic approach FAIRE-seq, with only a fraction of the amount of input tissue required. This approach is also compatible with CUT&RUN, which allows genome-wide mapping of histone modifications with less than 1/10th of the tissue input required for more conventional approaches such as Chromatin Immunoprecipitation Sequencing (ChIP-seq). Our protocol makes it possible to use newer, more sensitive enzymatic in situ approaches to interrogate gene regulatory networks during Drosophila metamorphosis.

| S-EPMC10208176 | biostudies-literature

Bulk Cut&run and Cut&tag

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CUT&RUN HUDEP1 OE SOX6-Flag

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Optimized CUT&RUN protocol for a non-histone protein in activated primary mouse B cells

Project description:Optimized CUT&RUN protocol for a non-histone protein in activated primary mouse B cells

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Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

2021-06-17 | GSE178343 | GEO

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