Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq

ABSTRACT: Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq

PROVIDER: PRJNA637506 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11932500.fastq.gz	Fastqsanger.gz
	SRR11932501.fastq.gz	Fastqsanger.gz
	SRR11932502.fastq.gz	Fastqsanger.gz
	SRR11932495.fastq.gz	Fastqsanger.gz
	SRR11932496.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq

Project description:Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq for Bombus terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology.

2020-10-02 | GSE151858 | GEO

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq.

Project description:Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. Although protein-coding genes in bumblebees have been extensively annotated, regulatory sequences of the genome, such as promoters and enhancers, have been poorly annotated. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we performed ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) on Bombus terrestris samples derived from four developmental stages: egg, larva, pupa, and adult, respectively. The ATAC-seq reads were mapped to the B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. We identified 36,390 chromatin accessible regions in total, including both shared and stage-specific chromatin accessible signals. Our study will provide an important resource, not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology throughout development.

| S-EPMC7588436 | biostudies-literature

ATAC-seq of Chamaelirium luteum to determine the accessible chromatin regions

Project description:To determine the accessible chromatin regions of Chamaelirium luteum genome, we performed the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to generate the genome-wide chromatin accessibility profile.

2025-11-13 | GSE285102 | GEO

Identification of accessible chromatin regions in response to cold stress in Vitis amurensis

Project description:We report the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) for high-throughput profiling of accessible chromatin regions after cold treatment in Vitis amurensis

2021-11-12 | GSE122487 | GEO

ATAC-seq of Chamaelirium luteum to determine the accessible chromatin regions

Project description:ATAC-seq of Chamaelirium luteum to determine the accessible chromatin regions

| PRJNA1201177 | ENA

Bos taurus ATAC-seq across 88 tissue samples to profile open chromatin regions in the cattle genome

Project description:We performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) using 88 tissue samples to profile open chromatin regions in the cattle genome.

2023-08-24 | E-MTAB-11825 | biostudies-arrayexpress

The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)

Project description:In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. ATAC-seq was performed in these embryos at various stages in preimplantation development.

2016-06-15 | E-GEOD-66581 | biostudies-arrayexpress

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

2022-02-23 | GSE197224 | GEO

Regions of accessible chromatin in adult mushroom body neurons of Drosophila melanogaster [Trx_ATAC]

Project description:We have analyzed regions of accessible chromatin in adult mushroom body neurons of Drosophila melanogaster of a control genetic background using ATAC-seq.

2025-01-14 | GSE273839 | GEO

Genome-wide identification of accessible chromatin regions by ATAC-seq upon induction of the transcription factor bZIP11 in Arabidopsis.

Project description:Basic leucine zipper 11 (bZIP11) is a transcription factor that is activated under low energy conditions in plants and plays a crucial role in enabling plants to adapt to starvation situations. Although previous results indicate that bZIP11 regulates chromatin accessibility based on evidence obtained from single genomic loci, to what extent this transcription factor regulates the chromatin landscape at the whole genome level remains unknown. Here we addressed this by performing an ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) on Arabidopsis thaliana (Arabidopsis) leaf protoplasts to obtain a profile of chromatin patterning in response upon bZIP11 induction. We identified, on average, 10,000 differentially accessible regions upon bZIP11 induction, corresponding to over 8,420 different genes out of the 25,000 genes present in the Arabidopsis genome. Our study provides a resource for understanding how bZIP11 regulates the genome at the chromatin level and provides an example of the impact of a single transcription factor on a whole plant genome.

| S-EPMC10374617 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data