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Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II]

ABSTRACT: Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II]

PROVIDER: PRJNA643828 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12137022_1.fastq.gz	Fastqsanger.gz
	SRR12137022_2.fastq.gz	Fastqsanger.gz
	SRR12137023_1.fastq.gz	Fastqsanger.gz
	SRR12137023_2.fastq.gz	Fastqsanger.gz
	SRR12137024_1.fastq.gz	Fastqsanger.gz

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Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II]

Project description:The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Three biological replicates were assigned for each group and in total 13 groups were prepared for ATAC-seq libraries. We mapped about 30 million reads per sample to D. discoideum with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed D. discoideum have dispartate chromatin accessibility regions throughout the genome.

2021-04-21 | GSE153733 | GEO

Chromatin accessibility in D. discoideium (AX2) in different developmental stages

Project description:The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Two biological replicates were assigned for each group and in total 8 groups were prepared for ATAC-seq libraries. We mapped about 10 million reads per sample to D. discoideum with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed D. discoideum have dispartate chromatin accessibility regions throughout the genome.

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Single-cell transcriptome analysis in D. discoideum (AX4) in different developmental stages

Project description:Single-cell transcriptome analysis in D. discoideum (AX4) in different developmental stages

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Genome-wide chromatin accessibility data from cultured human fetal lung tip-derived organoids at different stages of lung development

Project description:Human fetal lung tip cells were purifed from developing human lungs at pseudoglandular and canalicular stages and in vitro cultured as organoids. Chromatin accessibility data for each organoid line at different stages were profiled by ATAC-seq.

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Chromatin accessibility at four key stages of turbot development, from phylotypic to post-metamorphic stages [ATAC-seq]

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Project description:Landscape of chromatin accessibility across tissues and developmental stages is essential to elucidate the transcriptional regulation in various biological processes and phenotypes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development have been seldomly investigated. Here, we profiled open chromatin maps and transcriptional features of the heart, kidney, liver, lung, skeletal muscle, and spleen tissues in newborn pigs and that of porcine liver tissue at suckling and adult stages using ATAC-seq and rRNA-depleted RNA-seq, respectively. Employing a union set of protein coding genes (PCGs) and two kinds of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue or developmental stage. The PCGs with tissue-specific accessible promoters, as expected, had active transcription and were relevant to tissue-specific functions. Other non-coding tissue-specific peaks were involved in both physical activities and morphogenesis in the neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands the understanding of epigenetic regulation in mammalian tissue functions and organ development, which can benefit both economic trait improvement and better biomedical use of pigs.

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ATAC-seq data of Amphimedon queenslandica (Demosponge species) through eight developmental stages, from white stage (cleavage) to adult

Project description:We report a comprehensive DNA accessibility profile of the Demosponge species Amphimedon queenslandica using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) through six embryonic developmental stages, a larval stage and adult stage. We assessed the dynamics of chromatin accessibility and identified 40,218 consensus peaks, 4,751 of them were differentially accessible in at least one developmental stage. Cis-regulatory elements were more dynamically regulated while proximal elements were more likely to be constitutively active. Furthermore, we identify a shift towards repressive chromatin in mid and late developmental stages which coincide with the increase in expression of genes of Metazoan origin. Finally, we show that cis-regulatory regions are differentially enriched in different Transcription Factor binding sites (TFBS) which demarcate three main stages of development and importantly, they are predictive of cis-regulatory regions in other animal species but not in Capsaspora owczarzaki, a close relative of animals.

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Chromatin accessibility in D. discoideium (AX2) in different developmental stages

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Chromatin accessibility in the mouse intestinal epithelium across different regions and life stages

Project description:We compare the epigenomes of mouse intestinal epithelial cells at different intestinal regions and life stages of the mouse. We use a sequencing assay for transposase accessible chromatin (ATAC-seq) to determine highly accessible genomic regions. We determine regions that are differentially accessible between intestinal regions (duodenal crypt, duodenal villus, and colon) and between life stages (12-to-15-day-old/juvenile, 90-day-old/adult, and 21-month-old/geriatric).

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