Assessing chromatin accessibility in maize using ATAC-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1061549 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27443449_1.fastq.gz | Fastqsanger.gz | |||
| SRR27443449_2.fastq.gz | Fastqsanger.gz | |||
| SRR27443450_1.fastq.gz | Fastqsanger.gz | |||
| SRR27443450_2.fastq.gz | Fastqsanger.gz | |||
| SRR27443451_1.fastq.gz | Fastqsanger.gz |
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Project description:Assessing chromatin accessibility in maize with ATAC-seq
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Project description:The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. We demonstrate a streamlined ATAC-seq protocol for maize in which nuclei purification can be achieved without cell sorting, and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, provides a precise and efficient assessment of the maize chromatin landscape.
2024-01-10 | GSE252638 | GEO
Project description:Maize (Zea mays) is one of the most important crop in the world. Better understanding the maize chromatin architecture points to novel approaches to improve crop yield. Here, we describe the first ATAC-seq protocol to assess the maize genome. Fresh leaf tissue was gently chopped by a blade to release intact nuclei which later were fractionated using Percoll-sucrose gradient. The isolated nuclei were treated with a transposase that fragments and tags the genome; these fragments were subjected to two rounds of PCR to generate the ATAC-seq library. In the first round of PCR, these fragments were amplified with 5 cycles and sequencing barcodes were added. A fraction of the first PCR product was subjected to qPCR to determine the optimal amplification cycle number in the second round of PCR. The library quality can be assessed by a Bioanalyzer prior to sequencing. The distinct bands indicated good quality. After sequencing, the computational analysis of fragment size distribution may show patterns of periodicity that is a characteristic to ATAC-seq libraries. In our preliminary analysis, we found that 85% percent of the identified regions deviate from closed regions previously identified by MNase-seq, suggesting that the ATAC-seq library preparation procedure described here is effective in identifying open chromatin regions of the maize genome.
2019-01-23 | GSE120491 | GEO
Project description:Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.
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Project description:A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we define the chromatin accessibility and transcriptional landscape controlling this process in thirteen primary cell types that traverse the hematopoietic hierarchy. Exploiting the finding that enhancer landscapes better reflect cell identity than mRNA levels, we enable "enhancer cytometry" for accurate enumeration of pure cell types from complex populations. We further reveal the lineage ontogeny of genetic elements linked to diverse human diseases. In acute myeloid leukemia, chromatin accessibility reveals distinctive regulatory evolution in pre-leukemic HSCs (pHSCs), leukemia stem cells, and leukemic blasts. These leukemic cells demonstrate unique lineage infidelity, confirmed by single cell regulomes. We further show that pHSCs have a competitive advantage that is conferred by reduced chromatin accessibility at HOXA9 targets and is associated with adverse patient outcomes. Thus, regulome dynamics can provide diverse insights into human hematopoietic development and disease. Single-cell ATAC-seq of LMPPs, Monocytes, LSCs and Luekemic blast cells.
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Project description:Analysis of chromatin accessibility in primary GCTB samples with ATAC-seq
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Project description:Open or accessible regions of the genome are the primary positions of binding sites for transcription factors and chromatin regulators. Transposase-accessible chromatin sequencing (ATAC-seq) can probe chromatin accessibility in the intact nucleus. Here, we describe a protocol to generate ATAC-seq libraries from fresh Arabidopsis thaliana tissues and establish an easy-to-use bioinformatic analysis pipeline. Our method could be applied to other plants and other tissues and allows for the reliable detection of changes in chromatin accessibility throughout plant growth and development. For complete details on the use and execution of this protocol, please refer to Wang et al. (2020).
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Project description:STAT4 dynamically interacts with the genomic landscape and functions in modulating chromatin accessibility to influence gene expression. We aimed to evaluate the impact of STAT4 on chromatin accessibility of colonic lamina propria ILC1s. To address this aim, we sorted ILC1s from the colonic LP of unmanipulated C57BL/6 and STAT4-/- mice and performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq).
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Project description:Chromatin accessibility profiling by ATAC-seq
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