Similar Datasets
Project description:We optimzed ATAC-seq library preparation for use with Drosophila melanogaster. The protocol addresses factors specific to fruit flies, such as the insect exoskeleton and smaller genome size. The optimized protocol provides guidelines for sample input, nuclei isolation, and enzymatic reaction times. The data included here were generated using our optimized library preparation workflow.
2022-04-20 | GSE197760 | 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: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.
2023-10-24 | GSE246106 | GEO
Project description:We develop a large-scale single-cell ATAC-seq method (txci-ATAC-seq) by combining Tn5-based pre-indexing with 10X Genomics barcoding. Leveraging this molecular hashing strategy, we demonstrate that txci-ATAC-seq enables the indexing of up to 200,000 nuclei across multiple samples in a single emulsion reaction, representing a ~22-fold increase in throughput compared to the standard workflow at the same collision rate. To improve the multiplexing capability of this new technique, we further develop a "phased" protocol variant (Phased-txci-ATAC-seq) that effectively decouples sample processing from library preparation and has the potential to profile up to 96 samples simultaneously. In this study, we profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16-/-) model. Our study of CC16-/- nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.
2023-10-25 | GSE231708 | GEO
Project description:Optimized ATAC-seq library preparation from Drosophila neurons
| PRJNA812007 | ENA
Project description:SUMOylation is thought to regulate chromatin structure and accessibility thus affecting gene expression. In order to assess these potential roles of SUMOylation in human pluripotent stem cells, ChiPS4 cells were treated with ML792 (selective SUMO E1 inhibitor) or DMSO (vehicle control) for the following times: 4, 8, 24 and 48h or left untreated for 48h. At each time point samples were collected for western blotting (control for the efficacy of treatment), RNA-seq (total RNA extracted using RNeasy Mini Kit) and ATAC-seq (using Omni-ATAC protocol, 3 replicates for each time point). Samples were further used for library preparation and sequenced using the Illumina NovaSeq 6000 S4.
2022-12-01 | E-MTAB-9961 | biostudies-arrayexpress
Project description:Cells were isolated from the back skin of 1-day old chicks after plucking down feathers. Cells were dissociated and enriched for epidermal cells according to a published protocol (PMID: 33157095). Single‐cell separation (10X Genomics Chromium), library preparation (10X Genomics Cell Ranger, version 3.0.2), sequencing (Illumina HiSeq 3000/4000) and data analysis (Seurat Version 3, Satija Lab, NY) were performed according to a published protocol (PMID: 31930613).
2021-03-24 | GSE169274 | GEO
Project description:Purpose: The goal of this study is to use chromatin accessibility data to study the information patterns of chromatin accessibility that encode TF-chromatin interactions. Methods: We generated chromatin accessibility data from the GM12878 lymphoblastoid cell line using a modified protocol where the ATAC-seq fragments are sonicated during the library preparation. The goal of the sonication step is to disrupt the observed fragment size distribution, therefore masking local TF-chromatin interactions encoded in the larger fragment sizes (e.g. nucleosome phasing) without affecting the levels of chromatin accessibility.
2020-12-21 | GSE135074 | GEO
Project description:We describe the NucleoATAC algorithm for high-resolution nucleosome positioning and occupancy determination using ATAC-seq. ATAC-seq was performed on Saccharomyces cerevisiae and Schizosaccaromyces pombe. Nucleosomes were called for both species as well as for the human GM12878 cell line using data from GSE47753. Additionally, ATAC-seq was performed on S. cerevisiae undergoing an osmotic stress time-course and nucleosomes were called for each time point.
2015-04-22 | E-GEOD-66386 | biostudies-arrayexpress
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