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Series GSE252638 Query DataSets for GSE252638
Status Public on Jan 10, 2024
Title Assessing chromatin accessibility in maize using ATAC-seq
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Overall design We perform the Maize seedling ATAC-Seq using only 2500 and 5000 nuclei, as well as the naked gDNA as control, in a total of three samples with two biological replicates, providing a new way to study the role of chromatin accessibility.
 
Contributor(s) Hsieh JA, Lin P, Wang C, Lee Y, Chang P, Lu RJ, Chen P, Wang Cr
Citation(s) 38863553
Submission date Jan 05, 2024
Last update date Jun 28, 2024
Contact name Pao-Yang Chen
E-mail(s) paoyang@gate.sinica.edu.tw
Organization name Academia Sinica
Department Institute of Plant and Microbial Biology
Street address 128 Sec. 2, Academia Rd, Nankang
City Taipei
ZIP/Postal code 11529
Country Taiwan
 
Platforms (1)
GPL25410 Illumina NovaSeq 6000 (Zea mays)
Samples (6)
GSM8004579 Maize ATAC-seq 2500 nuclei rep1
GSM8004580 Maize ATAC-seq 2500 nuclei rep2
GSM8004581 Maize ATAC-seq 5000 nuclei rep1
Relations
BioProject PRJNA1061549

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE252638_RAW.tar 211.5 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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