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Series GSE85203 Query DataSets for GSE85203
Status Public on Nov 30, 2016
Title Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes
Organisms Arabidopsis thaliana; Zea mays subsp. mays
Experiment type Other
Summary Chromatin structure plays a pivotal role in facilitating proper control of gene expression. The ability of transcription factors (TF) to bind cis-elements is often associated with accessible chromatin regions. Therefore, identification of these accessible regions throughout plant genomes is important to understanding the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes. However, in plants, the existence of cell walls, subcellular organelles and the lack of stable cell lines have prevented routine application of this technique. Here, we describe an assay combining ATAC-seq with Fluorescence-Activated Nuclei Sorting (FANS) to identify and map open chromatin and TF-binding sites in plant genomes. FANS-ATAC-seq compares favorably with published DNaseI sequencing (DNase-seq) results and it only requires 500-50,000 nuclei for accurate identification of open chromatin states.
Overall design Chromatin accessibility profiling (FANS-ATAC-seq) data collected from Arabidopsis 7-day old Col-0 whole seedlings, roots, 35S:H2AX-GFP/Col-0 whole seedlings, or 10-day old maize B73 overground parts. Replicates are included when available.
Please note that the *1million_reads raw data were used to generate the percentage of nuclear and organelle reads data, which is included in the associated manuscript as supplementary data table (therefore not included in the GEO records).
Contributor(s) Schmitz RJ, Lu Z
Citation(s) 27903897
Submission date Aug 04, 2016
Last update date May 15, 2019
Contact name Robert J Schmitz
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
Platforms (2)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL22285 Illumina NextSeq 500 (Zea mays subsp. mays)
Samples (14)
GSM2260231 Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep1
GSM2260232 Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep2
GSM2260233 Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep1
BioProject PRJNA336549
SRA SRP080945

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Supplementary file Size Download File type/resource
GSE85203_RAW.tar 1.7 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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