R. Assessing chromatin accessibility in maize using ATAC-seq. Preprint at bioRxiv https://doi.org/10.1101/526079 (2019). Yu, H. G., Hiatt, E. N., Chan, A., Sweeney, M. & Dawe, R. K. Neocentromere-mediated chromosome movement in maize. J. Cell Biol. 139, 831–840 (1997). ...
(ATAC-seq peaks) and TF-binding loci was tested using a per chromosome randomization of TF-binding loci (the number of overlaps as the evaluation function and 10,000 permutations). The observed value appears far from the limit of the threshold (Pvalue < 0.01) of the random distribution...
To further dissect the functional roles of SAM-related homeobox TFs, we gathered comprehensive RNA-seq, ribosome profiling (Ribo-seq), and ATAC-seq datasets collected from various B73 tissues: leaves, SAM, internodes, stems, tassels and endosperm (Additional file 11: Table S10). We defined 18...
Results: We identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatorial epigenome features around these OCRs using ChIP-seq, Bisulfite-seq, and RNA-seq datasets. Our integrative analysis of coordinated ...
Table S1. scRNA-seq and protoplasting-responsive genes datasets, related to Figures 1 and S1–S3 Table S2. scRNA-seq validation by FACS RNA & ATAC-seq, related to Figures 2 and S3 Table S3. scRNA-seq applications, related to Figures 3, 4, and S4 Table S4. Primers, sgRNAs sequences...
RNA-seq Ten tissues were sampled throughout development for evidence-based gene annotation including the following: (1) primary root and (2) coleoptile at 6 days after planting; (3) base of the 10th leaf, (4) middle of the 10th leaf, and (5) tip of the 10th leaf at the Vegetative ...
To better understand how C 4 photosynthesis is regulated at the transcriptional level, we performed RNA‐seq, ATAC‐seq, ChIP‐seq and Bisulfite‐seq (BS‐seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that ...
We construct a dynamic regulome for 27 members of three SAM-related homeobox subfamilies (KNOX, WOX, and ZF-HD) through machine-learning models for the detection of TF targets across different tissues and stages by combining tsCUT&Tag, ATAC-seq, and expression profiling. This dynamic regulome ...
2d). This region was also reported as a chromatin accessibility landscape as determined by the Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) data from a public repository (Supplementary Fig. 4). In addition, this region was identified to have a H3K27me3-HiChIP loop ...
5c) was determined by considering the likelihood of overlap between the ear tissue ATAC-seq dataset and each ARF dataset using the bedtools fisher function from bedtools v2.24.0. Diffbind v2.0.2 occupancy analysis67 was used to generate the consensus clade A-only, clade B-only and shared ...