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Series GSE243806 Query DataSets for GSE243806
Status Public on Apr 28, 2024
Title aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs
Organisms Citrus sinensis; Dianthus caryophyllus; Populus; Arabidopsis thaliana; Brassica napus; Glycine max; Solanum lycopersicum; Solanum tuberosum; Oryza sativa; Saccharum officinarum; Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. aChIP precisely profiles histone modifications in all 14 tested EIPOs and identifies transcription factor and chromatin-modifying enzyme binding sites. In addition, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared with previous methods in vegetative tissues. aChIP reveals the histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Altogether, aChIP is a powerful, efficient and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs.
 
Overall design We demonstrate the widespread utility of advanced ChIP-seq (aChIP) by profiling diverse chromatin proteins in 14 representative EIPOs including the extremely challenging dry seeds. aChIP shows excellent efficiency and sensitivity in vegetative tissues compared with previous methods. Finally, we profiled the landscape of histone modifications and unveiled their potential functions in rapeseed dry seeds and germinated seeds. Collectively, the data illustrate the great potential of using aChIP to unveil the intricacies of chromatin biology and shed light on their biological functions in plants, particularly within EIPOs.
Web link https://www.nature.com/articles/s41477-024-01743-7
 
Citation(s) 39179701
Submission date Sep 22, 2023
Last update date Oct 25, 2024
Contact name Wenying Zhong
E-mail(s) wenyingzhong@webmail.hzau.edu.cn
Organization name Huazhong Agricultural University
Street address Lion Rock Street
City Wuhan
ZIP/Postal code 430072
Country China
 
Platforms (11)
GPL25410 Illumina NovaSeq 6000 (Zea mays)
GPL26208 Illumina NovaSeq 6000 (Arabidopsis thaliana)
GPL27660 Illumina NovaSeq 6000 (Oryza sativa)
Samples (162)
GSM7795818 15d_maize_seeds_H3K27me3_aChIP-seq_rep1
GSM7795819 15d_maize_seeds_H3K27me3_aChIP-seq_rep2
GSM7795820 15d_maize_seeds_H3K4me3_aChIP-seq_rep1
This SuperSeries is composed of the following SubSeries:
GSE243804 aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [ChIP-Seq]
GSE243805 aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [RNA-Seq]
Relations
BioProject PRJNA1020073

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

Supplementary file Size Download File type/resource
GSE243806_RAW.tar 100.3 Mb (http)(custom) TAR (of BROADPEAK, NARROWPEAK)
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