NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE243804 Query DataSets for GSE243804
Status Public on Apr 28, 2024
Title aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [ChIP-Seq]
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
Summary Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.
 
Overall design Chromatin Immunoprecipitation followed by seqencing (ChIP-seq) for histone modifications (H3K4me3 and H3K27me3), transcription factors (RNAPII and CAMTA3), DNA binding proteions (MBD7) and chromatin enzymes (DME) in different economically important plant organs (EIPOs) and vegetative tissues.
 
Contributor(s) Zhang Q, Zhong W, Zhao L
Citation missing Has this study been published? Please login to update or notify GEO.
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 (154)
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 SubSeries is part of SuperSeries:
GSE243806 aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs
Relations
BioProject PRJNA1020082

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
GSE243804_RAW.tar 100.3 Mb (http)(custom) TAR (of BROADPEAK, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap