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Series GSE232347 Query DataSets for GSE232347
Status Public on May 16, 2024
Title ISRH-seq: a sensitive and robust methodology for R-loop profiling
Organism Oryza sativa
Experiment type Other
Summary R-loops serve as key modulators in various biological processes in humans and plants.Current high-throughput methodologies for R-loop profiling have their own intrinsic pros and cons. Therefore, any robust, sensitive, and amenable methods, complementary and/or advantageous to existing methodologies, are much needed for advancing R-loop biology. We here present an RNase H based cleavage combined with DNA polymerase-mediated in situ biotin-dATP/dCTP labeling of newly synthesized DNA for sequencing, termed ISRH-seq, an antibody-independent approach for strand-specific mapping of R-loops. After conducting a parallel comparison with DRIP-seq, we found that ISRH-seq can identify more R-loop peaks with the same sequencing depth. Moreover, ISRH- and DRIP-specific R-loops had distinct genomic and epigenetic features, exhibited distinct relationships with expression of overlapping genes, and functional divergence. Importantly, we found that ISRH-seq can be scalable down to 250-100ng DNA input, indicative of a robust and sensitive high-throughput methodology. In addition, it can be applied for R-loop profiling under stress conditions. Thus, our study provides a valuable orthogonal methodology for comprehensive profiling of R-loops in plants. It could be easily adapted to other non-plant systems, especially for these biologically important tissues or cell types with limited cell numbers, thereby advancing understanding of R-loop biology.
 
Overall design ISRH-seq
 
Contributor(s) Zhang W, Yang Y, Wu J, Li M
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Submission date May 11, 2023
Last update date May 16, 2024
Contact name Wu Jing
E-mail(s) wj_0922@yeah.net
Organization name Nanjing Agricultural University
Street address No.1 Weigang, Nanjing, Jiangsu
City Nanjing
ZIP/Postal code 210000
Country China
 
Platforms (1)
GPL27660 Illumina NovaSeq 6000 (Oryza sativa)
Samples (18)
GSM7329017 ISRH-seq_8μg_rep1
GSM7329018 ISRH-seq_8μg_rep2
GSM7329019 ISRH-seq_5μg_rep1
Relations
BioProject PRJNA971645

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Supplementary file Size Download File type/resource
GSE232347_RAW.tar 1.3 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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