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Sample GSM7329031 Query DataSets for GSM7329031
Status Public on May 16, 2024
Title ISRH-seq_salt_rep1
Sample type SRA
 
Source name seeding
Organism Oryza sativa
Characteristics tissue: seeding
cell line: seeding
cell type: seeding
genotype: WT
treatment: three-day-salt treated
Growth protocol spread into nutrient soil in the pot or hydroponics for 150 mM NaCl treatment for continuing to grow in the greenhouse at 28-30°C and 14 h/10 h light-dark cycle
Extracted molecule genomic DNA
Extraction protocol Purified genomic DNA was fragmented into size as 200-500bp using a sonicator. 100ng, 250ng, 500ng, 3 µg, 5 µg and 8 µg fragmented DNA was used for RNase H in combination with DNA polymerase I for in situ labeling with a total 200 µl reaction at 16℃ for 2h
Streptavidin bound biotin labeled DNA strand was used for single-stranded DNA library preparation using scale ssDNA-seq Lib Prep Kit for Illumina V2 (RK20228, ABclonal Technology, China)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Sequenced reads were trimmed for adaptor sequences using Fastp
Bowtie2(version 2.2.5)was used for aligning clean reads to the rice reference genome (MSU version7.0) with default parameters
R-loop peak calling was performed using MACS2 (version 2.1.4)
Assembly: MSU v7.0
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: ISRH-seq
 
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
 
Platform ID GPL27660
Series (1)
GSE232347 ISRH-seq: a sensitive and robust methodology for R-loop profiling
Relations
BioSample SAMN35052001
SRA SRX20301924

Supplementary file Size Download File type/resource
GSM7329031_ISRH-seq_salt_rep1.bw 75.6 Mb (ftp)(http) BW
GSM7329031_ISRH-seq_salt_rep1.peaks.txt.gz 836.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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