|
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 |