|
| Status |
Public on May 16, 2024 |
| Title |
ISRH-seq_250ng_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seeding
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: seeding
cell line: seeding
cell type: seeding
genotype: WT
|
| 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 |
SAMN35052004 |
| SRA |
SRX20301921 |
