 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 11, 2024 |
| Title |
S6-ssDRIP-seq-3T3-DMSO |
| Sample type |
SRA |
| |
|
| Source name |
NIH/3T4
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NIH/3T4
genotype: WT
treatment: DMSO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed by 0.5% SDS and digested with 0.1mg/mL proteinase K (TransGen Biotech#: GE201-01) at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method.
Genomic DNA was directly sonicated to 250 bp using ME220 (Covaris, 70 W, 20% Duty factor, 1000 cycles per burst, 130 s, at 4–20°C) before DRIP. After DRIP with antibody S9.6, Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences) was used for library preparation following the manufacturer’s manual.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
library strategy: ssDRIP-seq
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads with low quality and adaptor contamination were trimmed, and short reads less than 50 pb were filtered by Trim Galore (version 0.6.7)
After trimming, clean reads were aligned to the genomes (BW25113 genome for E. coli, GRCh38 genome for humans, mm10 genome for mice) with Bowtie 2 (version 2.2.5) using local alignment mode.
Assembly: BW25113 genome for E. coli, GRCh38 genome for humans, mm10 genome for mice.
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Nov 30, 2022 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Changbin Sun |
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Department |
Agricultural Genomics Institute at Shenzhen
|
| Lab |
Guangdong Laboratory of Lingnan Modern Agriculture
|
| Street address |
Dapeng
|
| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE219069 |
ssDRIP-seq: a high-throughput method for R-loop mapping and quantitative assessment |
| GSE219071 |
mDRIP-seq is a high-throughput method for quantitative R-loop landscape profiling |
|
| Relations |
| BioSample |
SAMN31944400 |
| SRA |
SRX18430876 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6767123_S6-ssDRIP-seq-3T3-DMSO_RPGC_bin5_cRloop.bw |
89.8 Mb |
(ftp)(http) |
BW |
| GSM6767123_S6-ssDRIP-seq-3T3-DMSO_RPGC_bin5_wRloop.bw |
89.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
