NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6767120 Query DataSets for GSM6767120
Status Public on Jun 11, 2024
Title S3-ssDRIP-seq-HEK293T-DMSO
Sample type SRA
 
Source name HEK293T
Organism Homo sapiens
Characteristics cell line: HEK293T
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 GPL24676
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 SAMN31944403
SRA SRX18430873

Supplementary file Size Download File type/resource
GSM6767120_S3-ssDRIP-seq-HEK293T-DMSO_RPGC_bin5_cRloop.bw 36.4 Mb (ftp)(http) BW
GSM6767120_S3-ssDRIP-seq-HEK293T-DMSO_RPGC_bin5_wRloop.bw 36.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap