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Sample GSM3772635 Query DataSets for GSM3772635
Status Public on Sep 20, 2019
Title DRIP enriched and RNaseH treated
Sample type SRA
Source name NTERA-2 cell line
Organism Homo sapiens
Characteristics treatment: +S9.6 +RNaseH
Extracted molecule genomic DNA
Extraction protocol Pelleted cells were lysed with Proteinase K and 20% SDS. Nucleic acids were extracted using phenol:chloroform:isoamyl alcohol and phase separated using phase lock tubes. Samples were then digested using restriction enzyme cocktails then treated with sodium bisulfite in a non-denaturing way.
SMRTbell libraries were constructed using Pacific Bioscience's amplicon template preparation protocol.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model PacBio RS II
Data processing Library strategy: SMRF-seq
Pacbio reads were pre-processed into CCS reads using Pacbio SMRT Link v6.0 (default parameters).
Raw Pacbio CCS reads were mapped using bismark v0.20.0 with the following parameters: -q --score-min L,0,-0.3 --rdg 5,3 --rfg 5,3 --ignore-quals
SMRF-seq peaks were called using a sliding window algorithm with the following parameters: minimum cytosine conversion threshold of 55% and peak length of 100bp.
DRIPc-seq reads were trimmed with fastq-mcf v2.4.4 and mapped with bowtie2 v2.2.6 (sDRIP-seq) with defaulte parameters.
Genome_build: hg19
Supplementary_files_format_and_content: GFF files were generated using sliding window algorithm; Each row represents the coordinates of an R-loop peak in a specific read (read names are specified in column 9). DRIPc-seq bedGraph files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; Scores (Column 4) indicate tag per million (x30).
Submission date May 16, 2019
Last update date Sep 20, 2019
Contact name Frederic Chedin
Organization name UC Davis
Department MCB
Lab Chedin
Street address 1 Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platform ID GPL21311
Series (1)
GSE130726 High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation
BioSample SAMN11663716
SRA SRX5849994

Supplementary file Size Download File type/resource
GSM3772635_PCB6.gff.gz 8.9 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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