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| Status |
Public on Sep 20, 2019 |
| Title |
DRIP enriched |
| Sample type |
SRA |
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| Source name |
NTERA-2 cell line
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| Organism |
Homo sapiens |
| Characteristics |
treatment: +S9.6
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
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| 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).
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| Submission date |
May 16, 2019 |
| Last update date |
Sep 20, 2019 |
| Contact name |
Frederic Chedin |
| E-mail(s) |
[email protected]
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| Organization name |
UC Davis
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| Department |
MCB
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| Lab |
Chedin
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| Street address |
1 Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL21311 |
| Series (1) |
| GSE130726 |
High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation |
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| Relations |
| BioSample |
SAMN11663719 |
| SRA |
SRX5849991 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3772632_PCB1.gff.gz |
2.5 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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