|
| Status |
Public on May 01, 2024 |
| Title |
OS152, nuclei, m6dA methylated, rep3, 2.2 polymerase |
| Sample type |
SRA |
| |
|
| Source name |
F
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: F
cell line: OS152 cell line
cell type: metastatic osteosarcoma cell line
genotype: MYC amplified, CN40
treatment: m6dA methylated
|
| Treatment protocol |
Isolated OS152 nuclei were methylated (10uL EcoGII per 1-2e6 nuclei) with non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 1.16mM (NEB) after 15 minutes.
Isolated nuclei (methylated or unmethylated) were tagmented with H-Tn5-R27S,E54K,L372P (QB3 MarcoLab) at 55°C for 1hr.
|
| Growth protocol |
OS152 cells were cultured in standard 1x DMEM supplemented with 10% Fetal Bovine Serum and 1% 100x Penicillin-Streptomycin-Glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tagmented nuclei were pre-treated with 10uL RNaseA at 37°C for 15 minutes, then purified with 2.5uL Proteinase K (20mg/mL), 2.5uL 10% SDS, and 2.5uL 0.5mM EDTA at 60°C for 1-2 hours with continuous shaking at 1000 rpm. DNA was extracted with 2x SPRI bead cleanup.
Tagmented fragments were gap-repaired using Phusion DNA polymerase and Taq Ligase, or T4 DNA polymerase and Ampligase, at 37ºC for 1hr, digested with Exonuclease III at 37ºC for 1hr, then cleaned up using Ampure PB. Library quality was assessed with Qubit 1x High Sensitivity DNA Assay and Agilent Bioanalyzer High Sensitivity DNA kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Sequel II |
| |
|
| Description |
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF.
|
| Data processing |
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular consensus sequences (CCS) using ccs (v6.4.0) with kinetic information
Extracting kinetic information from CCS reads using the SAMOSA-ChAAT computational pipeline
Aligning CCS reads to a modified version of the hg38 reference genome with the contaminant contig KI270752.1 removed using pbmm2 (v.1.9.0)
Assembly: hg38
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Supplementary files format and content: *_zmwinfo.pickle: Python pickle containing a dataframe with length, # of passes, and mean IPD per base per CCS read
|
| |
|
| Submission date |
Feb 14, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Arjun S Nanda |
| Organization name |
Gladstone Institutes / UCSF
|
| Department |
Gladstone Institute for Data Science & Biotechnology
|
| Lab |
Ramani Lab
|
| Street address |
1700 Owens St
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL28352 |
| Series (2) |
| GSE225311 |
Direct transposition of native DNA for sensitive multimodal single-molecule sequencing III |
| GSE225314 |
Direct transposition of native DNA for sensitive multimodal single-molecule sequencing |
|
| Relations |
| BioSample |
SAMN33294078 |
| SRA |
SRX19368009 |
