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Sample GSM6422266 Query DataSets for GSM6422266
Status Public on Aug 08, 2022
Title OS152, nuclei, m6dA methylated, rep4
Sample type SRA
 
Source name OS152 cell line
Organism Homo sapiens
Characteristics Sex: 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
OS152_PR30_plusM
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
Library strategy: SMRT-Tag Library Preparation
 
Submission date Jul 31, 2022
Last update date Feb 18, 2023
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)
GSE210136 Direct transposition of native DNA for sensitive multimodal single-molecule sequencing I
GSE225314 Direct transposition of native DNA for sensitive multimodal single-molecule sequencing
Relations
BioSample SAMN30072547
SRA SRX16745138

Supplementary file Size Download File type/resource
GSM6422266_SAMOSA-Tag.OS152_PR30_plusM_full.pickle.gz 14.0 Gb (ftp)(http) PICKLE
GSM6422266_SAMOSA-Tag.OS152_PR30_plusM_zmwinfo.pickle.gz 16.4 Mb (ftp)(http) PICKLE
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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