|
| Status |
Public on Feb 18, 2022 |
| Title |
DT40 |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblast
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: DT40
cell type: avian leukosis virus (ALV)-induced bursal lymphoma
|
| Treatment protocol |
Asynchronously growing cells were treated with 20 µM of 5-ethynyl-2′-deoxyuridine (EdU) for 2 min when 70-80 % confluent (0.8 millions of cells per ml)
|
| Growth protocol |
DT40 cells were cultured in RPMI 1640 medium supplemented with 10% Fetal Bovine Serum (FBS), 1% chicken serum, 50µM of betamercaptoethanol and penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Okazaki fragments were isolated by sucrose gradient size-fractionation of genomic DNA followed by click-chemistry biotinylation and streptavidin capture of EdU-labelled DNA as described previously (PMID: 26751768).
Okazaki fragments were treated with NaOH to remove 5' RNA, 5' phosphorylated with T4 polynucleotide kinase (PNK), hydridized and ligated to double-stranded adapters, followed by ampfication and bar-coding in PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DT40 OK-seq
|
| Data processing |
Library strategy: OK-seq
bcl2fastq2 v2.15.0 (demultiplex)
Cutadapt 1.3 (adapter trimming)
FastQC 0.10.1 (quality control)
BWA 0.7.4 (mapping) then merge the original BAM with re-amplificated BAM together by samtools
home-made script for replication fork direction (RFD)
Genome_build: Galgal4
Supplementary_files_format_and_content: bigwig file for forward and reverse strand and RFD profile
|
| |
|
| Submission date |
Feb 15, 2022 |
| Last update date |
Feb 18, 2022 |
| Contact name |
Chunlong Chen |
| E-mail(s) |
chunlong.chen@curie.fr
|
| Organization name |
Institut Curie
|
| Department |
UMR3244
|
| Street address |
26 rue d’Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE196761 |
Genome-wide replication fork directionality measured by strand-specific sequencing of Okazaki fragments in chicken lymphoma cells (DT40). |
|
| Relations |
| BioSample |
SAMN25965008 |
| SRA |
SRX14187411 |
