|
| Status |
Public on Jan 26, 2022 |
| Title |
WT-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
WT
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: 30min S-phase at 25C with 400ug/mL BrdU
|
| Treatment protocol |
Cells are arrested in G1 with alpha factor; 400ug/mL of BrdU was added 30min before release from G1 , cells were released into pre-warmed media containing 400ug/mL BrdU.
|
| Growth protocol |
yeast were grown at 25C in rich media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted as in Replicon-seq protocol after calcium induction of MNase
Library was constructed using SQK-SKL109 or SQK-SKL110 kit (Oxford Nanopore)
Nanopore MinION FLO-MIN106 flow cells R9
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Description |
cell were arrested with alpha factor, released in presence of 400ug/mL brdu at 25C, and collected at 30min after release for replicon-seq experiment
|
| Data processing |
Base calling was performed using Guppy (Oxford Nanopore)
Reads were mapped to the genome using Minimap2
BrdU containing reads were call using DNAscent V2, reads were split into 250bp interval to assign as BrdU positive or negative reads, BrdU score was then calculated, and only reads with a BrdU > or = 0.5 were selected
Custom genome was constructed from Nanopre reads using Canu.
|
| |
|
| Submission date |
Jan 19, 2022 |
| Last update date |
Jan 26, 2022 |
| Contact name |
clemence claussin |
| E-mail(s) |
claussin.clemence@gmail.com
|
| Organization name |
Memorial sloan kettering cancer center
|
| Department |
molecular biology
|
| Lab |
whitehouse iestyn
|
| Street address |
1275 York Avenue
|
| City |
new york |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL25739 |
| Series (1) |
| GSE194025 |
Single-molecule mapping of replisome progression |
|
| Relations |
| BioSample |
SAMN25124851 |
| SRA |
SRX13834080 |
