|
| Status |
Public on Sep 02, 2022 |
| Title |
fast5 Pol2REL_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MATa
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: MATa
genotype: MATa pol2-REL::Kan MCM4-N-ter-MNase LEU2::BrdU-Inc URA3::GPD-TK7
treatment: G1 arrested with alpha factor and released with BrdU at 25C
|
| 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 30C 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 |
Biological replicates for Pol2REL mutants
DNA replicons
MinION nanopore
|
| 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
position and orientation of the reads primers were defined using LAST ( kielbasa et al, 2011)
Assembly: Custom genome was constructed from Nanopre reads using Canu.
|
| |
|
| Submission date |
Aug 26, 2022 |
| Last update date |
Sep 02, 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) |
| GSE212101 |
Balanced act of a leading strand DNA polymerase specific domain and its exonuclease domain promotes genome-wide replication fork symmetry |
|
| Relations |
| BioSample |
SAMN30521761 |
