|
| Status |
Public on Jan 26, 2022 |
| Title |
WT-RNAseq-2 |
| Sample type |
SRA |
| |
|
| Source name |
WT
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: 30min S-phase at 25C with 15min pulsed labelled of 4-thiouracil
|
| Treatment protocol |
Cells were arrested into G1 phase with alpha factor, 15min after release from G1, 4-thiouracil was added to the culture to labelled nascent RNAs, cells were collected 30min after alpha factor release.
|
| Growth protocol |
yeast were grown at 25C in rich media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using invitrogen extraction kit and as described in Baptista and Devys, 2018; mRNA was enriched using NEB mRNA selection kit #E7490S
Library was constructed using SQK-DSC109 library kit (Oxford Nanopore)
Nanopore MinION FLO-MIN106 flow cells R9
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
RNAs were pulsed labeled for 15min, 15min after released with
|
| Data processing |
Base calling was performed using Guppy (Oxford Nanopore)
Reads were mapped to the genome using Minimap2
position and orientation of the reads primers were defined using LAST ( kielbasa et al, 2011)
|
| |
|
| 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 |
SAMN25124847 |
| SRA |
SRX13834084 |
