|
| Status |
Public on May 26, 2018 |
| Title |
wee1-50_delta_mutant 34C Pu-seq |
| Sample type |
SRA |
| |
|
| Source name |
wee1-50_delta_mutant
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: YAK257
genotype/variation: h-, Wee1-50, rnh201::HYG, cdc6L591G ade6-704, leu1-32, ura4-D18
|
| Growth protocol |
Cells were grown on 34C in YPD media to log phase. For ‘wt’ datasets two strains were used, both strains containing rnh201 deletion together with either polymerase δ (cdc6-L591G) or polymerase ε (cdc20-M630F) mutations. These strains incorporate more rNTPs on the strands synthetized by the mutant polymerase. These sites can be mapped by Pu-seq. For the wee1-50, set2Δ and wee1-50 set2 Δ datasets the two strains also contained these mutations along with rnh201 and cdc6-L591G or cdc20-M630F.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was prepared using the QIAGEN 100/G Genomic-tip. The isolated DNA was then subjected to alkali treatment (0.3 M NaOH, 2h 55°C) which digested the DNA at the positions of rNTP incorporation and also separated the double strands. The resulting ssDNA fragments were size selected on agarose gel (fragments between 300-500bp were isolated).
Polymerase usage sequence (Pu-seq) technique was performed as previously described (Daigaku et al., 2015 and Keszthelyi et al. 2015)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
rNTP-pol-d-wee1-50-34C_S7
|
| Data processing |
library strategy: Polymerase usage sequence (Pu-seq)
The reads were mapped using bowtie2
Origin positions and efficiencies were determined using the tools published and described in detail in Daigaku et al., 2015 and Keszthelyi et al. 2015. with default variables except for the ‘percentile threshold for origins’ option was set to 0.2 = 20th percentile.
Genome_build: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets)
Supplementary_files_format_and_content: Bedgraph files contain the position and the efficiency of the origins.
|
| |
|
| Submission date |
Apr 27, 2018 |
| Last update date |
May 26, 2018 |
| Contact name |
Andrea Keszthelyi |
| E-mail(s) |
ak483@sussex.ac.uk
|
| Organization name |
University of Sussex
|
| Department |
Genome Damage and Stability Centre
|
| Lab |
G4.15
|
| Street address |
University of Sussex, Sussex House, Falmer
|
| City |
Brighton |
| ZIP/Postal code |
BN1 9RH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE113747 |
An essential role for dNTP homeostasis following CDKinduced [Pu-seq] |
|
| Relations |
| BioSample |
SAMN08993099 |
| SRA |
SRX4003439 |
