|
| Status |
Public on Apr 19, 2018 |
| Title |
SynII_G2 |
| Sample type |
SRA |
| |
|
| Source name |
genomic DNA from G2 cells enriched by FACS from asynchronous culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: SynII_corrected
relevant genotype: his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 SynII-Y::URA3
|
| Treatment protocol |
Cells were sorted by DNA content, selecting S phase and G2 phase cells
|
| Growth protocol |
Cells were harvested from mid-log phase cultures grown in YPD media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells obtained from FACS were resuspended in 500 µL of 1.2 M sorbitol, 200 mM Tris-HCl (pH7.5), 20 mM EDTA, 0.1% b-mercaptoethanol. Cells were spheroplasted with Zymolyase and then treated with SDS, Proteinase K and RNase A. DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to Illumina instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
In the processed data file the values for each chromosome were generated by dividing by 2.7
|
| Data processing |
Reads were mapped to the references genome sequence (using the Stampy package).
Samtools view was used to filter reads, retaining uniquely mapped reads with each segment properly aligned according to the aligner (-f 2) and with high mapping quality (-q 50).
Replication timing profile was generated by normalizing the replicating (S phase) sample to the non-replicating (G2) sample in 1 kb windows.
Windows where fewer than 250 reads were mapped in either sample were excluded.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor.
Genome_build: SynII_genome_complete.fa
Supplementary_files_format_and_content: Processed files (*.wig) are available as Series supplementary files.
|
| |
|
| Submission date |
Nov 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Conrad A Nieduszynski |
| Organization name |
Earlham Institute
|
| Lab |
DNA replication & genome stability
|
| Street address |
Norwich Research Park
|
| City |
Norwich |
| ZIP/Postal code |
NR4 7UZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE89611 |
Deep functional analysis of synII, a 770 kb synthetic yeast chromosome |
|
| Relations |
| BioSample |
SAMN05991006 |
| SRA |
SRX2333019 |
