|
| Status |
Public on Mar 29, 2019 |
| Title |
80% BrdU / 20% T media (control input) |
| Sample type |
SRA |
| |
|
| Source name |
genomic DNA from cells grown in YPG media containing 100 uM of 80% BrdU and 20% thymidine for 24 hours
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YVL11
relevant genotype: MATa ADE2 cdc21::kanMX leu2::LEU2-GAL-hENT1 LYS2 RAD5 trp1::TRP1-GAL-dNK ura3-1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested, spun down, washed in water, and then 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 and ONT instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Illumina sequencing reads from control input sample
|
| Data processing |
Illumina: sequencing reads were demultiplexed and the barcode sequences were trimmed using the FASTX toolkit
Illumina: Sequencing reads were mapped to the sacCer3 genome assembly using bowtie2
Illumina: Read tag counts were determined for the 5’ end of uniquely mapping reads without mismatches in 100 bp nonoverlapping regions
Illumina: The ratio between IP and Input sample was calculated for each bin, excluding bins that had less than 20% of the expected number of reads in the input sample
Illumina: Ratios were median-smoothed over 1 kb windows
Nanopore: Basecalling was perform with Albacore
Nanopore: Aligned reads to sacCer3 reference using minimap2
Nanopore: Detected BrdU in reads using D-NAscent
Nanopore: D-NAscent converts called BrdU sites to psl files
Nanopore: D-NAscent converts regions of called BrdU into bedgraphs
Genome_build: sacCer3
Supplementary_files_format_and_content: bed files show either BrdU-seq data or D-Nascent origin calls
Supplementary_files_format_and_content: bedgraphs show either BrdU calls or fork direction
Supplementary_files_format_and_content: psl files show hard call BrdU detectiondata
|
| |
|
| Submission date |
Oct 29, 2018 |
| Last update date |
Mar 29, 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 |
GPL19756 |
| Series (1) |
| GSE121941 |
Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads |
|
| Relations |
| BioSample |
SAMN10343418 |
| SRA |
SRX4952556 |
