|
| Status |
Public on May 12, 2017 |
| Title |
Rad18-proficient,70 min, IP |
| Sample type |
SRA |
| |
|
| Source name |
Genomic DNA from rad18+ cells 70 min after cdc25 G2 arrest and release
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: YDP18
genotype/variation: h- smt-0 leu1-32 ade6-704 leu1::[leu1-adh:hENT1] his7+ adh1::hsv-TK cdc25-22
cell type: Rad18-proficient
protocol: cdc25 G2 arrest and release
time (after release): 70 min
chip antibody: anti-BrdU antibody (BD biosciences, catalog# 347580)
|
| Growth protocol |
Cells were synchronized in G2 phase by cdc25 block, released into meduim containing 0.5 micro-M of BrdU and sampled at 70 min after release
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was subjected to immunoprecipitation with anti-BrdU antibody. The yielded single-stranded DNA was converted to double strands, which were used for Illumina library preparation using NEBNext® Ultra™ DNA Library Prep Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
rad18-plus-70min-IP
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig
|
| Data processing |
Sequence pair-end reads were mapped to the S. pombe reference genome using bowtie2 with 50bp-triming of 3'-side of R1 and R2 reads.
Pairs of sequence reads which were properly aligned were selected based on 0x2 bit of the flag paramer of each pair.
Pairs of sequence read mapping to a single genomic location: 300-bp bin were summed.
Normalized numbers were generated by dividing the sequence pair counts at each bin by the total number of reads.
Replication progression was calculated (see the original paper) for each 300 bp region of the genome (termed local replication rate) when the whole genome was either 25, 50 or 75% replicated.
Genome_build: ASM294v2.23
Supplementary_files_format_and_content: Wig files, datasets of local replicarion rates across the genome
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasukazu Daigaku |
| E-mail(s) |
yasukazu.daigaku@jfcr.or.jp
|
| Organization name |
Japanese Foundation for Cancer Research
|
| Department |
Cancer institute
|
| Lab |
Cancer Genome Dynamics
|
| Street address |
3-8-31 Ariake Koto-ku
|
| City |
Tokyo |
| ZIP/Postal code |
1358550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE70033 |
The role of PCNA ubiquitylation during unperturbed genome replication in S.pombe |
|
| Relations |
| BioSample |
SAMN03782962 |
| SRA |
SRX1066392 |
