|
| Status |
Public on Nov 10, 2022 |
| Title |
Sample 29_dbf4-Zn*2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: MPy76
antibody: Non
genotype: dbf4-Zn*2 (H680C)
treatment: hydroxyurea
|
| Treatment protocol |
Cells were arrested with α-factor (~5 nM ) and incubated for ~4 h at 23 °C then released in fresh YEPD containing 400 μg/mL BrdU, 200 μg/mL Pronase and 200 mM hydroxyurea. Harvested cells after 60min of incubation.
|
| Growth protocol |
10–20 mL of cells were grown per sample to OD ~ 0.5 in YEPD at 23 °C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were resuspend in 500 μL genomic lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
BrdU-IP sequencing
|
| Data processing |
library strategy: BrdU-IP-seq
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: S228C
Supplementary files format and content: binned.bed files
|
| |
|
| Submission date |
Oct 10, 2022 |
| Last update date |
Nov 12, 2022 |
| Contact name |
Meghan V Petrie |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Southern California
|
| Department |
Molecular Biology
|
| Street address |
1050 Childs Way
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089-2910 |
| Country |
USA |
| |
|
| Platform ID |
GPL26302 |
| Series (1) |
| GSE215190 |
Dbf4 Zn-finger motif is specifically required for stimulation of Ctf19-activated origins in S. cerevisiae |
|
| Relations |
| BioSample |
SAMN31231912 |
| SRA |
SRX17843592 |
