 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 20, 2019 |
| Title |
GDpol1-4A-5-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
GDpol1-4A-5
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain/background: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB
genotype/variation: GAL1-DHFR-pol1-4A
|
| Treatment protocol |
Add rapamycin for one hour.
|
| Growth protocol |
30°C, grow overnight in YEP + 3% raffinose + 0.5% galactose until log phase then switched into various galactose concentrations + 3% raffinose for four hours.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Okazaki Fragments
|
| Data processing |
Bowtie2 (version 2.2.3) was used to align paired-end fastq files to the S. cerevisiae reference genome.
Sam files were converted to bam files using samtools, then reads were sorted.
Bam files were converted to bed files using bedtools paired end function and PCR duplicates were removed.
Printed columns for the chromosome, position of the start and stop of the read, and the strand information into output bed files.
Genome_build: Yeast S288C, build R64-1-1
Supplementary_files_format_and_content: bed files: chromosome, start and end positions of mapped reads, strand information.
Supplementary_files_format_and_content: OEM_position_timing.xls: Origin location (chromosome and base pair), origin efficiency metric for all replicates and conditions: calculated using methodology from (McGuffee et al. (2013) Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Mol Cell 50, 123-135), and timing of origin firing during S phase (early or late).
|
| |
|
| Submission date |
May 20, 2019 |
| Last update date |
May 21, 2019 |
| Contact name |
Duncan Smith |
| E-mail(s) |
duncan.smith@nyu.edu
|
| Phone |
212-992-6595
|
| Organization name |
New York University
|
| Department |
Dept. of Biology/Center for Genomics and Systems Biology
|
| Street address |
1009 Silver Center, 100 Washington Sq E
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE115897 |
Separable recruitment of DNA Polymerase α for leading- and lagging-strand replication initiation |
|
| Relations |
| BioSample |
SAMN11790873 |
| SRA |
SRX5872578 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3785201_GDpol1-4A-5-rep2.bed.gz |
17.7 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
