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Sample GSM6625541 Query DataSets for GSM6625541
Status Public on Nov 10, 2022
Title Sample 34_fkh1∆fkh2-dsm_rep2
Sample type SRA
 
Source name Yeast cells
Organism Saccharomyces cerevisiae
Characteristics strain: HYy218
antibody: Non
genotype: fkh1{delta}fkh2-dsm
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 SAMN31231907
SRA SRX17843597

Supplementary file Size Download File type/resource
GSM6625541_fkh1fkh2dsm_rep2_To.bed.gz 1.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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