NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7847988 Query DataSets for GSM7847988
Status Public on Apr 17, 2024
Title pob3_H3K4me3_ChIP rep1
Sample type SRA
 
Source name fission yeast
Organism Schizosaccharomyces pombe
Characteristics cell line: fission yeast
strain: 392
genotype: pob3
treatment: H3K4me3_ChIP
Treatment protocol BrdU was added to a final concentration of 650 μM at 25minutes after the temperature shift.
Growth protocol Strains containing the cdc25-22 temperature-sensitive mutant were first grown at permissive temperature (25°C) until the early-mid log phase (OD 0.2~0.4). Cultures were then incubated at 36°C for 4 hours to arrest cells at the G2 phase of the cell cycle. Cells were then shifted to 25°C to allow them to enter the S phase synchronously.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked at 60 minutes after temperature shift with the addition of 1% formaldehyde and incubated for 20 minutes with shaking at 25°C. Immunoprecipitation was performed as described in ChIP. Crosslinking was reversed by Chelex-100. Briefly, total and ChIP DNA were incubated at 100°C for 5 minutes and then immediately cooled on ice for 5 minutes. DNA was diluted ten times with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v)), and incubated with BrdU antibody (BD Bioscience 555627) for two hours at 4°C. Next, Sepharose Protein G beads (Cytiva 17-0618-01) were added and incubated for an additional one hour at 4°C. The beads were then washed three times with BrdU IP buffer and once with TE. Finally, DNA was eluted with TES and purified with the QIAGEN MinElute PCR Purification kit (Qiagen 28004).
Accel­NGS 1S Plus DNA library kit (Swift Bioscience, 10096).
eSPAN-seq
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description synchronized to G2 ending, nascent DNA on S10 min
Data processing mapped to pombe reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Origins were called by MACS2 from BrdU-IP
Assembly: pombe, ASM294v2
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position
 
Submission date Oct 18, 2023
Last update date Apr 17, 2024
Contact name zhiguo zhang
Organization name Columbia University
Department Pediatric and Genetics and Development
Lab Irving Cancer Research Center
Street address 1130 St. Nicholas Avenue
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL20584
Series (1)
GSE237770 Coordination of histone chaperones for parental histone segregation and epigenetic inheritance
Relations
BioSample SAMN37877415
SRA SRX22130967

Supplementary file Size Download File type/resource
GSM7847988_YM205_WT_H3K56ac_eSPAN.tar.gz 116.0 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap