|
| Status |
Public on Apr 17, 2024 |
| Title |
dpb4D_H3K4me3_ChIP rep1 |
| Sample type |
SRA |
| |
|
| Source name |
fission yeast
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell line: fission yeast
strain: 324
genotype: dpb4D
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 |
SAMN37877471 |
| SRA |
SRX22130959 |
