|
| Status |
Public on Feb 02, 2024 |
| Title |
Mcm2_220818_WT_S |
| Sample type |
SRA |
| |
|
| Source name |
SPPN3a
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPPN3a
genotype: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcm2-GFP:kan cdc25-22 otr1R(Sph1)::ura4+
chip antibody: Abcam anti-GFP 290
growth: Growth in YEA 36degreeC and 26degreeC
fixation: 3percent PFA
|
| Growth protocol |
Growth in EMM and YEA, 26°C and 36°C, 30°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked using 3% PFA at room temperature for 30 min. Cells were spun at 2,000g for 10 min and pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 300–600 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mcm2_220818_WT_S
|
| Data processing |
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
|
| |
|
| Submission date |
Sep 05, 2023 |
| Last update date |
Feb 02, 2024 |
| Contact name |
Shiv Grewal |
| E-mail(s) |
grewals@mail.nih.gov
|
| Phone |
240-760-7553
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
Laboratory of Biochemistry and Molecular Biology
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL20584 |
| Series (2) |
| GSE242353 |
Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance [ChIP-seq] |
| GSE242431 |
Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance |
|
| Relations |
| BioSample |
SAMN37285310 |
| SRA |
SRX21637806 |
