|
| Status |
Public on Aug 05, 2024 |
| Title |
H3K9me3_snf5_CDx2_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ snf5-3xHA-chp1CD-FLAG-chp1CD::KanMX6
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SpRKS325
chip antibody: Abcam anti-H3K9me3 8898
growth: Growth in YEA 30C
fixation: 3% PFA
|
| Growth protocol |
Growth in YEA at 30°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked using 3% PFA at room temperature or 18°C for 30 min. Cells were spun at 3000rpm for 5 min washed 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 200–700 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 MiSeq |
| |
|
| Description |
H3K9me3_snf5_CDx2_Rep1
|
| Data processing |
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs from ChIPseq were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li, H. & Durbin, 2009). Macs2 (Zhang, Y. et al. 2008) was used to process the resulting BAM files to product bedgraphs normalized to input and untagged controls. Deeptools (Ramirez et al. 2016) bamCoverage was used to generate CPM normalized bedgraphs for input and untagged BAMS.
Assembly: S. pombeV2 reference with the sequence of the full 40 kbmatregion provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).
|
| |
|
| Submission date |
Jun 06, 2024 |
| Last update date |
Aug 05, 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 |
GPL16192 |
| Series (1) |
| GSE269243 |
Nucleosome remodeler exclusion by histone deacetylation enforces heterochromatic silencing and epigenetic inheritance |
|
| Relations |
| BioSample |
SAMN41708244 |
| SRA |
SRX24823476 |
