|
| Status |
Public on Sep 09, 2020 |
| Title |
wt 1mM H2O2_H3K9me2 |
| Sample type |
SRA |
| |
|
| Source name |
S. pombe cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: h- ED972 wild-type (wt)
phenotype: wild-type phenotype
treatment: treated with 1 mM H2O2 for 18 hr
chip antibody: 5.1.1 mouse monoclonal anti-H3K9me2 antibody kindly provided by Takeshi Urano (Nakagawachi et al. 2003. Oncogene)
|
| Treatment protocol |
Cells were fixed with 1% formaldehyde for 15 min at room temperature
|
| Growth protocol |
Cells were grown in liquid yeast extract plus supplements (YES) media at 32C to a concentration of 5x10^6-1x10^7 cells/mL
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed by bead beating and chromatin was sheared by sonication. Lysates were incubated with antibody and Protein-G Dynabeads overnight. Immunoprecipitated genomic DNA was recovered using PCR purification columns.
Libraries were prepared for Illumina sequencing with 1-5 ng of ChIP or 10 ng of input DNA using NEXTflex adaptors and Ampure XP beads. Barcoded libraries were pooled and sequenced following Illumina HiSeq 2000, NextSeq or MiniSeq workflows.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP DNA
|
| Data processing |
ChIP-Seq: Raw reads were de-multiplexed and trimmed using Trimmomatic (v0.35) to remove adapter contamination and regions of poor sequencing quality. Trimmed reads were aligned to the S. pombe reference genome (972h-, ASM294v2.20) using Bowtie2 (v2.3.3). Resulting bam files were processed using Samtools (v1.3.1) and picard-tools (v2.1.0) for sorting, removing duplicates and indexing. Ratios IP/input were calculated using BamCompare (deepTools v2.0) in SES mode for normalisation.
sRNA-Seq: Raw reads were de-multiplexed. Raw reads were trimmed using Cutadapt (v1.17) to remove adapters and filter out reads <19 nt and >25 nt. Filtered fastq files were then processed using SCRAM and coverage files (.csv) at defined locations (cen1L, hba1 locus, ncRNA394 locus) were obtained.
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: ChIP-Seq: bigWig files of ratio IP/input. sRNA-Seq: csv files indicating coverage over specific genomic locations (cen1L / hba1locus / ncRNA394 locus).
|
| |
|
| Submission date |
Oct 04, 2019 |
| Last update date |
Mar 03, 2021 |
| Contact name |
Sito Torres-Garcia |
| E-mail(s) |
j.torres@ed.ac.uk
|
| Organization name |
Wellcome Centre for Cell Biology. University of Edinburgh
|
| Lab |
Allshire Lab
|
| Street address |
6.4 Michael Swann Building. Max Born Crescent
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3BF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE138436 |
Epigenetic gene silencing by heterochromatin primes fungal resistance |
|
| Relations |
| BioSample |
SAMN12912276 |
| SRA |
SRX6950751 |
