|
| Status |
Public on Feb 17, 2022 |
| Title |
sj_dcr1_1_ChIP_Seq_Input |
| Sample type |
SRA |
| |
|
| Source name |
S. japonicus cell culture
|
| Organism |
Schizosaccharomyces japonicus |
| Characteristics |
strain: EHB3054
genotype: h- mat-P2028 dcr1-dis::natMX6 mpe1-R77W ura4-D3 ade6(sj)-domE
chip antibody: Input
|
| Treatment protocol |
Cells were fixed with 1% formaldehyde for 15 min at room temperature
|
| Growth protocol |
Cells were grown in YES at 32C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed using a bead beater (Biospec products) for 4 x 2min, and lysates were sonciated using a Bioruptor twin (Diagenode) for 7 x 4min cycles (30 secs on/30 secs off on 'high' power). Samples were pre-cleared with Protein-G Agarose for 1 hour, then incubated with fresh Protein-G agarose and antibody overnight. Beads were washed, then crosslinks were reveresed at 65°C, before contaminating RNA was removed using RNaseA. Proteins were digested with Proteinase K and immuniprecipatated genomic DNA was recovered using PCR purifcation columns (Qiagen).
Libraries were constructed using the NEBNext Library Prep Master Mix Set (NEB) according to manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads were filtered for quality and adapter using Trim Galore! (v0.4.3.1), reads that became shorter than 20nt were discarded
Trimmed reads were aligned to the S. japonicus reference genome (SJ5) using Bowtie2 (v2.3.4.3)
Coverage bigWig files were generated for each sample using bamCoverage (v3.3.2.0.0). RPKM was used for normalisation with a bin size of 50bp.
Ratios IP/Input were calculated using bigwigCompare (v3.3.2.0.0)
Ratios [H3K9/Input]/[H3/Input] were calculated using bigwigCompare (v3.3.2.0.0)
Genome_build: GCA_000149845.2
Supplementary_files_format_and_content: bedgraph files plotting the ratio of [H3K9me2/Input]/[H3/Input] for each sample
|
| |
|
| Submission date |
Oct 11, 2021 |
| Last update date |
Feb 17, 2022 |
| Contact name |
Elizabeth H Bayne |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Edinburgh
|
| Department |
Institute of Cell Biology
|
| Lab |
Roger Land Building
|
| Street address |
Alexander Crum Brown Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3FF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30837 |
| Series (2) |
| GSE185663 |
Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [ChIP-Seq] |
| GSE185665 |
Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus |
|
| Relations |
| BioSample |
SAMN22215331 |
| SRA |
SRX12571146 |
