|
| Status |
Public on Nov 27, 2023 |
| Title |
Y1FIPuntreatedn2 |
| Sample type |
SRA |
| |
|
| Source name |
h? rpb1-Y1F::natMX6; rpb3-HA:kanMX6
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell line: Y1F
genotype: h? rpb1-Y1F::natMX6; rpb3-HA:kanMX6
chip antibody: HA (Millipore Sigma Roche ROAHA
treatment: none
|
| Treatment protocol |
HU was added to one of the cultures to a final concentration of 12 mM, and incubation was continued for 4 hours.
|
| Growth protocol |
S. pombe strains expressing rpb3-HA were grown to OD600 of 0.2 in 100 mL YES at 30oC and then split into two 50 mL cultures.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1.5x10^7 cells from each sample were then crosslinked with 1% formaldehyde. Extracts were prepared by bead beating and were sonicated in a Bioruptor (Diagenode; UCD-200).
ChIP-seq libraries were prepared with 2 ng of input or IP DNA using the NEBNext Ultra II DNA Library kit for Illumina (New England Biolabs).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
1165_IP_C_n2
1165_IPINratio_C_n2_SESscaled.bw
|
| Data processing |
Quality of the reads was determined using FastQC prior to and after trimming with TrimGalore (0.6.6)(Babraham Institute Bioinformatics https://www.bioinformatics.babraham.ac.uk/).
The trimmed reads were aligned to the reference S. pombe ASM294v2 genome using bowtie2
Aligned, deduplicated bam files were sorted and indexed in samtools
The deeptools package (version 2.0) was then used to derive bigWig files corresponding to IP/input ratios for each sample, and to scale based on read depth using the SES method.
A median genic Rpb3-HA occupancy across all protein-coding genes was computed for each bigWig file; this value was set to 1 for the wild-type control and used to scale the other bigWig files using wiggletools
Assembly: ASM294v2
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Nov 21, 2023 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Jason Tanny |
| E-mail(s) |
jason.tanny@mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Pharmacology and Therapeutics
|
| Street address |
3655 Prom Sir William Osler room 132
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL30067 |
| Series (1) |
| GSE248360 |
The Rtf1/Prf1-dependent histone modification axis and Rpb1 C-terminal domain phosphorylation counteract multi-drug resistance in fission yeast [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN38345451 |
| SRA |
SRX22593037 |
