|
| Status |
Public on Dec 12, 2018 |
| Title |
Tup11_glycerol_CHIP_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole cell
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: D96_Tup11-TAP
genotype: h+ ura4-d18 leu1-32 ade6-m216 tup11::TAP-KanMX6
chip antibody: Protein A (clone SPA-27, Sigma P2921)
|
| Treatment protocol |
Cells were crosslinked for 30 mins in 1% formaldehyde. Following this the crosslinking reaciton was quenched with glycine
|
| Growth protocol |
Cells were cultured in YES 3% glucose for four hours at 32 degrees before being collected by centrifugation, washed twice in sterile water and shifted to YES 3% glucose, YES 3% sucrose, or YES 3% glycerol and cultured at 32 degrees for a further four hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared according to Wong et al. 2013 Curr Protoc Mol Biol Chapter 7:Unit 7 11
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP
Tup11_glycerol_IDR_filtered.narrowPeak
|
| Data processing |
basecalls were performed using Illumina CASAVA v1.8.4 pipeline
raw reads were cleaned using Cutadapt v1.9.1 with default parameters and assessed for quality using FastQC
cleaned reads were aligned to the S. pombe ASM294v2.25 genome using Bowtie2 v2.3.1 with the following parameters: --very-sensitive- local --minins 0 --maxins 600 -t --threads 8.
ChIP-seq peak calling was performed for transcription factor ChIPs using MACS2 v2.1.1 with the following parameters: -bw 300 --gsize 12.5E6 -B -q 0.01 -m 4 50 -extsize 150 —fix- bimodal. The Irreproducible Discovery Rate (IDR) statistic v2.0.2 (https://github.com/nboley/idr) was calculated for pairs of ChIP-seq replicates and used to filter MACS2 peak calls for reproducible and high quality peaks.
bigwigs were generated for RNA-PolII Ser5 ChIPs using deeptools BAM compare
Genome_build: ASM294v2
Supplementary_files_format_and_content: peak files contain high confidence peaks that passed IDR thresholds per sample
|
| |
|
| Submission date |
Dec 11, 2018 |
| Last update date |
Dec 14, 2018 |
| Contact name |
Dane Aaron McKay Vassiliadis |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Melbourne
|
| Street address |
Parkville VIC 3000
|
| City |
Melbourne |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17225 |
| Series (2) |
| GSE123614 |
A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe [ChIP-seq] |
| GSE123633 |
A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe |
|
| Relations |
| BioSample |
SAMN10579542 |
| SRA |
SRX5124655 |
