|
| Status |
Public on Mar 24, 2023 |
| Title |
S.islandicus.LAL141.SIRV2.2hpi.ChIP-seq.Cbp1.replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
microbial cells
|
| Organism |
Sulfolobus islandicus LAL14/1 |
| Characteristics |
genotype: WT
chip antibody: Cbp1
cell type: microbial cells
treatment: SIRV2 infected 2hpi
|
| Treatment protocol |
Four 250 mL cultures of S. islandicus LAL14/1 were grown in rich medium at 76 °C under agitation for approximately 12 h. When the optical density (OD) reached 0.2, two of the cultures were infected with SIRV2 using a multiplicity of infection (MOI) of 10, while the other two served as uninfected controls. After 2 hours post-infection (hpi), 200 mL aliquots were rapidly transferred to flasks, placed on heated magnetic stirring plates and cross-linked with stabilized formaldehyde solution to a final concentration of 0.4%.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen QIAquick PCR purification
NEBNext Ultra II DNA library prep kit for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
19272X21
NovaSeq SP Reagent Kit v1.5_50x50 bp Sequencing
|
| Data processing |
Paired-end reads were mapped using Bowtie v1.1.2 [30] with parameters -v 2 -m 1 --fr allowing only for uniquely mapped read pairs to be included
We sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 150 bp, sd 20 bp) using a custom R script (https://github.com/fblombach/ChIP-seq/blob/master/read_sampling.R)
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width), chromatin input samples for these IPs were previously deposited at NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141286)
Assembly: NC_021058.1 (S. islandicus LAL14/1) and AJ344259.1 (SIRV2)
Supplementary files format and content: bigwig files with occupancy normalised against the chromatin input samples, scaled by the Signal Extraction Scaling method
|
| |
|
| Submission date |
Feb 24, 2023 |
| Last update date |
Mar 24, 2023 |
| Contact name |
Finn Werner |
| E-mail(s) |
[email protected]
|
| Organization name |
University College London
|
| Department |
Institute of Structural and Molecular Biology
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL32880 |
| Series (2) |
| GSE226024 |
ChIP-seq data for Cbp1 and RNA polymerase in Sulfolobus islandicus LAL14/1 |
| GSE226026 |
Cbp1-Cren7 chromatinization of CRISPR arrays favours transcription from CRISPR leaders over cryptic promoters. |
|
| Relations |
| BioSample |
SAMN33434788 |
| SRA |
SRX19495038 |
