|
| Status |
Public on Dec 12, 2023 |
| Title |
P23-45_5min_input |
| Sample type |
SRA |
| |
|
| Source name |
bacterial
|
| Organism |
Thermus thermophilus HB8 |
| Characteristics |
infection: P23-45 bacteriophage
cell type: bacterial
time: 5 min
chip antibody: none
|
| Growth protocol |
Bacterial cells were grown in an orbital shaker at 70°C in liquid medium (0.8% tryptone, 0.4% NaCl, 0.2% yeast extract, 0.5 mM MgSO4, and 0.5 mM CaCl2 in “Vittel” mineral water). Cells were grown until an optical density at 600 nm of around 0.2 and infected with P23-45 bacteriophage at a multiplicity of infection 10. At 5, 20, and 40 min post infection 200 ml of cells were collected.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Infected cells were fixed with 1% formaldehyde for 20 minutes. The cross-linking reaction was stopped by the addition of dry glycine up to the final concentration of 0.5 M. Cells were incubated for 20 min with agitation. The cells were harvested by centrifugation and washed twice with ice-cold TBS (10 mM Tris-HCl pH 7.6, 150 mM NaCl). The cells were lysed and DNA was sheared by sonication to an average size of 200 – 500 bp. Immunoprecipitation was performed using corresponding antibodies and Sera-Mag SpeedBeads Protein A/G Sepharose magnetic beads (GEHealth).
DNA libraries were generated by the Skoltech Genomics Core Facility using Swift Accel-NGS 1S Kit (Swift Biosciences) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The adapters and low-quality sequences were eliminated by the Skoltech Genomics Core Facility.
ChIP-seq reads were aligned to P23-45 genome with the second long terminal repeat ommited ([1...83630] of the GenBank accession OP542242) using bowtie2 (version 2.4.1).
Samtools (version 1.10) software was used to convert .sam files to .bam format and to filter the reads. Filtering was performed using the following parameters: -F 4 (to remove all unmapped reads), -f 2 (to keep only the reads mapped in a proper pair), -q 1 (to skip the alignments with mapQuality < 1).
BedGraph files were generated using MACS2 (version 2.2.7.1) with default settings.
Assembly: GenBank accession OP542242
Supplementary files format and content: bedGraph
|
| |
|
| Submission date |
Oct 14, 2022 |
| Last update date |
Dec 12, 2023 |
| Contact name |
Rob Lavigne |
| E-mail(s) |
rob.lavigne@kuleuven.be
|
| Organization name |
KU Leuven
|
| Department |
Biosystems
|
| Lab |
Laboratory of Gene Technology
|
| Street address |
Kasteelpark Arenberg 21
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL32745 |
| Series (2) |
| GSE215810 |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA-polymerases encoded by P23-45 bacteriophage |
| GSE215812 |
T. thermophilus infected with phage P23-45 |
|
| Relations |
| BioSample |
SAMN31285976 |
| SRA |
SRX17893296 |
