|
| Status |
Public on Dec 12, 2023 |
| Title |
P23-45_t5_control |
| Sample type |
SRA |
| |
|
| Source name |
bacterial
|
| Organism |
Thermus thermophilus HB8 |
| Characteristics |
infection: P23-45 bacteriophage
strain: HB8
cell type: bacterial
treatment: no enrichment
|
| Growth protocol |
Thermus thermophilus strain HB8 was grown until exponential phase and infected with P23-45. A culture sample was taken 5 minutes post-infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol method, followed by Dnase I treatment. The enriched sames were subjected to an enrichment procedure based on streptavidin beads to enrich for primary RNA transcripts. For the control samples the enrichment steps were omitted.
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In paralel, the control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded according to the Oxford Nanopore Technologies cDNA-PCR protocol (SQK-PCS109 combined with SQK-PBK004). The amplified cDNA samples were pooled together in a final library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Live basecalling and demultiplexing on the PromethION 24 device in high accuracy mode using the Guppy software.
Identification and orientation of full-length reads using Pychopper (v2.5.0) and adapters were removed using Cutadapt (v2.7).
eads were mapped against the reference genomes of Thermus thermophilus HB8 (NC_006461.1) and phage P23-45 (OP542242) using minimap2. For mapping against the phage genome, the second long terminal repeat was omitted (mapping region [1...83630])
Peak calling using termseq-peaks scripts.
Assembly: GenBank accession OP542242 (phage P23-45) and NC_006461.1 (T. thermophilus HB8)
Supplementary files format and content: Narrowpeak files generated by peak calling
|
| |
|
| Submission date |
Oct 14, 2022 |
| Last update date |
Dec 12, 2023 |
| Contact name |
Rob Lavigne |
| E-mail(s) |
[email protected]
|
| 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 |
GPL32746 |
| Series (2) |
| GSE215811 |
ONT-cappable-seq for P23-45 bacteriophage 5 min post-infection |
| GSE215812 |
T. thermophilus infected with phage P23-45 |
|
| Relations |
| BioSample |
SAMN31285979 |
| SRA |
SRX17893304 |
