|
| Status |
Public on Jun 24, 2022 |
| Title |
t10_enriched |
| Sample type |
SRA |
| |
|
| Source name |
Pseudomonas aeruginosa
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: US449
infection: Pseudomonas virus LUZ7
time: 10 minutes post-infection
treatment: enriched for primary RNAs
|
| Growth protocol |
P. aeruginosa cells were grown to exponential phase in LB medium and infected with phage LUZ7 at an MOI of 50 to ensure synchronous infection. Culture samples were collected at 0 minutes, and 5, 10 and 20 minutes post-infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.
Total RNA was enriched for primary transcripts using an adapted version of the (SMRT)-cappable-seq enrichment protocol. In parallel, control samples were not enriched but subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded according to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCS109 combined with SQK-PBK004). The amplified cDNA samples were pooled together in a final library and loaded on a promethION flowcell.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Data processing |
Library strategy: ONT-cappable-seq
Live basecalling and demultiplexing by PromethION 24 device
Identification and orientation of full-length reads using Pychopper (v2.5.0)
Read trimming using Cutadapt (v2.7)
Mapping of reads against reference genomes of P. aeruginosa US449 and LUZ7 using minimap2
Peak calling using termseq-peaks script
Genome_build: CP091880; NC_013691.1
Supplementary_files_format_and_content: Narrowpeak files generated by peak calling
|
| |
|
| Submission date |
Feb 16, 2022 |
| Last update date |
Jun 24, 2022 |
| 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 |
GPL31946 |
| Series (1) |
| GSE196845 |
Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages |
|
| Relations |
| BioSample |
SAMN25995407 |
| SRA |
SRX14201139 |
