|
| Status |
Public on Jun 04, 2020 |
| Title |
Neg control PAO1 rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Pseudomonas aeruginosa PAO1 growing exponentially in LB
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
infection time: 0 min
|
| Treatment protocol |
Viral infection as described in Blasdel et al. 2018, Preparing cDNA libraries from lytic phage-infected cells for whole transcriptome analysis by RNA-Seq, Springer
|
| Growth protocol |
LB exponential growth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organic extraction
truseq stranded mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads quality control performed with trimmomatic, seqtk, and fastqc
Alignment to reference genome using TopHat2 with stranded (filename includes .str) and non-stranded depending on sample
Read counts using HTSeq-count
Normalization of counts within the triplicates of a given condition using TPM
Host DGE comparing late infection with no infection was performed as described in Blasdel et al. 2018 (Preparing cDNA libraries from lytic phage-infected cells for whole transcriptome analysis by RNA-Seq, Springer)
Genome_build: Pseudomonas aeruginosa PAO1 with accession number NC_002516.2, and PA5oct denovo assembled genome (see related publication)
Supplementary_files_format_and_content: Phage PA5oct count tables and normalization in xlsx format, host DGE count tables and normalization in xlsx format
|
| |
|
| Submission date |
Apr 23, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Cedric Lood |
| E-mail(s) |
[email protected]
|
| Organization name |
KU Leuven
|
| Department |
Division of Animal and Human Health Engineering
|
| Lab |
Laboratory of Gene Technology
|
| Street address |
Kasteelpark Arenberg 20 - box 2460
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE130190 |
Genomic, transcriptomic, and structural analysis of Pseudomonas virus PA5oct highlights the molecular complexity among Jumbo phages |
|
| Relations |
| BioSample |
SAMN11482257 |
| SRA |
SRX5728481 |
