|
Status |
Public on Jun 04, 2020 |
Title |
Neg control PAO1 rep 1 |
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 |
SAMN11482349 |
SRA |
SRX5728479 |