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Sample GSM3733640 Query DataSets for GSM3733640
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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