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| Status |
Public on Jul 07, 2017 |
| Title |
Host-P4_0_rep2 |
| Sample type |
SRA |
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| Source name |
Pseudomonas aeruginosa PAK
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| Organism |
Pseudomonas aeruginosa |
| Characteristics |
subsp.: Host PAK
strain: PAK
time point: 0 min post infection
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| Treatment protocol |
Synchronous infection with bacteriophage PAK_P4 for 0min, 3,5min or 13min (MOI = 50) and halted by rapid cooling in diluted phenol
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| Growth protocol |
Pseudomonas cells were grown in LB supplemented with 10mM MgCl2 at 37°C until OD600nm ̴ 0,3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were then lyzed in TRIzol,® total RNA was purified through a standard organic extraction and ethanol precipitation followed by DNase treatment (TURBO DNAse®) and rRNA depletion (Ribo-Zero rRNA Removal Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols using the Truseq stranded RNA seq kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Host RNA recovered after 0min post infection
processed data file: Host-infect-P4_T0-T13_statistics.xls
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced were mapped to Pseudomonas aeruginosa PAK whole genome sequence or Phage P4 sequence complemented by the manually annotated ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES -l 20
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 13M value as a reference for reporting the expression data of 0M.
Genome_build: Pseudomonas aeruginosa PAK (KK037225.1), Pseudomonas phage PAK_P4 (NC_022986)
Supplementary_files_format_and_content: Genome annotation (Gene ID), Raw Counts (0M, 13M), Normalized Counts (0M, 13M), Statistics (FC, pvalue, significant)
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| Submission date |
Aug 24, 2016 |
| Last update date |
Jul 07, 2017 |
| Contact name |
Monot Marc |
| E-mail(s) |
mmonot@pasteur.fr
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| Phone |
+33145688390
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| Organization name |
Institut Pasteur
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| Department |
Genomes and Genetics
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| Lab |
Biomics
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| Street address |
25, rue du docteur roux
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| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL18644 |
| Series (1) |
| GSE86022 |
Biological characterization of virulent therapeutic bacteriophage PAK_P4 infecting Pseudomonas aeruginosa |
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| Relations |
| BioSample |
SAMN05629254 |
| Supplementary data files not provided |
| Raw data provided as supplementary file |
| Processed data are available on Series record |
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