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| Status |
Public on Mar 02, 2022 |
| Title |
proQ mutant with empty vector 3 |
| Sample type |
SRA |
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| Source name |
Bacterial cells
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| Organism |
Pasteurella multocida |
| Characteristics |
strain: AL3358
treatment: AL2973 proQ mutant with vector pPBA1100S; SpecR
genotype: proQ mutant
expression: lack of ProQ protein
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| Treatment protocol |
None
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| Growth protocol |
Grown to OD600=0.6 in Heart Infusion Broth
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| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol:Choloform extraction
Agilent SureSelect Strand-Specific RNA Library Prep kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
PE3
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| Data processing |
raw fastq files were aligned to the Pasturella multocida reference VP191,(NZ_CP048792.1) and aligned using R subread (Liao, Smyth, and Shi 2019).
Reads were quantified with featureCounts (Liao, Smyth, and Shi 2014) producing the raw gene count matrix. The QC for the raw genes counts matrix and various quality control metrics were summarised in a MultiQC report (Ewels et al. 2016).
Raw counts were then analyzed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: Pasturella multocida reference VPM191,(NZ_CP048792.1)
Supplementary_files_format_and_content: raw gene counts, text file, comma separated
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| Submission date |
Feb 16, 2022 |
| Last update date |
Mar 02, 2022 |
| Contact name |
Deanna S Deveson Lucas |
| Organization name |
Monash University
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| Lab |
Monash Bioinformatics Platform
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| Street address |
15 Innovation walk, Monash University, Clayton
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| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
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| Platform ID |
GPL31945 |
| Series (1) |
| GSE196834 |
The role of the RNA chaperone protein ProQ in Pasteurella multocida |
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| Relations |
| BioSample |
SAMN25991640 |
| SRA |
SRX14200135 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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