|
| Status |
Public on Dec 04, 2020 |
| Title |
Δghk replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Sgg UCN34 Δghk
|
| Organism |
Streptococcus gallolyticus UCN34 |
| Characteristics |
deleted gene: gallo_rs10345 (ghk)
|
| Growth protocol |
The WT strain and the three regulatory mutants Δgsp, Δghk and Δgrr were inoculated at DO=0,1 in liquid THY (10mL) from fresh agar plates and incubated without agitation at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At DO(600)=0,5, RNA were extracted with the MP Biomedicals™ FastRNA™ Pro Blue Kit and treated with DNase (Invitrogen™ Ambion™ TURBO DNA-free Kit) to remove residual DNA. DNase was inactivated with the DNase inactivation reagent present in the kit.
rRNA were depleted from 0,5 μg of total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. Sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit (20020595) following the manufacturer’s instructions (Illumina). The directional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies) and concentrations measured with the Qubit® dsDNA HS Assay Kit (ThermoFisher). Sequences of 65 bases were generated on the Illumina Hiseq 2500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Product of the deleted gene: Gallocin histidine kinase (Ghk), a putative histidine kinase that likely respond to GSP concentration by activating Grr
14-3
|
| Data processing |
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11 . Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome (NC_013798.1, from NCBI).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g locus_tag -s 1).
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the WT, 13, 14 and 15 biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Streptococcus gallolyticus UCN34 (NC_013798.1, from NCBI)
Supplementary_files_format_and_content: Output file from DESzq2
|
| |
|
| Submission date |
Apr 09, 2020 |
| Last update date |
Dec 04, 2020 |
| Contact name |
Rachel Legendre |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut Pasteur
|
| Department |
Research and Resource Center for Scientific Informatics
|
| Lab |
Hub of Bioinformatics and Biostatistics
|
| Street address |
28, rue du docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75724 |
| Country |
France |
| |
|
| Platform ID |
GPL28370 |
| Series (1) |
| GSE148401 |
A dedicated three component regulatory system (GSP/Ghk/Grr) activates gallocin transcription in Streptococcus gallolyticus UCN34 |
|
| Relations |
| BioSample |
SAMN14568308 |
| SRA |
SRX8090664 |
