|
| Status |
Public on Nov 04, 2024 |
| Title |
2603V/R ∆covR RNA-seq Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
2603V/R
|
| Organism |
Streptococcus agalactiae |
| Characteristics |
strain: 2603V/R
genotype: {delta}covR
|
| Treatment protocol |
Bacterial pellets are washed with cold PBS containing RNA stabilization reagents (RNAprotect, Qiagen) before flash freezing and storage at -80°C.
|
| Growth protocol |
Bacterial cultures in rich media (THY) incubated at 37°C in static condition are harvested in exponential growth phase (OD600 = 0.5).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA are extracted after cell wall mechanical lysis with 0.1 µm beads (Precellys Evolution, Bertin Technologies) in RNApro reagent (MP Biomedicals), and purified by chloroform extraction and ethanol precipitation.
Depletion of rRNA (FastSelect Bacterial, Qiagen) and libraries construction ((TruSeq Stranded mRNA, Illumina) are done following manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2603VR_DcovR_Rep2
|
| Data processing |
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.10. Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 2.5.1, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 2.0.0 from Subreads package (parameters: -t locus_tag -g ID -s 1).
Count data were analyzed using R version 4.0.5 and the Bioconductor package DESeq2 version 1.30.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed with(out) applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological condition. 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.
Assembly: Streptococcus agalactiae NEM316 (NCBI RefSeq NC_004368)
Assembly: Streptococcus agalactiae 2603 (NCBI RefSeq NC_004116)
Assembly: Streptococcus agalactiae A909 (NCBI RefSeq NC_007432)
Supplementary files format and content: DESeq 2 output matrix
|
| |
|
| Submission date |
Jun 10, 2024 |
| Last update date |
Nov 04, 2024 |
| Contact name |
Rachel Legendre |
| E-mail(s) |
rachel.legendre@pasteur.fr
|
| 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 |
GPL29157 |
| Series (2) |
| GSE269472 |
Virulence regulates and boosts CRISPR-Cas9 immunity in Group B Streptococcus [RNA-seq] |
| GSE269473 |
Virulence regulates and boosts CRISPR-Cas9 immunity in Group B Streptococcus. |
|
| Relations |
| BioSample |
SAMN41772687 |
| SRA |
SRX24857679 |
