|
| Status |
Public on Apr 25, 2024 |
| Title |
NEM316 ∆gdpP Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Streptococcus agalactiae NEM316 |
| Characteristics |
cell type: bacterial cell
genotype: {delta}gdpP
|
| 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 |
NEM316.complete.txt
|
| 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 BM110 (from NCBI id=318722, NCBI RefSeq reference NZ_LT714196)
Assembly: Streptococcus agalactiae NEM316 (from NCBI id=165229, NCBI RefSeq reference NC_004368)
Supplementary files format and content: DESeq 2 output matrix
|
| |
|
| Submission date |
Mar 21, 2024 |
| Last update date |
Apr 25, 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 |
GPL34325 |
| Series (1) |
| GSE262190 |
Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group B Streptococcus |
|
| Relations |
| BioSample |
SAMN40570180 |
| SRA |
SRX24017370 |
