|
| Status |
Public on Oct 15, 2024 |
| Title |
delta_ctrC, post exponential, rep4 |
| Sample type |
SRA |
| |
|
| Source name |
L. longbeachae strain NSW150
|
| Organism |
Legionella longbeachae NSW150 |
| Characteristics |
cell type: L. longbeachae strain NSW150
genotype: delta_ctrC
|
| Treatment protocol |
not applicable
|
| Growth protocol |
Bacteria were streaked onto BCYE plates and grown for three days at 37°C. From these plates, BYE liquid medium was inoculated and bacteria were grown to exponential phase (OD600 2.0-2.5), post-exponential phase (OD600 3.7-4.2) or stationary phase (overnight) and bacterial pellets were snap-frozen before processing for RNAseq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiazol and miRNA Mini kit (Qiagen)
1 ug of total RNA was then used in Illumina’s TruSeq mRNA Library kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
post exponential phase
|
| Data processing |
Basecalls performed using CASAVA version 1.9
Adapters removal with cutadapt software version 1.15
Trimming of the reads using Sickle version 1.33 (https://github.com/najoshi/sickle), with a quality threshold of 20 (-q 20). Reads shorter than 20nucleotides were removed
Clean reads were aligned to the Legionella longbeachae NSW150 sequence using Bowtie2 (version 2.3.4.3) and only uniquely mapped reads were kept for the counts
Reads count with featureCounts programm (from the Subreads package version 1.6.3). We used --primary option and stranded counts (option -s 1)
Differential analysis between the different conditions was performed with the R package Sartools (version 1.3.0) using DESeq2 methods. The “median” option was used to compute size factors
Assembly: refSeq : GCF_000091785.1, NC_013861.1
Supplementary files format and content: tabular text file with read count (column 2), sequence accession numbers (columns 3, 4), localisation of the features (columns 5, 6, 7), locus_tag of the features (column 8)
|
| |
|
| Submission date |
Jul 15, 2024 |
| Last update date |
Oct 15, 2024 |
| Contact name |
Christophe Rusniok |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut Pasteur
|
| Department |
Genomes et Genetique
|
| Lab |
Unite de Biologie des Bacteries Intracelulaires
|
| Street address |
25, 28 rue du Docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL34703 |
| Series (1) |
| GSE272232 |
The unique Legionella longbeachae capsule favors intracellular replication and immune evasion |
|
| Relations |
| BioSample |
SAMN42492811 |
| SRA |
SRX25325669 |
