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| Status |
Public on Oct 09, 2020 |
| Title |
lomA mutant_RNA m2011-3 |
| Sample type |
SRA |
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| Source name |
lomA mutant
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| Organism |
Leptospira interrogans serovar Manilae |
| Characteristics |
strain: UP-MMC-NIID LP
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| Treatment protocol |
no treatment
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| Growth protocol |
Exponential-phase cultures at 30°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected by centrifugation and pelleted cells were resuspended in TRIzol. RNA was then purified according to the manufacturer's instructions (Invitrogen, Saint Aubin, Ile de France, France). DNA was degraded by using a Turbo DNA-free kit according to the manufacturer's instructions (Invitrogen).
From 0.5 μg of total RNA, we depleted ribosomal RNAs using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. On these rRNA-depleted RNAs, the sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
lomA mutant_RNA
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| Data processing |
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
Bowtie version 1.2 with default parameters, was used for alignment on the reference genome (L. interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform).
Genes were counted using featureCounts version 1.4.6-p35from Subreads package (parameters: -t CDS -g locus_tag -s 1)
Count data were analyzed using R version 3.5.15and the Bioconductor packageDE Seq2 version 1.20.0f. 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 WT, complemented strain, and lomA. 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: interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform
Supplementary_files_format_and_content: tabulated files from DESeq2
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| Submission date |
Oct 15, 2019 |
| Last update date |
Oct 09, 2020 |
| Contact name |
Rachel Legendre |
| E-mail(s) |
rachel.legendre@pasteur.fr
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| Organization name |
Institut Pasteur
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| Department |
Research and Resource Center for Scientific Informatics
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| Lab |
Hub of Bioinformatics and Biostatistics
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| Street address |
28, rue du docteur Roux
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| City |
Paris |
| ZIP/Postal code |
75724 |
| Country |
France |
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| Platform ID |
GPL21582 |
| Series (1) |
| GSE138917 |
A pathogen-specific 4mC methyltransferase is critical for epigenetic regulation and virulence of Leptospira interrogans |
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| Relations |
| BioSample |
SAMN13035668 |
| SRA |
SRX7000051 |
| 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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