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| Status |
Public on Apr 26, 2023 |
| Title |
T0, J085, 3 |
| Sample type |
SRA |
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| Source name |
Bacterial culture
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| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
time: T0
cell type: Bacterial culture
strain: J085
genotype: WT
medium: MH
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Part of the transposon mutant libraries were used for gDNA extraction using Qiagen DNeasy® Blood & Tissue Kit as per manufacturer’s instructions.
Sequencing libraries were prepared using Agilent’s sureselect XT2 Kit with custom RNA baits designed to hybridize the edges of the Mariner transposon. The 100 ng protocol was followed as per manufacturer’s instructions. A total of 12 cycles were used for library amplification. Agilent’s 2100 bioanalzyer was used to verify the size of the pooled libraries and their concentration.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
0 vs. 16 J085
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| Data processing |
Library strategy: Tn-Seq
Reads were then filtered through transposon mapping to ensure the presence of an informative transposon/genome junction using a previously described mapping algorithm (Pierlé et al., 2014, Negro et al., 2019).
Informative reads were extracted and mapped. Reads were counted when the junction was reported as mapped inside the ORF of a gene plus an additional 50 bp upstream and downstream. Normalization calculations were applied according to van Opijnen et al., 2009
Expansion or decrease of fitness of mutants was calculated in fold changes with normalized insertion numbers. Baggerly’s test on proportions was used to determine statistical significance as well as a Bonferroni correction.
Assembly: NC_002506 and NC_002505
Supplementary files format and content: Matrix table with insertion numbers and insertion reads for every gene and sample
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| Submission date |
Mar 10, 2022 |
| Last update date |
Apr 26, 2023 |
| Contact name |
André Carvalho |
| E-mail(s) |
andre-filipe.paulino-carvalho@pasteur.fr
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| Organization name |
Institut Pasteur
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| Street address |
28 Rue du Dr Roux
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| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL32053 |
| Series (1) |
| GSE198341 |
Transposon Insertion Sequencing to study the genetic interactions between V. cholerae WT cells and two mutant strains in absence or presence of subinhibitory doses of tobramycin |
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| Relations |
| BioSample |
SAMN26564462 |
| SRA |
SRX14428803 |
| 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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