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| Status |
Public on Jul 18, 2017 |
| Title |
The Yersinia pestis NlpD Lipoprotein is important for iron assimilation and is functionally linked to the twin-arginine translocation system |
| Organism |
Yersinia pestis |
| Experiment type |
Expression profiling by array
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| Summary |
Cultures of Y. pestis Kimberley53 (Kim53) virulent strain and Kim53∆nlpD were grown in heart infusion broth supplemented with 0.2% xylose and 2.5 mM CaCl2 for 5 h at 37°C, 200rpm. Total RNA samples were extructed and used for cRNA synthesis and labelling (using Cy3-CTP and Cy5-CTP). cRNA of two independent samples from each strain were labeled and hybridized to custom made Agilent 8x15K slide. Goal: Identifing alterations in gene expression profile between the wild-type Kim53 virulent strain and Kim53∆nlpD. Those altered mRNA transcrips will be used for better understanding of the cause for Kim53∆nlpD attenuation.
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| Overall design |
Y. perstis two independent biological replicates were performed. Extracted total RNA were used for cRNA synthesis and labeling with Cy3/Cy5-CTP, hybridized to Agilent custom-made 8x15K slide format.
For bacterial total RNA preparation, bacterial colonies were grown on BHIA plats for 48 h at 28°C , harvested and diluted in heart infusion broth (HIB) supplemented with 0.2% xylose and 2.5 mM CaCl2 to an OD660 of 0.01 and grown over night at 28°C in a shaker (200 rpm). The resulting cultures were diluted in fresh broth to an OD660 of 0.05 and allowed to grow for 5 h at 37°C. Aliquots of ~5×108 cfu were collected by centrifugation and cells were used for RNA preperation from Y. pestis Kimberley53 (Kim53) virulent strain and Kim53∆nlpD (fully attenuated) strain. Differential expression was evaluate using linear models for designed microarray experiments. Genes with differences corresponding to P<0.05 in either the high or the low photomultiplicator scans and that had signal to control or control to signal ratios ³2.0 were considered to be differentially regulated.
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| Contributor(s) |
Tidhar A, Levy Y, Zauberman A, Vagima Y, Gur D, Aftalion M, Israeli O, Chitlaru T, Ariel N, Flashner Y, Shafferman A, Zvi A, Mamroud E |
| Citation missing |
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| |
| Submission date |
Jul 17, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Avital Tidhar |
| E-mail(s) |
avitalt@iibr.gov.il
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| Phone |
972-8-9381509
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| Organization name |
Israel Institute for Biological Research
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| Department |
Biochemistry and molecular Genetics
|
| Street address |
P.O.B 19
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| City |
Ness-Ziona |
| ZIP/Postal code |
7410001 |
| Country |
Israel |
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| Platforms (1) |
| GPL21664 |
Agilent-020624 Yersinia pestis 8x15K array |
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| Samples (4)
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| GSM2704877 |
Y. pestis, Kim53 28°C vs. Kim53 37°C |
| GSM2704878 |
Y. pestis, Kim53 37°C vs.Kim53∆nlpD 28°C |
| GSM2704879 |
Y. pestis, Kim53∆nlpD 28°C vs.Kim53∆nlpD 37°C |
| GSM2704880 |
Y. pestis, Kim53∆nlpD 37°C vs.Kim53 28°C |
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| Relations |
| BioProject |
PRJNA394674 |
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