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| Status |
Public on Feb 01, 2018 |
| Title |
RNA-sequencing based analysis of Listeria monocytogenes 10403S and H7858 and corresponding ΔsigB mutants under exposure to pH 5.5 with or without bile |
| Organism |
Listeria monocytogenes |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S and H7858 and corresponding ΔsigB mutants under exposure to pH 5.5 with or without bile. RNA-seq was performed on all strains and conditions in four independent biological replicates. Indexed and purified cDNA libraries (12 libraries per strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 100-bp per read). Reads alignment was carried out using the Burrows-Wheeler Aligner (BWA). Differential expression of genes in different strains and conditions was statistically assessed using the BaySeq method.
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| Overall design |
Transcriptome profiles of L. monocytogenes 10403S and H7858 and corresponding ΔsigB mutants under exposure to pH 5.5 with or without bile were generated by deep sequencing, in quadruplicate, using Illumina Hiseq 2500.
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| |
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| Contributor(s) |
Guariglia V |
| Citation(s) |
29467736 |
| |
| Submission date |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Veronica Guariglia |
| E-mail(s) |
vg93@cornell.edu
|
| Phone |
6072805390
|
| Organization name |
Cornell University
|
| Department |
Food Science
|
| Street address |
320 Stocking Hall
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14850-6302 |
| Country |
USA |
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| Platforms (1) |
| GPL21330 |
Illumina HiSeq 2500 (Listeria monocytogenes) |
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| Samples (32)
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| Relations |
| BioProject |
PRJNA401799 |
| SRA |
SRP117040 |
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