|
| Status |
Public on Jan 11, 2018 |
| Title |
wt_A_1 |
| Sample type |
SRA |
| |
|
| Source name |
10403S wild type
|
| Organism |
Listeria monocytogenes |
| Characteristics |
strain background: 10403S
genotype/variation: wild type
growth phase: exponential growth in LB
molecule subtype: rRNA-depleted RNA
|
| Growth protocol |
A single colony of the indicated strain was inoculated into brain-heart infusion medium (BHI) supplemented with 100μg/mL streptomycin and grown for 20h shaking at 37⁰C. Bacteria were then washed in PBS and diluted 1:100 into LB medium and grown 3.5 hours at 37⁰C shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were lysed and RNA extracted using the FastPrep RNApro solution and lysing matrix B according to the manufacturer's instructions.
Libraries were prepared by the Harvard Medical School Biopolymers Facility using Illumina kits according to the manufacturers instructions. Briefly, ribosomal RNA was removed from the samples using the Ribo-Zero™ rRNA Removal kit for Gram-positive bacteria, and the samples were the prepared for strand-specific RNA sequencing using the PrepX RNA-Seq Library Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling was performed using Illumina Real Time Analysis software
Sequences were trimmed of adaptor sequences and filtered for low quality sequence and then aligned to the Listeria monocytogenes EGD-e genome using CLCBio Genomics Workbench version 7.5.1. Reads were not mapped to rRNA features to account for variability in rRNA-depletion efficiency between samples.
Differential gene expression analysis was performed using the DGE (edgeR) package in CLCBio Genomics Workbench version 7.5.1.
Genome_build: NC_003210.1
Supplementary_files_format_and_content: A single tab-delimited text file broken down by feature. Contains differential gene expression analysis between the two strains as well as total counts and RPKM values for each feature in each sample.
|
| |
|
| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Grubaugh |
| E-mail(s) |
[email protected]
|
| Phone |
617-432-4157
|
| Organization name |
Harvard Medical School
|
| Department |
MBIB
|
| Lab |
Higgins
|
| Street address |
77 Ave Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21330 |
| Series (1) |
| GSE98373 |
Identification of trancripts regulated by the Listeria monocytogenes two-component system regulator VirR by RNA-seq |
|
| Relations |
| BioSample |
SAMN06854112 |
| SRA |
SRX2771236 |
