|
| Status |
Public on Oct 30, 2019 |
| Title |
Sample 6: Wild-Type Dark 3 |
| Sample type |
SRA |
| |
|
| Source name |
Wild-Type Dark
|
| Organism |
Listeria monocytogenes |
| Characteristics |
strain: EGDe
growth condition: Dark
|
| Treatment protocol |
Cultures were divided in two in darkness, with one aliquot kept in darkness and the other exposed to 0.6 mW cm2 470 nm light for 20 min.
|
| Growth protocol |
Cells were cultured in BHI broth at 30°C to OD600 ~0.2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were stabilised in RNAlater and RNA was extracted using Rneasy mini prep kit (Qiagen). The NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (Illumina) was used to prepare the cDNA fragment libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the complete sequenced genome of reference strains EGDe (ENSEMBL ASM19603v1) using Bowtie 2 v 2.2.4 with standard parameters and --sensitive-local (Langmead and Salzberg 2012).
BAM alignment files were used as input for read counting using htseq-count (HTSeq version 0.6.0) (Anders et al. 2015).
Differential expression analyses were performed using DESeq2 in R v 3.2.2 (Love et al. 2014).
The differential expression was reported as log2 fold changes, wtih p-values adjusted by the DESeq2 default Benjamini-Hochberg (BH) adjustment method and genes with a >2-fold change in expression and a p-value < 0.05 were considered as DE.
Supplementary_files_format_and_content: Comma separated text files.
|
| |
|
| Submission date |
May 09, 2019 |
| Last update date |
Oct 30, 2019 |
| Contact name |
Amber Louise Dorey |
| E-mail(s) |
amber.dorey@nuigalway.ie
|
| Organization name |
National University of Ireland Galway
|
| Department |
Microbiology
|
| Lab |
Bacterial Stress Response Group
|
| Street address |
University Road
|
| City |
Galway |
| State/province |
Galway |
| ZIP/Postal code |
H91 CF50 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL26477 |
| Series (1) |
| GSE130971 |
Blue Light Sensing in Listeria monocytogenes Is Temperature-Dependent and the Transcriptional Response to It Is Predominantly SigB-Dependent |
|
| Relations |
| BioSample |
SAMN11613169 |
| SRA |
SRX5940116 |
