|
| Status |
Public on May 16, 2024 |
| Title |
d1759b |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria cells
|
| Organism |
Listeria monocytogenes serotype 4b str. F2365 |
| Characteristics |
cell type: Bacteria cells
genotype: gltC mutant strain
treatment: 8 mM Hydrogen peroxide treatment
|
| Treatment protocol |
Three replicates each of (1) WT (2)d1031 and (3) d1759 were treated with 8 mM Hydrogen peroxide
|
| Growth protocol |
Listeria monocytogenes F2365 (n=6) were cultured overnight and were diluted 1:10 in BHI and incubated at 37 °C with shaking for ~1 h to reach OD600 ~ 0.2-0.3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the FastRNA spin kit for microbes and the FastPrep-24 instrument (MP Biomedicals, Santa Ana, CA) following manufacturer's instruction
Library construction and sequencing was performed by Novogen
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
FPKM.xls
d1759vsWT_deg_all
|
| Data processing |
CLC Genomic Workbench 24.0.1
Clean sequence reads were obtained by triming reads containing adapter and removing poly-N sequence and reads with low-quality
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of the reference genome and aligning clean reads to reference genome were used on Bowtie2
Raw reads were filtered by (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); and (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
The RNA-seq reads were assembled according to the reference genomes using Rockhopper(R. McClure, et al, 2013)
Assembly: AE017262.2
Supplementary files format and content: d1031vsWT_deg_all.xls: differentially expressed genes
Supplementary files format and content: d1759vsWT_deg_all.xls: differentially expressed genes
|
| |
|
| Submission date |
May 16, 2024 |
| Last update date |
May 16, 2024 |
| Contact name |
Hossam Abdelhamed |
| E-mail(s) |
abdelhamed@cvm.msstate.edu
|
| Organization name |
CVM
|
| Street address |
Wise drive
|
| City |
Mississippi State |
| ZIP/Postal code |
39762 |
| Country |
USA |
| |
|
| Platform ID |
GPL34483 |
| Series (1) |
| GSE267669 |
Catabolite control protein C (CcpC) contributes to virulence and hydrogen peroxide-induced oxidative stress responses in Listeria monocytogenes |
|
| Relations |
| BioSample |
SAMN41425923 |
| SRA |
SRX24584220 |
