|
| Status |
Public on Mar 25, 2024 |
| Title |
ureC::bla_LB+urea_biol_rep_3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial
|
| Organism |
Proteus mirabilis |
| Characteristics |
cell type: bacterial
genotype: ureC::bla
strain: HI4320
condition: LB +urea
|
| Treatment protocol |
1 mL of each culture was preserved in 2 mL of RNAprotect Bacterial Reagent. After incubating for ~15 minutes at room temperature, samples were centrifuged, supernatants removed, and pellets frozen at -20°C for at least one day.
|
| Growth protocol |
Overnight cultures of bacterial strains were sub-cultured in duplicate in 3 mL LB buffered with 250 mM HEPES and incubated at 37°C with aeration. After 2 hours, one culture of each strain was supplemented with urea to a final concentration of 50 mM while the other culture remained unperturbed. Samples were collected after 15 minutes of growth post-urea addition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy kit (Qiagen). Samples were incubated with lysozyme (0.5 mg/mL) for 15 minutes with agitation to lyse cells. Subsequent RNA isolation was performed according to the manufacturer’s instructions. Genomic DNA was depleted using the Turbo-DNAfree Kit (Invitrogen). rRNA was removed using the NEBNext rRNA Depletion Kit (bacteria).
Sequencing libraries were prepared using the xGen Broad-range RNA Library Prep (IDT) and xGen Normalase UDI Primer Plate 1 (IDT) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ureC_urea-induced_transcriptome.xlsx
ureC_urea_vs_ureR_urea.xlsx
ureC_urea_vs_WT_urea.xlsx
|
| Data processing |
Geneious Prime 2022.1 software was used for data analysis (www.geneious.com). Reads were paired as fastq files and were imported into Geneious Prime using the average insert size for each sample.
The BBduk plug-in was used to remove Illumina adapter sequences and perform quality trimming (maq=20, maxns=1, trimq=14, minlength=20).
Trimmed reads were mapped to the HI4320 genome (GenBank: NC_010554.1) using the Geneious read mapper.
Geneious calculated expression levels of genes in each sample, and the DeSeq2 plug-in was used to calculate differential expression (fit type=parametric).
Assembly: NCBI Reference Sequence: NC_010554.1
Supplementary files format and content: Excel files containing differential gene expression data between the two indicated samples, as calculated by DeSeq2.
|
| |
|
| Submission date |
Jan 31, 2024 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Madison Fitzgerald |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Department |
Microbiology & Immunology
|
| Lab |
Mobley
|
| Street address |
1150 W. Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL33818 |
| Series (1) |
| GSE254779 |
Proteus mirabilis UreR Coordinates Cellular Functions required for Urease Activity |
|
| Relations |
| BioSample |
SAMN39710785 |
| SRA |
SRX23485169 |
