|
| Status |
Public on Jun 18, 2024 |
| Title |
RU11/001 ΔldtR- Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Sinorhizobium meliloti RU11/001 |
| Characteristics |
cell type: Bacterial
genotype: deltaldtR
treatment: Bromfield overlay
|
| Treatment protocol |
N/A
|
| Growth protocol |
TYC-Sm liquid cultures (24 hours) were subcultured into Bromfield overlay plates at OD600 = 0.002 and incubated at 30C for 17 hours, to an OD600 of 0.20-0.25. Cultures were standardized to 2 ml at an OD600 = 0.20.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the Rneasy Protect Bacteria Mini Kit (Qiagen) according to the manufacturer's protocol. For each sample, 1.25 µg total RNA was provided for rRNA depletion and library preparation.
RNA libraries were prepared with the TruSeq Stranded mRNA library preparation kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
| |
|
| Description |
DESeqs2_Analysis
|
| Data processing |
Onboard adapter trimming was performed.
Sequences were quality-trimmed using the BBDuk plugin in Geneious Prime® 2023.2.1 (base quality score cutoff of 20 and minimum sequence length of 30 nt).
Cleaned reads were mapped to the S. meliloti RU11/001 genome in Geneious Prime® 2023.2.1 using the Geneious RNA mapper with default settings.
Differential expression analysis was performed using the DESeqs2 plugin in Geneious Prime® 2023.2.1.
Assembly: Sinorhizobium meliloti RU11/001 (GenBank accession number GCA_001050915.2)
Supplementary files format and content: Excel (.xls) files containing raw read counts, TPM, RPKM, and TPKM for all six samples, one file per sample
Supplementary files format and content: Excel (.xls) file containing the full DESeqs2 analysis results for all six samples
|
| |
|
| Submission date |
Dec 21, 2023 |
| Last update date |
Jun 18, 2024 |
| Contact name |
Birgit E Scharf |
| E-mail(s) |
bscharf@vt.edu
|
| Phone |
1-540-231-0757
|
| Organization name |
Virginia Tech
|
| Department |
Biological Sciences
|
| Lab |
Scharf
|
| Street address |
970 Washington St SW
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24060 |
| Country |
USA |
| |
|
| Platform ID |
GPL34034 |
| Series (1) |
| GSE251837 |
The motility defect caused by absence of the transcriptional regulator LdtR in Sinorhizobium meliloti is restored by mutations in the motility genes motA and motS |
|
| Relations |
| BioSample |
SAMN39059317 |
| SRA |
SRX22998432 |
