|
| Status |
Public on Sep 09, 2022 |
| Title |
LVS ∆rpsU2 pF C |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Francisella tularensis subsp. holarctica LVS |
| Characteristics |
cell type: bacterial cell
growth phase: mid-log
genotype: {delta}rpsU2 pF
|
| Growth protocol |
Cells were collected from mid-log cultures (OD600 0.3-0.4).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nucleic acids were isolated using the Direct-Zol RNA purification kit (Zymo Research) according to the manufacturer’s protocol. Purified nucleic acids were treated with RQ1 Dnase (Promega) for 1 hour at 37°C and RNA was purified with the Direct-Zol RNA purification kit.
Approximately 1.5 μg of RNA isolated as above was sent to the Microbial Genome Sequencing Center (MiGS). After using RiboZero Plus rRNA depletion, libraries were made using Illumina Stranded RNA library preparation and sequenced for a minimum of 12 million paired end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
mapping: bowtie2 version 2.2.4 (bowtie2 -N 1 -L 20 -i S,1,0.50 -D 20 --non-deterministic --no-mixed --no-discordant --no-unal )
read counting: HTSeq version 0.11.2 (htseq-count -s reverse -a 1 -t gene -m intersection-nonempty --nonunique all -i locus_tag )
Differential gene expression analysis: DESeq2 version 1.32.0
Assembly: NC_007880
Supplementary files format and content: tab-delimited text files include read count for each feature
|
| |
|
| Submission date |
Aug 08, 2022 |
| Last update date |
Sep 09, 2022 |
| Contact name |
Kathryn M Ramsey |
| E-mail(s) |
kramsey@uri.edu
|
| Organization name |
University of Rhode Island
|
| Department |
CMB / BPS
|
| Lab |
Ramsey Lab
|
| Street address |
7 Greenhouse Road
|
| City |
Kingston |
| State/province |
RI |
| ZIP/Postal code |
02881 |
| Country |
USA |
| |
|
| Platform ID |
GPL32555 |
| Series (1) |
| GSE210766 |
A ribosomal protein homolog modulates gene expression and virulence in a bacterial pathogen |
|
| Relations |
| BioSample |
SAMN30196775 |
| SRA |
SRX16982856 |
