|
| Status |
Public on Jul 13, 2022 |
| Title |
SCHU S4, rep9 |
| Sample type |
SRA |
| |
|
| Source name |
SCHU S4
|
| Organism |
Francisella tularensis subsp. tularensis |
| Characteristics |
clade: Francisella tularensis subspecies tularensis subtype A.I
strain: SCHU S4
|
| Treatment protocol |
To preserve RNA integrity, bacterial cultures were added to RNAprotect Bacteria Reagent (Qiagen), as recommended by the manufacturer.
|
| Growth protocol |
Bacterial strains were cultured in BHI broth to mid-log growth phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the FastRNA Pro Blue Kit (MP Biomedicals), and then RNA was treated with DNase I and column purified, as recommended by the respective manufacturer.
To produce the the RNA-Seq libraries, ScriptSeq v2 Complete Library Preparation Kit for Bacteria (Epicentre) was utilized according to the manufacturer's instructions and included Ribo-Zero Ribosomal RNA (rRNA) Reagents for Bacteria to remove rRNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SCHUS4-9
|
| Data processing |
Trimmomatic was utilized to remove low-quality reads obtained by FastQC, and reads with less than 35 bp were removed from the analysis.
FastQC was applied again and alignments were obtained by using the TopHat2.
Bowtie 2 was utilized for indexing the genes.
Cufflink identified expressed genes and calculated transcript levels in the aligned reads within the TopHat2 generated Sequence Alignment/Map (SAM) formatted files.
Genes transcribed were measured using fragments per kilobase of exon per million (FPKM) reads.
Assembly: Francisella tularensis genome sequences were obtained from NCBI microbial genome database and had the following accession numbers: SCHU S4 (NC_006570.2), MA00-2987 (NZ_CP012372.1), WY96-3418 (NC_009257.1), and LVS (NC_07880.1).
Supplementary files format and content: Cufflinks FPKM data
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
Jul 13, 2022 |
| Contact name |
Robert Bristow Moore |
| E-mail(s) |
rmoore14@unl.edu
|
| Organization name |
University of Nebraska - Lincoln
|
| Department |
Biochemistry
|
| Lab |
Helikar Lab
|
| Street address |
1901 vine street
|
| City |
LINCOLN |
| State/province |
NE |
| ZIP/Postal code |
68504 |
| Country |
USA |
| |
|
| Platform ID |
GPL32256 |
| Series (1) |
| GSE202948 |
Arginine catabolism and polyamine biosynthesis pathway disparities within Francisella tularensis subpopulations |
|
| Relations |
| BioSample |
SAMN28233104 |
| SRA |
SRX15255169 |
