|
| Status |
Public on Jan 10, 2022 |
| Title |
krrA vehicle2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, pelleted
|
| Organism |
Bacillus anthracis |
| Characteristics |
strain: Sterne
genotype: {delta}krrA
growth media: LB
atomosphere: aerobic
growth temperature: 37°C
|
| Treatment protocol |
Samples were stored at -80°C prior to RNA extraction
|
| Growth protocol |
Bacteria were grown in BHIS medium at 37°C anaerobically or with 1.5% oxygen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit. DNA was removed by treatment with Invitrogen TURBO Dna-free kit and rRNA was depleted using the Invitrogen RiboMinus Transcriptome Isolation kit (bacteria) and the RiboMinus Concentration Module
Library construction was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
krrA vehicle
5425-HP-41
|
| Data processing |
Raw data files (.fastq) were imported into the CLC Genomics Workbench software (Version 20.0.1) platform for analysis. The Illumina paired reads option was chosen for import.
Imported reads were trimmed to remove adapters using CLC Genomics Workbench
To remove rRNA reads, all paired reads were aligned to a sequence list containing all rRNA sequences for each corresponding bacterial strain. Unmapped (non-rRNA) reads were collected and used for subsequent analysis. Steps were performed using CLC Genomics Workbench. Refrence genomes NC_009089 and NC_013315 were used for CD630 and CD196, respectively.
Expression values (as RPKM) for Gene Tracks were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench. For cross-comparison between strain a 'consensus genome' was generated by BLASTing every CD630 gene agains each CD196 gene and generating a gene track of the resulting consensus sequences.
Comparison of samples was performed using the "Differential Expression in Two Groups" function in CLC Genomics Workbench
Output was exported to MS Excel and manually curated if neccesary
|
| |
|
| Submission date |
Jan 07, 2022 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Hualiang Pi |
| E-mail(s) |
hualiangpi@gmail.com
|
| Organization name |
VUMC
|
| Street address |
1161 21st Avenue South
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL31186 |
| Series (2) |
| GSE193210 |
A Bacillus anthracis RNA binding protein post-transcriptionally regulates two component signaling through RNA turnover [RNA-Seq] |
| GSE193212 |
A Bacillus anthracis RNA binding protein post-transcriptionally regulates two component signaling through RNA turnover |
|
| Relations |
| BioSample |
SAMN24720681 |
| SRA |
SRX13653988 |
