|
| Status |
Public on Aug 11, 2021 |
| Title |
1D_wild_type |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Bordetella pertussis |
| Characteristics |
genotype: wild_type
|
| Treatment protocol |
2ml of cells harvested into 4ml RNA protect Bacteria (Qiagen)
|
| Growth protocol |
Wild type and mutant cells were grown to an OD600 0.6-0.7 in SS broth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cell pellets using RNAqueous RNA extraction kit (Ambion) following kit instructions, and DNA was removed using the TurboDNAse kit. Ribosomal RNA depletion was completed using the RiboZero Bacteria Kit (Illumina).
The KAPA Stranded Total RNA Kit (KAPA Biosystems) was used for library construction (single end reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Wild type B. pertussis
|
| Data processing |
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
Fastq file quality control was performed using FastQC v0.11.7
Fastq files were aligned to the B. pertussis genome using STAR v2.6.1a
BAM files were sorted as part of read alignment with STAR
Read count tables were generated using htseq-count v0.9.1
Genome_build: B. pertussis sp. Tohama I reference genome: https://www.ncbi.nlm.nih.gov/assembly/GCF_000195715.1
Supplementary_files_format_and_content: Tab delimited files containing uniquely mapped reads per gene for each sample
|
| |
|
| Submission date |
Jan 05, 2021 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Travis Blimkie |
| E-mail(s) |
travis.m.blimkie@gmail.com
|
| Organization name |
University of British Columbia
|
| Department |
MICB
|
| Lab |
REW Hancock Lab
|
| Street address |
2259 Lower Mall Research Station
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL29570 |
| Series (1) |
| GSE164312 |
RNase III and RNase E influence post-transcriptional regulatory networks involved in virulence factor production, metabolism and regulatory RNAs processing in Bordetella pertussis. |
|
| Relations |
| BioSample |
SAMN17219021 |
| SRA |
SRX9786642 |
