|
| Status |
Public on Aug 01, 2023 |
| Title |
VC Day4 biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
BCG Tokyo 172
|
| Organism |
Mycobacterium tuberculosis variant bovis |
| Characteristics |
strain: BCG Tokyo 172
treatment: Anhydrotetracycline 200ng/ml every 48 hours
genotype: WT
time: Day 4
|
| Treatment protocol |
For induction and maintainance of sgRNA and dcas9 expression the cultures were supplimented with Anhydrotetracycline at a final concentration of 200ng/ml every 48 hrs
|
| Growth protocol |
BCG cultures were grown in 7H9/ADC containing 20 µg/ml kanamycin and 50 µg/ml hygromycin as standing cultures at 37 degrees celcius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Direct-Zol RNA MiniPrep kit (Zymo research) following manufacturer's protocol
cDNA sample was randomly fragmented followed by 5' and 3' adapta ligation. Alternatively "tagmentation" was done to combine the fragmentation and ligation in a single more efficient step. Adapter-ligated fragments were then PCR amplified and gel purified
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
VC-MDP1_#1 cKD_day4.csv
|
| Data processing |
Mapped forward.fastq and reverse.fastq to Mycobacterium_bovis_bcg.ASM70565v1.dna.nonchromosomal.fa with default settings using BWA
Counted the number of reads in featureCounts in pair-end mode
Calculated significant differences between gene expression with DESeq2
Assembly: Mycobacterium_bovis_bcg.ASM70565v1.dna.nonchromosomal.fa
Supplementary files format and content: CSV format calculated by DESeq2
|
| |
|
| Submission date |
Jan 05, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Shaban Amina Kaboso |
| E-mail(s) |
kaboso90@gmail.com
|
| Organization name |
Niigata University
|
| Department |
Bacteriology
|
| Street address |
Asahimachi-Dori 1-757l, Chuo
|
| City |
Niigata |
| ZIP/Postal code |
951-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL33005 |
| Series (1) |
| GSE222247 |
Mycobacterial DNA binding protein 1 (MDP1) mediates gene regulation in Mycobacterium tuberculosis variant Bacillus Calmette-Guerin |
|
| Relations |
| BioSample |
SAMN32602400 |
| SRA |
SRX18945466 |
