|
| Status |
Public on Sep 28, 2023 |
| Title |
No drug 24h 2 |
| Sample type |
SRA |
| |
|
| Source name |
mc26230
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: mc26230
genotype: H37Rv deltaRD1 deltapanCD
treatment: None
time: 24h
|
| Treatment protocol |
Artemisinin and plant extracts were dissolved in DMSO. The concentrations of plant extracts indicated refer to the dry leaf mass used to make the extract, not the mass of the extract itself.
|
| Growth protocol |
Bacteria were grown in Middlebrook 7H9 supplemented with OADC, 0.2% glycerol, 0.05% Tween 80, and 24 μg/mL pantothenate (7H9) at 37 °C and 200 rpm. Bacteria were grown to mid-log phase, then diluted to OD 0.1 and treatments were applied.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5 ml of culture from the 24 hour time-points or 20 ml of culture from the 4 hour time-points was pelleted at 4 degrees, snap-frozen in liquid nitrogen, and stored at -80 until RNA extractions were performed. Pellets were resuspended in 1 ml Trizol or equivalent generic reagent, disrupted with a Fastprep 5G (MP Bio) using tubes pre-filled with 600 mg 100 um zirconium beads, molecular grade (OPS Diagnostics) for two cycles of 40 seconds each at 9 m/s. RNA was then extracted and purified with a Direct-Zol Kit (Zymo) including on-column DNase digestion.
rRNA was depleted using a set of biotinylated oligos designed as described in DOI 10.1128/mBio.00010-20. Paired-end Illumina sequencing libraries were constructed as described in DOI 10.1128/mBio.02012-21
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
No_drug_24h_2
GEO_featureCounts_table.txt
|
| Data processing |
Raw fastq files were demultiplexed using Cutadapt as in DOI 10.14806/ej.17.1.200.
Reads were aligned using BWA mem (DOI 10.1093/bioinformatics/btp324).
Reads aligned to genes were quantified using FeatureCounts (DOI 10.1093/bioinformatics/btt656).
Supplementary files format and content: GEO_featureCounts_table.txt is a tab-delimited text file that contains the output from running FeatureCounts on bam files generated from these fastq files. The FeatureCounts table can be used as input for DESeq2 for differential expression analysis.
|
| |
|
| Submission date |
Sep 28, 2023 |
| Last update date |
Sep 28, 2023 |
| Contact name |
Scarlet Shell |
| E-mail(s) |
sshell@wpi.edu
|
| Organization name |
Worcester Polytechnic Institute
|
| Department |
Biology and Biotechnology
|
| Lab |
Shell Lab
|
| Street address |
60 Prescott St, WPI
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL25317 |
| Series (1) |
| GSE244235 |
Transcriptomic response of Mycobacterium tuberculosis to artemisinin, Artemisia annua extract, and Artemisia afra extract |
|
| Relations |
| BioSample |
SAMN37575957 |
| SRA |
SRX21914572 |
