|
| Status |
Public on May 31, 2019 |
| Title |
DMSO C |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cell extract
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: Erdman
stress: hypoxia
treatment: DMSO
|
| Growth protocol |
Stationary phase M. tuberculosis was inoculated 1:100 into Sauton's media containing DMSO and incubated in a sealed vessel for 2 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were harvested from the culture by centrifugation, resuspended in Trizol and lysed by bead beating. RNA was extracted by chloroform extraction, followed by isopropanol precipitation, and the extracted RNA was resuspended in water. RNA integrity and concentration was measured with an Agilent Bioanalyzer.
RNA libraries were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Table S6 Hypoxic RNA Seq.xlsx
|
| Data processing |
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq2000.
Reads were aligned to M. tuberculosis genome NC_000962 using MAQ 0.7.1-9.
Differential expression analysis was performed using DESeq
Genome_build: NC_000962
Supplementary_files_format_and_content: DESeq analysis is presented in an excel format comparing expression in the C10-treated samples to DMSO-treated samples. Column A: Identification column indicates gene identification number and product; Column B: baseMean; C: baseMeanA; Column D: baseMeanB; Column E: Linear fold change comparing gene expression levels in C10-treated samples vs DMSO-treated samples; Column F: Log2 fold change comparing gene expression levels in C10-treated samples vs DMSO-treated samples; Column G: p value; Column H: adjusted p value; Column I: resVarA; Column J: resVarB; Column K: Functional category based on Mycobrowser annotation.
|
| |
|
| Submission date |
Apr 15, 2019 |
| Last update date |
May 31, 2019 |
| Contact name |
Gregory A Harrison |
| E-mail(s) |
gregoryharrison@wustl.edu
|
| Phone |
7086384787
|
| Organization name |
Washington University School of Medicine
|
| Department |
Molecular Microbiology
|
| Lab |
Stallings Lab
|
| Street address |
660 South Euclid Avenue
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18768 |
| Series (2) |
| GSE129830 |
RNA-sequencing of hypoxic Mycobacterium tuberculosis treated with C10 |
| GSE129835 |
Chemical disarming of isoniazid resistance in Mycobacterium tuberculosis |
|
| Relations |
| BioSample |
SAMN11419543 |
| SRA |
SRX5688215 |
