| Bacterial and Virus Strains |
|
|
| H37Rv (M. tuberculosis) |
D. Sherman lab |
N/A |
| Critical Commercial Assays |
|
|
| Ribo-Zero magentic kit bacteria |
Illumina |
Cat # MRZB12424 |
| TruSeq stranded mRNA library prep kit |
Illumina |
Cat # RS-122-2103 |
| Deposited Data |
|
|
| Hypoxia/reaeration RNA-Seq data |
Peterson et al., 2019 |
GEO: GSE116353
|
| TF-target gene network |
Peterson et al., 2019 |
http://networks.systemsbiology.net/mtb/data-center |
| Software and Algorithms |
|
|
| DuffyNGS |
Vignali et al., 2011 |
http://networks.systemsbiology.net/mtb/data-center |
| DESeq2 |
Love et al., 2014 |
https://github.com/mikelove/DESeq2 |
| DREM |
Schulz et al., 2012 |
https://sb.cs.cmu.edu/drem/ |
| Biotapestry |
Paquette et al., 2016 |
http://www.biotapestry.org/ |
| MATLAB R2014a |
N/A |
N/A |
| Adobe Illustrator CS6 |
N/A |
N/A |
| Inkscape 0.91 |
N/A |
N/A |
| Other |
|
|
| Fibox 4 oxygen meter with display |
PreSens |
Cat #200001478 |
| Polymer Optical Fiber for use with oxygen sensor |
PreSens |
Cat # 200000241 |
| Oxygen Sensor Spot |
PreSens |
Cat # 200000023 |
| Mass flow controller for Air |
Alicat Scientific |
Cat # MCW-100ACCM-D/5M,4IN, GAS: Air |
| Mass flow controller for Nitrogen |
Alicat Scientific |
Cat # MCW-100SCCM-D/5M,4IN, GAS: N2 |
| R notebook with scripts for performing computation analyses under “mtb hypoxia dormancy” |
This paper |
https://github.com/baliga-lab |
