Kupyaphores are counter regulatory zinc homeostatic metallophores required for Mycobacterium tuberculosis colonization

Github: viv3kanand/MTU-Manuscript

DOI: https://doi.org/10.1073%2Fpnas.2110293119

Citation: Mehdiratta K, Singh S, Sharma S, et al. Kupyaphores are zinc homeostatic metallophores required for colonization of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2022;119(8):e2110293119. doi:10.1073/pnas.2110293119

This repository documents the RNA-Seq and Operon analysis codes of Mycobacterium tuberculosis data.

Repository structure

.
├── README.md
└── data
│    └── ann
│        ├── Extract_ann.R
│        └── mtuTemp
│            ├── GCF_000195955.2_ASM19595v2_feature_table.txt.gz
│            ├── GCF_000195955.2_ASM19595v2_genomic.fna.gz
│            ├── GCF_000195955.2_ASM19595v2_genomic.gff.gz
│            ├── md5checksums.txt
│            ├── mtu.fna
│            ├── mtu.fna.fai
│            ├── mtu.gff
│            ├── mtu.ptt
│            └── mtu.rnt
│
└── DGE
│   ├── DGE.Rmd
│   └── Figures.Rmd
└── Operon
    ├── Rockhopper.ipynb
    ├── Results_cond0.1_6
    ├── Results_cond50_6
    └── Results_cond50_0.1