TB Systems Biology

TB Systems Biology is experimentally mapping and computationally modeling the molecular pathways of M. tuberculosis under conditions relevant to TB pathogenesis by performing systematic profiling using ChIP-seq, transcriptomics, proteomics, glycomics, metabolomics, and lipidomics during both in vitro and in vivo growth.

The following are data sets generated by TB Systems Biology with pointers to relevant publications about the data, pointers to the data, and sets of important genes/proteins identified by the set of experiments and the criteria for their selection.


Mycobacterium tuberculosis H37Rv

Reconstruction of the regulatory interaction network of M. tuberculosis

To systematically map transcription factor binding sites, ChIP-Seq data using FLAG-tagged transcription factors episomally expressed under the control of the mycobacterial tetracycline-inducible promoter will be generated. This method allows targeting all ~200 regulators in the M. tuberculosis genome in a consistent and comparable manner independent of regulatory function or the conditions under which each regulatory is expressed.

Deconstruction of the hypoxic response

Hypoxic time course experiments.


ChIP-Seq data in PATRIC

Sample name bigwig file View peaks
Rv0022c_58_6 download bigwig view peaks
Rv0023_52_4 download bigwig view peaks
Rv0042c_81_4_2 download bigwig view peaks
Rv0047c_53_1 download bigwig view peaks
Rv0067c_52_5 download bigwig view peaks
Rv0078_51_1 download bigwig view peaks
Rv0081_13_3 download bigwig view peaks
Rv0081_27_6 download bigwig view peaks
Rv0081_55_4 download bigwig view peaks
Rv0081_69_1 download bigwig view peaks
Rv0135c_49_7 download bigwig view peaks
Rv0195_82_5_2 download bigwig view peaks
Rv0232_16_6 download bigwig view peaks
Rv0238_77_4 download bigwig view peaks
Rv0273c_67_2 download bigwig view peaks
Rv0275c_79_3 download bigwig view peaks
Rv0302_66_6 download bigwig view peaks
Rv0324_17_7 download bigwig view peaks
Rv0324_35_1 download bigwig view peaks
Rv0324_37_4 download bigwig view peaks
Rv0324_37_6 download bigwig view peaks
Rv0324_70_4 download bigwig view peaks
Rv0330c_49_6 download bigwig view peaks
Rv0330c_82_5_3 download bigwig view peaks
Rv0348_60_7 download bigwig view peaks
Rv0353_81_3_3 download bigwig view peaks
Rv0465c_41_1 download bigwig view peaks
Rv0472c_81_3_2 download bigwig view peaks
Rv0474_14_6 download bigwig view peaks
Rv0494_17_1 download bigwig view peaks
Rv0494_71_1 download bigwig view peaks
Rv0576_53_3 download bigwig view peaks
Rv0599c_72_2_1 download bigwig view peaks
Rv0599c_72_2_2 download bigwig view peaks
Rv0602c_19_1 download bigwig view peaks
Rv0602c_40_8 download bigwig view peaks
Rv0653c_17_8 download bigwig view peaks
Rv0674_60_5 download bigwig view peaks
Rv0678_50_5 download bigwig view peaks
Rv0678_72_1 download bigwig view peaks
Rv0681_41_4 download bigwig view peaks
Rv0691c_63_3 download bigwig view peaks
Rv0757_18_6 download bigwig view peaks
Rv0757_18_8 download bigwig view peaks
Rv0767c_41_6 download bigwig view peaks
Rv0818_81_3_1 download bigwig view peaks
Rv0827c_16_7 download bigwig view peaks
Rv0827c_19_6 download bigwig view peaks
Rv0880_64_4 download bigwig view peaks
Rv0891c_61_7 download bigwig view peaks
Rv0967_61_5 download bigwig view peaks
Rv1019_60_6 download bigwig view peaks
Rv1033c_53_4 download bigwig view peaks
Rv1049_39_8 download bigwig view peaks
Rv1049_79_5 download bigwig view peaks
Rv1152_26_7 download bigwig view peaks
Rv1167c_40_2 download bigwig view peaks
Rv1167c_41_2 download bigwig view peaks
Rv1186c_80_7 download bigwig view peaks
Rv1219c_63_4 download bigwig view peaks
Rv1255c_18_7 download bigwig view peaks
Rv1353c_79_7 download bigwig view peaks
Rv1379_64_6 download bigwig view peaks
Rv1395_40_3 download bigwig view peaks
Rv1404_63_2 download bigwig view peaks
Rv1423_66_2 download bigwig view peaks
Rv1473A_76_5 download bigwig view peaks
Rv1556_66_3 download bigwig view peaks
Rv1657_24_4 download bigwig view peaks
Rv1674c_68_1 download bigwig view peaks
Rv1675c_65_3 download bigwig view peaks
Rv1719_66_1 download bigwig view peaks
Rv1773c_40_1 download bigwig view peaks
Rv1776c_64_5 download bigwig view peaks
Rv1816_60_4 download bigwig view peaks
Rv1828_70_7 download bigwig view peaks
Rv1846c_65_5 download bigwig view peaks
Rv1956_26_8 download bigwig view peaks
Rv1985c_24_7 download bigwig view peaks
Rv1985c_71_2 download bigwig view peaks
Rv1990c_37_7 download bigwig view peaks
Rv1994c_32_8 download bigwig view peaks
Rv2011c_83_1_2 download bigwig view peaks
Rv2017_81_2_3 download bigwig view peaks
Rv2021c_16_4 download bigwig view peaks
Rv2034_16_2 download bigwig view peaks
Rv2034_19_4 download bigwig view peaks
Rv2034_69_3 download bigwig view peaks
Rv2034_71_3 download bigwig view peaks
Rv2250c_80_6 download bigwig view peaks
Rv2258c_63_1 download bigwig view peaks
Rv2324_16_8 download bigwig view peaks
Rv2324_57_5 download bigwig view peaks
Rv2359_29_2 download bigwig view peaks
Rv2374c_45_4 download bigwig view peaks
Rv2488c_64_1 download bigwig view peaks
Rv2506_64_2 download bigwig view peaks
Rv2506_81_1_3 download bigwig view peaks
Rv2621c_26_1 download bigwig view peaks
Rv2640c_16_3 download bigwig view peaks
Rv2745c_13_4 download bigwig view peaks
Rv2760c_81_1_2 download bigwig view peaks
Rv2779c_64_3 download bigwig view peaks
Rv2779c_82_3_1 download bigwig view peaks
Rv2887_14_8 download bigwig view peaks
Rv2912c_83_5_2 download bigwig view peaks
Rv2989_15_8 download bigwig view peaks
Rv2989_69_4 download bigwig view peaks
Rv3050c_31_2 download bigwig view peaks
Rv3050c_57_4 download bigwig view peaks
Rv3058c_83_4_1 download bigwig view peaks
Rv3066_17_3 download bigwig view peaks
Rv3082c_83_4_2 download bigwig view peaks
Rv3095_34_6 download bigwig view peaks
Rv3133c_13_8 download bigwig view peaks
Rv3133c_27_8 download bigwig view peaks
Rv3133c_69_2 download bigwig view peaks
Rv3160c_29_1 download bigwig view peaks
Rv3167c_31_1 download bigwig view peaks
Rv3173c_81_4_1 download bigwig view peaks
Rv3183_17_4 download bigwig view peaks
Rv3219_26_2 download bigwig view peaks
Rv3246c_26_6 download bigwig view peaks
Rv3249c_28_4 download bigwig view peaks
Rv3249c_35_2 download bigwig view peaks
Rv3249c_71_4 download bigwig view peaks
Rv3260c_31_8 download bigwig view peaks
Rv3260c_83_1_1 download bigwig view peaks
Rv3291c_17_2 download bigwig view peaks
Rv3405c_17_6 download bigwig view peaks
Rv3416_48_4 download bigwig view peaks
Rv3417c_50_6 download bigwig view peaks
Rv3488_46_6 download bigwig view peaks
Rv3557c_65_4 download bigwig view peaks
Rv3557c_83_1_3 download bigwig view peaks
Rv3574_11_1 download bigwig view peaks
Rv3574_11_2 download bigwig view peaks
Rv3574_11_3 download bigwig view peaks
Rv3574_11_4 download bigwig view peaks
Rv3574_70_5 download bigwig view peaks
Rv3597c_28_8 download bigwig view peaks
Rv3597c_65_2 download bigwig view peaks
Rv3597c_70_3 download bigwig view peaks
Rv3676_83_3_1 download bigwig view peaks
Rv3736_83_3_2 download bigwig view peaks
Rv3744_83_3_3 download bigwig view peaks
Rv3765c_46_8 download bigwig view peaks
Rv3830c_83_5_1 download bigwig view peaks
Rv3833_83_2_3 download bigwig view peaks
Rv3849_59_5 download bigwig view peaks
Rv3849_71_5 download bigwig view peaks
Rv3855_23_8 download bigwig view peaks
Rv3855_71_6 download bigwig view peaks
Rv3862c_19_2 download bigwig view peaks

RNA-Seq data in PATRIC

Sample name bam file bai file bigwig file View alignments View coverage
SG2AT0 download bam download bai download bigwig view alignments view coverage
SG2AT1 download bam download bai download bigwig view alignments view coverage
SG2AT2 download bam download bai download bigwig view alignments view coverage
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SG2BT0 download bam download bai download bigwig view alignments view coverage
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SG2DT0 download bam download bai download bigwig view alignments view coverage
SG2DT1 download bam download bai download bigwig view alignments view coverage
SG2DT2 download bam download bai download bigwig view alignments view coverage
SG2DT3 download bam download bai download bigwig view alignments view coverage
SG2DT5 download bam download bai download bigwig view alignments view coverage
SG2DT7 download bam download bai download bigwig view alignments view coverage
SG2DT8 download bam download bai download bigwig view alignments view coverage
SG2DT9 download bam download bai download bigwig view alignments view coverage