tuberculosis. - OmicsDI

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Unknown (24397)
Genomics (6339)
Transcriptomics (1722)
Proteomics (452)
Metabolomics (58)
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Methylation profiling (18)
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Multiomics (2)

Organisms

Homo sapiens (675)
Mycobacterium tuberculosis (506)
Mus musculus (382)
Mycobacterium tuberculosis H37Rv (249)
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Danio rerio (34)
Mycobacterium tuberculosis CDC1551 (27)
Macaca mulatta (26)
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Staphylococcus aureus (16)
Mycobacterium avium subsp. paratuberculosis (14)
Oryctolagus cuniculus (14)
Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (11)
Mycobacterium avium (10)
Mycobacterium tuberculosis str. Erdman = ATCC 35801 (9)
Rattus norvegicus (8)
Mycobacterium avium subsp. paratuberculosis K-10 (8)
Thermus thermophilus HB8 (4)
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Corynebacterium pseudotuberculosis (2)
Drosophila melanogaster (2)
Arabidopsis thaliana (2)
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Plasmodium falciparum K1 (1)
Plasmodium falciparum NF54 (1)
Severe acute respiratory syndrome-related coronavirus (1)
Mammalia (1)

Organisms

Mycobacterium tuberculosis (874)
Homo sapiens (465)
Mus musculus (275)
Mycobacterium tuberculosis H37Rv (169)
Mycobacterium tuberculosis variant bovis (66)
Mycobacterium tuberculosis subsp. tuberculosis (37)
Mycobacterium tuberculosis variant bovis BCG (36)
Danio rerio (27)
Mycobacteroides abscessus (26)
Bos taurus (23)
Mycolicibacterium smegmatis (17)
Macaca mulatta (17)
Mycobacterium tuberculosis CDC1551 (14)
Mycobacterium tuberculosis H37Ra (13)
Macaca fascicularis (12)
Mycobacterium tuberculosis complex (10)
Mycobacterium (10)
Mycobacterium tuberculosis MC2_6020 (9)
Mycobacterium tuberculosis str. Erdman = ATCC 35801 (9)
Mycobacterium tuberculosis variant caprae (9)
human lung metagenome (9)
Mycobacterium tuberculosis variant africanum (8)
Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (8)
Mycobacterium marinum (8)
Oryctolagus cuniculus (8)
unidentified (7)
Mycolicibacterium smegmatis MC2 155 (6)
human sputum metagenome (5)
Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 (5)
Mycobacterium tuberculosis complex sp. (4)

Repository

ENA (6182)
geo (1319)
biostudies-arrayexpress (607)
pride (274)
MassIVE (54)
iProX (53)
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dbGaP (16)
PAXDB (13)
PeptideAtlas (13)
ExpressionAtlas (12)
jPOST (10)
PanoramaPublic (7)
GNPS (6)
NODE (6)
EVA (2)
Cell Collective (1)

Tissue

Cell culture (44)
Macrophage (30)
Prokaryotic cell (11)
Blood serum (10)
Cultured cells (9)
Bacterial cells (6)
Blood (6)
Blood plasma (6)
Cell line cell (5)
Blood (4)
Lung (4)
Monocyte (4)
Urine (3)
Blood cell (3)
Cell suspension culture (3)
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Bronchoalveolar lavage (2)
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Permanent cell line cell (2)
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Bacterial protein (1)
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Bone marrow-derived macrophage (1)
Brain (1)

Disease

Tuberculosis (62)
Pulmonary tuberculosis (30)
Tuberculosis (28)
Normal (3)
Meningeal tuberculosis (2)
Secondary progressive multiple sclerosis (1)
Tuberculosis and treatment for 3 months (1)
Tuberculosis and treatment for 6 months (1)
Latent tuberculosis infection (1)
Latent tuberculosis (1)
Alzheimers disease (1)
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Influenza (1)
Juvenile idiopathic arthritis (1)
Escherichia coli infection (1)
Kawasaki disease (1)
Urinary bladder cancer (1)
Multibacillary (1)
Fish tuberculosis (1)
HIV-Tuberculosis with Immune Reconstitution Inflammatory Syndrome (1)
Non-diabetic (1)
Psoriatic arthritis (1)

Technology Type

Mass Spectrometry (299)
Shotgun proteomics (162)
Bottom-up proteomics (41)
Data-dependent acquisition (26)
ESI (25)
Mass spectrometry (19)
Gel-based experiment (18)
Data-independent acquisition (16)
Affinity purification coupled with mass spectrometry proteomics (15)
SWATH MS (15)
Top-down proteomics (10)
Mass spectrometry assay (7)
Affinity proteomics (3)
HDMSE (3)
All-ion fragmentation (2)
Mass spectrometry imaging (2)
SRM/MRM (2)
Affymetrix Genome-Wide Human SNP Array 6.0 Genotypes (1)
Affymetrix 500K (1)
NMR spectroscopy (1)
EI (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
Immunopeptidomics (1)

Instrument Platform

NextSeq 500 (20)
Illumina NovaSeq 6000 (16)
Illumina HiSeq 2500 (12)
Illumina HiSeq 2000 (12)
Illumina NovaSeq X (7)
Agilent 2100 Bioanalyzer (3)
NanoDrop (3)
Chemostat (3)
Bioanalyser (3)
Illumina MiSeq (3)
NextSeq 550 (3)
Nanodrop N1000 spectrophotometer (2)
Bellco roll-in incubator (2)
Variable Atmosphere Incubator (2)
NA (2)
Ion Torrent Proton (2)
Illumina DNA Prep sample preparation kits (Illumina Inc., San Diego, CA, USA). Final libraries concentrations and size were assessed with Quant-IT DNA Assay Kit and Agilent 4200 Tapestation System (Agilent Technologies, Milan, Italy), (1)
QIAamp DNA minikit, Qiagen, Germany (1)
Rstudio (1)
Microbeads (1)
GeneChip Instrument System (1)
Affymetrix mouse gene 1.0 ST arrays (1)
Qubit 2.0, Agilent 2100 (1)
Model 450 Fluidics Station/Affymetrix GeneChip Scanner 3000 TG System (1)
Agilent® 2100 Bioanalyzer Instrument (1)
None (1)
QuantStudioTM 12K Flex system (1)
AB SOLiD 3 Plus System (1)
Affymetrix 428 (1)
Axon 4000B scanner (1)

Publication Date

2025 (208)
2021 (175)
2024 (162)
2014 (150)
2013 (144)
2026 (143)
2018 (139)
2023 (134)
2010 (132)
2022 (130)
2020 (126)
2012 (113)
2019 (104)
2016 (103)
2015 (96)
2017 (86)
2011 (61)
2009 (57)
2008 (56)
2007 (45)
2005 (9)
2006 (8)
2004 (2)
2003 (2)

UNIPROT ID/AC

35KD_MYCTU (11)
A85A_MYCTU (11)
A85B_MYCTU (11)
A85C_MYCTU (11)
ACNA_MYCTU (11)
ACPM_MYCTU (11)
I6X8D2 (1)
P9WPB3 (1)
Q79FX8 (1)
P0CH91 (1)
Q79FX6 (1)
P9WPB1 (1)
P9WQD9 (1)
P9WQD7 (1)
P9WGR1 (1)
O53580 (1)
P9WNG3 (1)
I6Y778 (1)
P9WGR9 (1)
P9WGT3 (1)
P9WNG5 (1)
P9WNZ3 (1)
P9WNZ7 (1)
P9WPB5 (1)
P9WQD3 (1)
P9WQH7 (1)
O53578 (1)
P9WQH9 (1)
P96890 (1)
P95029 (1)

CHEBI ID

CHEBI:30769 (11)
CHEBI:15741 (10)
CHEBI:30915 (9)
CHEBI:18012 (7)
CHEBI:15351 (5)
CHEBI:15346 (5)
CHEBI:16891 (4)
CHEBI:30887 (4)
CHEBI:6650 (4)
CHEBI:30744 (4)
CHEBI:15380 (4)
CHEBI:16265 (2)
CHEBI:33231 (1)
CHEBI:38068 (1)
CHEBI:35222 (1)
CHEBI:22036 (1)
CHEBI:12742 (1)
CHEBI:33442 (1)
CHEBI:45607 (1)
CHEBI:12757 (1)
CHEBI:12760 (1)
CHEBI:13394 (1)
CHEBI:10833 (1)
CHEBI:57540 (1)
CHEBI:13393 (1)
CHEBI:10786 (1)
CHEBI:527887 (1)
CHEBI:21901 (1)
CHEBI:44214 (1)
CHEBI:44215 (1)

Metabolite Name

L-Proline (5)
L-Threonine (5)
Xanthine (5)
L-Tyrosine (5)
L-Phenylalanine (5)
3-Hydroxybenzaldehyde (4)
Succinic acid (4)
L-Asparagine (4)
Sebacic acid (4)
Adenosine (4)
Adipic acid (4)
L-Serine (4)
Guanosine (4)
Uridine (4)
L-Valine (4)
Inosine (4)
Hypoxanthine (4)
2(3H)-Benzothiazolethione (3)
L-Norleucine (3)
Glycine (3)
L-Alanine (3)
Uracil (3)
Betaine (3)
S-Adenosylhomocysteine (3)
L-Lysine (3)
Citrulline (3)
5-Hydroxy-L-tryptophan (3)
2-Isopropylmalic acid (3)
Taurine (3)
Deoxycholic acid (3)

First Public Date

2013 (1509)
2014 (1267)
2025 (455)
2024 (428)
2026 (400)
2023 (314)
2021 (311)
2022 (266)
2019 (256)
2018 (246)
2020 (244)
2017 (199)
2015 (140)
2016 (118)
2012 (20)
2011 (6)
2010 (3)

Modelling Approach

Ordinary differential equation model (7)
Computational model (6)
Constraint-based model (6)

Study status

Enrolling by invitation (1)
Terminated (1)
Active, not recruiting (1)
Recruiting (1)

Lab affiliation

Professor, Microbiology, Immunology, and Pathology Mycobacteria Research Laboratories Scientific Director, Rocky Mountain Regional Biocontainment Laboratory Editor-in-chief, BMC Mycobacteria (4)
1DST/NRF Centre of Excellence in Biomedical Tuberculosis research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa (3)
Colorado State University (3)
Global Health Institute, EPFL, Lausanne, Switzerland (3)
Massachusetts Institute of Technology (3)
OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands (3)
Associate Professor School of Life Sciences University of Hawaii at Manoa (2)
DST/NRF Centre of Excellence in Biomedical Tuberculosis research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa (2)
Department of Chemical and Systems Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa (2)
Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town (2)
ETH Zurich (2)
Farnusch Kaschani, Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (2)
Institute of Biochemistry and Biophysics, Polish Academy of Sciences (2)
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (2)
Institute of Microbiology (2)
Max Perutz Labs, Vienna, Austria (2)
Ph.D., Professor, Vice Dean (2)
Rutgers Robert Wood Johnson Medical School Department of Biochemistry and Molecular Biology (2)
School of Biological and Behavioural Sciences Queen Mary University of London (2)
School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL) (2)
Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University (2)
Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China (2)
Translational Health Science and Technology Institute (2)
1 Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China 2 Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200049, PR China 3 Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China. (1)
1. Africa Health Research Institute, Durban, South Africa 2. 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA 3. Center for AIDS Research and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA (1)
1. Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia 2. The University of Sydney, Discipline of Infectious Diseases & Immunology and Sydney Institute for Infectious Diseases, Camperdown, NSW 2050, Australia (1)
1Departments of Medicine & 2Pathology, Case Western Reserve University and University Hospitals Case Medical Center; 3Department of Molecular Biology & Microbiology Case Western Reserve University School of Medicine, Cleveland, Ohio 44106,USA. (1)
A.N. Bach Institute of Biochemistry, Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences, Leninsky pr., 33, 119071, Moscow, Russia (1)
Aix-Marseille Univ, CNRS, LISM, IMM FR3479, 13009 Marseille, France (1)
Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique (1)

Keyword

Remicade (1)
CGD Infection (1)
Chorionic Granulomatous Disease (1)
CGD (1)
Volatile Organic Compounds (1)
Nano-sensors (1)
Electronic nose (1)
Digestive cancers (1)
Perla Occipital System (1)
Inflammatory Bowel Disease (1)
IBD (1)
Infliximab (1)

IsPrivate

False (22)

Model Flag

Non Kinetic (7)

Submitter Keywords

Ersilia (6)
Machine Learning Model (6)
FAIR-AIML (2)
FROG (2)
Manuscript Accepted (1)
Immuno-oncology (1)

Classification

bacteria (3611)
fungi (3)
viruses (3)

Modification

15.994915 (2)
Not available (2)
2x(15)N labeled L-lysine (1)
42.010565 (1)
4x(15)N labeled L-arginine (1)
57.021464 (1)
58.005479 (1)
6x(2)H labeled dimethylated L-arginine (1)
N6-dimethyl-L-lysine (1)

Study type

Transcription profiling by array (423)
RNA-seq of coding RNA (78)
Unknown experiment type (12)
ChIP-seq (10)
Other (8)
DNA-seq (8)
Proteomic profiling by array (7)
RNA-seq of total RNA (7)
High-throughput sequencing (4)
CLIP-seq (4)
Comparative genomic hybridization by array (4)
MicroRNA profiling by array (4)
Methylation profiling by array (4)
RNA-seq of non coding RNA (4)
ChIP-chip by tiling array (3)
Human - One-color microarray (3)
Transcription profiling by tiling array (3)
Observational (3)
Baseline (2)
One-color microarray (2)
Human - High-throughput sequencing (2)
Animal - High-throughput sequencing (2)
ChIP-chip by array (2)
Transcription profiling by RT-PCR (2)
RIP-seq (2)
RNA-seq of coding RNA from single cells (2)
Two-color microarray (1)
RNAi profiling by array (1)
Bisulfite-seq (1)
Ribo-seq (1)

Release Date

2025 (2528)
2022 (2447)
2021 (2384)
2023 (2339)
2024 (2141)
2020 (2008)
2019 (1626)
2018 (1515)
2017 (1271)
2016 (1115)
2015 (1051)
2014 (899)
2013 (704)
2012 (546)
2011 (463)
2010 (432)
2026 (308)
2009 (287)
2008 (247)
2007 (149)
2006 (128)
2005 (89)
2003 (64)
2004 (53)
2002 (50)
2001 (49)
2000 (36)
1999 (34)
1998 (31)
1997 (4)

Location

Latvia (1)
South Korea (1)
Germany (1)
United States (1)
Austria (1)
France (1)

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Time course RNA-seq of Mycobacterium tuberculosis exposed to nitric oxide.

Mycobacterium tuberculosis is an intracellular human pathogen with the ability to resist and adapt to many adverse conditions it encounters upon infection. Among these, overcoming the production of nitric oxide by macrophages could be key for M. tuberculosis success. We have challenged M. tuberculo...

ORGANISM(S): Mycobacterium tuberculosis H37Rv

2017-08-29 | E-MTAB-5557 | biostudies-arrayexpress

The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis [ChIP-Seq]

The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead to compromised production of pathogen-specif...

ORGANISM(S): Mycobacterium tuberculosis H37Rv

2014-06-02 | E-GEOD-54239 | biostudies-arrayexpress

Dual RNA-seq of M. tuberculosis H37Rv infecting macrophage-like THP-1 cells during 48h

Transcriptional changes during early infection of macrophage-like THP-1 cell line with pathogenic bacterium Mycobacterium tuberculosis. RNAseq samples were taken at 0h (THP-1 cells growing in the RPMI medium), and after 4h, 24h and 48h post infection. Bacterial enrichment was performed to increase t...

ORGANISM(S): Homo sapiens

2017-08-01 | E-MTAB-5287 | biostudies-arrayexpress

Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus

Tuberculosis (TB) is still a major global health challenge, killing over 1.5 million people each year, and hence, there is a need to identify and develop novel treatments for Mycobacterium tuberculosis (M. tuberculosis). The prevalence of infections caused by nontuberculous mycobacteria (NTM) is als...

ORGANISM(S): Mycobacterium tuberculosis

2024-03-01 | E-MTAB-13761 | biostudies-arrayexpress

Role of M. tuberculosis in CO sensing

This SuperSeries is composed of the following subset Series: GSE11095: Dose response of carbon monoxide treatment of M. tuberculosis GSE11096: Role of M. tuberculosis dosS and dosT in CO sensing Refer to individual Series

ORGANISM(S): Mycobacterium tuberculosis

2008-05-28 | E-GEOD-10897 | biostudies-arrayexpress

The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis [RNA-Seq]

ORGANISM(S): Mycobacterium tuberculosis H37Rv

2014-06-02 | E-GEOD-54240 | biostudies-arrayexpress

Functional Genomics Reveals Extended Roles of the Mycobacterium tuberculosis Stress Response Factor sigmaH

DNA Microarray based comparison of M. tuberculosis and its isogenic delta-sigmaH mutant for an extended period of time, using a diamide-stress and removal strategy (post-diamide stress or PDS) Raw data has been requested of, but not provided by, the submitter. Two strains, M. tuberculosis vs delta-...

ORGANISM(S): Mycobacterium tuberculosis

2010-06-24 | E-GEOD-15608 | biostudies-arrayexpress

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis; insights for early bactericidal activity

Background: Pyrazinamide (PZA) plays an essential part in the shortened 6-month tuberculosis (TB) treatment course due to its activity against slow-growing, semi-dormant organisms. We tested the paradigm that PZA preferentially targets slow growing cells of Mycobacterium tuberculosis that remain aft...

ORGANISM(S): Mycobacterium tuberculosis H37Rv

2016-03-25 | E-MTAB-4093 | biostudies-arrayexpress

MntR(Rv2788): a transcriptional regulator that controls manganese homeostasis in Mycobacterium tuberculosis.

Transcriptional profiling of SirR and manganese regulated expression of genes in Mycobacterium tuberculosis strains comparing high manganese vs. low manganese in Rv (wild type Mycobacterium tuberculosis) and ST70 (mntR mutant strain of Mycobacterium tuberculosis) Two strains each with two conditions...

ORGANISM(S): Mycobacterium tuberculosis

2015-12-08 | E-GEOD-70812 | biostudies-arrayexpress

Role of M. tuberculosis dosS and dosT in CO sensing

Transcriptional profiling of M. tuberculosis dosR and dosS mutants and wild type growing in log phase treated with carbon monoxide or nitric oxide versus untreated controls Keywords: Genetic modification Two condition experiment, DETANO treated cells at 100 uM or CO treated cells at 20000 ppm versus...

ORGANISM(S): Mycobacterium tuberculosis

2008-05-28 | E-GEOD-11096 | biostudies-arrayexpress

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33079 Results

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