Mycobacterium avium
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ABSTRACT:
PROVIDER: PRJNA447977 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization
2007-04-27 | GSE7622 | GEO
Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization Each isolate was competitively hybridized against Map K10 with a minimum of 2 dye flip hybridizations per isolate.
2010-06-11 | E-GEOD-7622 | biostudies-arrayexpress
Project description:Detection of species-specific proteotypic peptides for accurate and easy characterization of infectious non-tuberculous mycobacteria such as Mycobacterium avium subsp. paratuberculosis, Mycobacterium marinum and Mycobacterium vaccae is essential. Therefore, we carried out reanalysis of publicly available M. avium subsp. paratuberculosis, M. marinum and M. vaccae proteomic dataset PXD027444, PXD003766 and PASS00954 by proteome database search and followed by spectral library generation. The raw DDA data were searched against their respective reference proteome databases using Proteome Discoverer and FragPipe. The resulting peptide spectrum matches were converted into a spectral library using BiblioSpec.
2024-03-07 | PXD045965 | Pride
Project description:Mycobacterium avium subsp. paratuberculosis Raw sequence reads
| PRJNA632696 | ENA
Project description:We focused on how Mycobacterium avium subsp. paratuberculosis influences the subsequent host response to investigate the host immunopathology accompanying the host anti-mycobacterial immune response during Mycobacterium avium subsp. paratuberculosis infection in spleen of mice.
2014-10-31 | GSE62836 | GEO
Project description:We focused on how Mycobacterium avium subsp. paratuberculosis influences the subsequent host response to investigate the host immunopathology accompanying the host anti-mycobacterial immune response during Mycobacterium avium subsp. paratuberculosis infection in spleen of mice. We analyzed altered transcription in the spleen of mice at 3, 6, and 12 weeks following Mycobacterium avium subsp. paratuberculosis infection.
2014-10-31 | E-GEOD-62836 | biostudies-arrayexpress
Project description:Mycobacterium avium is one of the prominent disease causing bacteria in humans. It causes lymphadenitis, chronic pulmonary and extrapulmonary and disseminated infections in adults, children and immunocompromised humans. M. avium has ~4,500 predicted gene models, out of which not all are identified at proteomic level. Proteomic database search followed by proteogenomic analysis helps in the correction of gene models, identification of novel exons/genes, variant proteins. As part of this study, we performed proteomic analysis of M. avium cultures by data-dependent acquisition (DDA) and data-independent acquisition (DIA) method followed by proteogenomic analysis of M. avium proteomic data. M. avium culture was subjected to proteomic sample preparation. The resulting peptides were acquired in 120min DDA (12 bRPLC) and DIA method using EASY nLC 1200 liquid chromatogram system coupled to Orbitrap Fusion Tribrid mass spectrometer. The resulting DDA raw files were searched sequentially against the M. avium proteome database, Mycobacterium tuberculosis H37Rv and Ra proteome database (Mtb), M. avium genome six-frame translated proteome and variant proteins database, respectively. The database search result was converted into a spectral library and used for DIA data search for the validation of GSSPs and variant peptides. The database search of M. avium DDA has resulted in the identification of 2,954 M. avium proteins, 128 Mtb proteins, 174 GSSPs (M. avium genome six-frame translated proteome) and 795 SNPs corresponding to 612 proteins (variant proteins database), respectively. The M. avium proteome database search has covered 62.09% of the proteome with the identification of 2,954 proteins out of 4,757 proteins in the database. From the manual categorization of 174 GSSPs, we observed 23 N-terminal extensions, 142 pseudogene coding peptides and one each novel exon and short peptide, respectively.
2023-03-17 | PXD032067 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE32241: Differentially regulated genes induced in Mycobacterium avium subspecies paratuberculosis by in vitro acid-nitrosative multi-stress GSE32242: Differentially regulated genes induced in Mycobacterium avium subspecies paratuberculosis by in vitro infection of THP-1 human macrophage cell line Refer to individual Series
2012-05-31 | E-GEOD-32243 | biostudies-arrayexpress
Project description:Detection of species-specific proteotypic peptides for accurate and easy characterization of infectious non-tuberculous mycobacteria such as Mycobacterium avium subsp. paratuberculosis is essential. Therefore, we conducted an in-depth global proteomic experiment using M. avium subsp. paratuberculosis ATCC 19698 (Map) strain followed by proteome database search and spectral library generation. The lysate was subjected to in-solution proteomic sample preparation and fractionated using an offline C18 StageTip. Each fraction was acquired in technical triplicates using a 180 min data-dependent acquisition (DDA) method in Orbitrap Fusion Tribrid (Thermo Scientific) mass spectrometer. The resulting raw DDA data were searched against the M. avium subsp. paratuberculosis proteome database using Proteome Discoverer and FragPipe. The resulting peptide spectrum matches were converted into a spectral library using BiblioSpec.
2024-03-07 | PXD040589 | Pride
Project description:To investigate the changes in global transcriptome expression of HSCs following infection, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified HSCs (SP KSL CD150+) isolated from naive or Mycobacterium avium infected mice
2017-01-04 | GSE89364 | GEO