Ontology highlight
ABSTRACT:
PROVIDER: PRJNA983112 | 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:To understand nontuberculous mycobacterial (NTM) pathogenesis, we evaluated immune responses to Mycobacterium avium (Mav) in asymptomatic individuals with a previous history of M. avium complex lung disease (MACDZ). We analyzed global gene expression in paired Mav-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls.
2022-10-28 | GSE212384 | 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: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: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:Investigation of whole genome gene expression level changes in BMDM adhered for 4 or 18hrs to Lab Tek Chamber slides pre-coated with 4ug/ml of human serum albumin (HSA) (control protein) or purified human C1q and treated with lipopolysaccharide (LPS: 20ng/ml) Mycobacterium avium 101 (M avium) or apoptotic Jurkat T cells. BMDM were obtained from C57Bl/6 and generated as previously described in Bohlson, SS, Strasser, JA, Bower JJ, Schorey J S 2001 Role of complement in Mycobacterium avium pathogenesis: in vivo and in vitro analyses of the host response to infection in the absence of complement component C3 Infec Immun 69: 7729-7735. Mybacterium avium 101 was obtained from Dr Jeff Schorey (University of Notre Dame). The human Jurkat T cell line was obtained from ATCC (Manassas, VA) and induced to undergo apoptosis with dexamethasone as described in Lillis, AP, Greenlee, M C, Mikhailenko I, Pizzo, S V, Tenner, A J, Strickland, D K, Bohlson, S S 2008 Murine Low-Density Lipoprotein Receptor-Related Protein 1 (LRP) Is Required for Phagocytosis of Targets Bearing LRP Ligands but Is Not Required for C1q-triggered Enhancement of Phagocytosis J Immunol 181: 364: 373. A six chip study using total RNA from 5 separate cultures of BMDM adhered to HSA for 4 hrs, 5 separate cultures of BMDM adhered to C1q for 4 hrs, 5 separate cultures of BMDM adhered to HSA for 4 hrs and infected with M avium at a 1:500 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to C1q for 4hrs and infected with M avium at a 1:500 ratio ofBMDM to M avium, 5 separate cultures of BMDM adhered to HSA for 4 hrs and infected with M avium at a 1:1000 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to HSA for 4 hrs and treated with 20ng/ml LPS, 5 separate cultures of BMDM adhered to C1q for 4 hrs and treated with 20ng/ml LPS, 5 separate cultures of BMDM adhered to HSA for 4 hrs and treated with 20ng/ml LPS and co-cultured with apoptotic Jurkat cells at a 1:3 ratio of BMDM to apoptotic cells, 5 separate cultures of BMDM adhered to C1q for 4 hrs and treated with 20ng/ml LPS and co-cultured with apoptotic Jurkat cells at a 1:3 ratio of BMDM to apoptotic cells, 5 separate cultures of BMDM adhered to HSA for 18 hrs, 5 separate cultures of BMDM adhered to C1q for 18 hrs, 5 separate cultures of BMDM adhered to HSA for 18 hrs and infected with M avium at a 1:500 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to C1q for 18hrs and infected with M avium at a 1:500 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to HSA for 18 hrs and infected with M avium at a 1:1000 ratio of BMDM to M avium. The chip utilized for these studies is a mouse whole-genome 12-plex expression microarray design by NimbleGen designed from the MM9 genome Candidate probe sequences were verified to have no cross-hybridization to human (HG19) or Mycobacterium avium (NC_008595) targets Note: Study sample BMDM_HSA & M avium (1:500)_18hr_rep2 was not included in this submission due to quality control concerns.
2012-03-01 | E-GEOD-35280 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in BMDM adhered for 4 or 18hrs to Lab Tek Chamber slides pre-coated with 4ug/ml of human serum albumin (HSA) (control protein) or purified human C1q and treated with lipopolysaccharide (LPS: 20ng/ml) Mycobacterium avium 101 (M avium) or apoptotic Jurkat T cells. BMDM were obtained from C57Bl/6 and generated as previously described in Bohlson, SS, Strasser, JA, Bower JJ, Schorey J S 2001 Role of complement in Mycobacterium avium pathogenesis: in vivo and in vitro analyses of the host response to infection in the absence of complement component C3 Infec Immun 69: 7729-7735. Mybacterium avium 101 was obtained from Dr Jeff Schorey (University of Notre Dame). The human Jurkat T cell line was obtained from ATCC (Manassas, VA) and induced to undergo apoptosis with dexamethasone as described in Lillis, AP, Greenlee, M C, Mikhailenko I, Pizzo, S V, Tenner, A J, Strickland, D K, Bohlson, S S 2008 Murine Low-Density Lipoprotein Receptor-Related Protein 1 (LRP) Is Required for Phagocytosis of Targets Bearing LRP Ligands but Is Not Required for C1q-triggered Enhancement of Phagocytosis J Immunol 181: 364: 373.
2012-03-01 | GSE35280 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
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