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Human gut metagenome

ABSTRACT: Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria; 16S metagenomics of healthy Japanese individual derived-gut microbiome

PROVIDER: PRJDB6814 | ENA |

REPOSITORIES: ENA

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Bacteria

Project description:Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria; Whole genome sequencing of novel bacterial isolates

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Questioning the purity of the media - Extracellular small non-coding RNA contaminants in fetal bovine serum and serum-free media

Project description:In the research field of extracellular vesicles (EVs), the use of EV-depleted fetal bovine serum (FBS) for in vitro studies is highly recommended to eliminate the confounding effects of media derived EVs. EV-depleted FBS may either be prepared by ultracentrifugation or bought commercially, nevertheless these depletion methods do not guarantee an RNA-free preparation. In this study we have addressed the RNA contamination issue in FBS, ultracentrifuged EV-depleted FBS, commercially available EV-depleted FBS, and also from our recently developed filtration based EV depleted FBS. Commercially available serum-free, xeno-free defined media were also screened for RNA contamination.

2019-04-30 | GSE120594 | GEO

Evaluation of commercially available small RNA methods for plant samples

Project description:Evaluation of commercially available small RNA methods for plant samples

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Mus musculus

Project description:Comparison of commercially available histone antibodies

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Microarray of human microvascular brain endothelial cell line hCMEC/D3 cultured in EndoGRO or EBM-2 medium

Project description:hCMEC/D3 cell line can be cultured in 2 distinct commercially available media. The objective here was to determine the differences such media induced.

2021-08-23 | E-MTAB-10813 | biostudies-arrayexpress

Fungal community from commercially available Reishi products

Project description:Fungal community from commercially available Reishi products Metagenome

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Nitric oxide exposure induces production of Rpf-dependent differentially culturable mycobacteria

Project description:Rationale: Tuberculosis has a devastating impact on global health by claiming nearly 1.4 million lives each year. During infection Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, produces heterogenous populations some of which don’t produce colonies on agar but grow in liquid media and often require supplementation with culture supernatants or recombinant Resuscitation-promoting factor, thus defined as differentially culturable bacilli. Objectives: to evaluate whether exposure to nitric oxide (NO), a well-known host defence molecule, alters mycobacterial growth phenotypes and drives generation of Rpf-dependent differentially culturable bacilli. Methods: a novel NO donor was synthesised and tested against Mtb and Mycobacterium bovis BCG in vitro, followed by growth assays, flow cytometry analysis and assessment of transcriptomic responses. Resuscitation-promoting factor (Rpf) inhibitors were used to characterise the role of Rpf proteins in the reactivation of NO-treated mycobacteria. Mycobacterial phenotypes were also investigated during infection of THP-1 macrophages activated with retinoic acid and vitamin D3. Measurements and Main Results: differentially culturable mycobacteria were generated after exposure to the novel NO donor or during infection of activated THP-1 cells. Resuscitation of these differentially culturable bacilli was largely abolished by specific Rpf inhibitors. Transcriptomic analysis revealed redox-associated stress signatures mediated by SigH and SigF, with significant down-regulation of ribosome and cell wall architecture genes, including rpfA, rpfB and rpfE, and induction of genes involved in response to thiol stress, sulphur metabolism and iron acquisition. Conclusion: Our study provides mechanistic insights into the generation of Rpf-dependent Mtb during tuberculosis and outlines a critical role of NO in this process.

2023-09-01 | E-MTAB-10776 | biostudies-arrayexpress

Transcription profiling of 22 Pancreatic Cancer Cell Lines

Project description:We used microarrays to analyze the global expression patterns for 22 commercially available pancreatic cancer cell lines 22 pancreatic cancer cell lines were grown to 80% confluence in DMEM/FBS/PenStrep media and then harvested for total RNA

2010-05-27 | E-GEOD-21654 | biostudies-arrayexpress

In vitro differentiation of rat multipotent adult porgenitor cells to smooth muscle like cells

Project description:The aim of the study was to characterize the molecular mechanism involved in TGF-ß mediated smooth muscle formation in vitro. We employed rat bone marrow derived Oct4 expressing clones of multipotent adult progenitor cells (rMAPC). We subjected these cells to differentiation towards smooth muscle cell as previously reported using TGF-ß1. The differentiation process reuires 6 days with media change every 2 days followed by RNA harvest. RNA was isolated using commercially available kits (Qiagen RNA easy micro kit). RNA integrity and quality was assessed prior to labeling and hybridization. As a control RNA from rat aortic smooth muscle cells was commercially obtained.

2012-10-09 | GSE32990 | GEO

S-Trap is an ultrafast sample preparation approach for shotgun proteomics

Project description:The success of shotgun proteomic analysis depends largely on how samples are prepared. Current approaches such as gel-, solution- or filter-based, although being extensively employed in the field, are time-consuming and less effective with respect to the repetitive sample processing, recovery, and overall yield. As an alternative, suspension trapping (S-Trap) filter is commercially available very recently in the format of single or 96-well filter plate. In contrast to conventional filter aided sample preparation (FASP) approach, which utilizes a molecular weight cutoff (MWCO) membrane as the filter and requires hours of processing before digestion-ready proteins can be obtained, S-Trap employs a three-dimensional porous material as filter media, and traps particulate protein suspension with subsequent depletion of interfering substances and in-filter digestion. Due to the large (sub-micron) pore size, each centrifugation cycle of S-Trap filter only takes around 1 minute, which significantly reduces the total processing time from approximately 3 hours by FASP to less than 15 minutes, suggesting an ultrafast sample preparation approach for shotgun proteomics. Here, for the first time, we comprehensively evaluate the performance of individual S-Trap filter and 96-well filter plate in the context of global protein identification and quantitation using whole cell lysate and clinically relevant sputum samples.

2019-03-28 | PXD010237 | Pride

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