Metagenomic analysis of Egyptian mummies
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ABSTRACT:
PROVIDER: PRJEB33848 | ENA |
REPOSITORIES: ENA
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Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress
Project description:LC-MS/MS-based Proteomic analysis of an archaeological Ptolemaic Egyptian vase. Other complementary analyses performed: aDNA on chloroplasts, metabolomics LC-MS/MS, SR-FTIR microscopy, SR-XRD.
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Project description:Interventions: Group 1: Surgical patients undergoing surgery for colorectal cancer: immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa, and saliva samples perioperatively and during oncologic follow-up.
Group 2: oncologic patients with chemo- / immune therapy without recent surgery:
Immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa and saliva samples during therapy and oncological follow-up.
Group 3: healthy controls:
Immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa, and saliva samples at the time of screening colonoscopy.
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Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: diagnostic
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Project description:Abstract from accompanying publication: "Bats host a number of viruses that cause severe disease in humans without experiencing overt symptoms of disease themselves. While the mechanisms underlying this ability to avoid sickness are not known, deep sequencing studies of bat genomes have uncovered genetic adaptations that may have functional importance in the antiviral response of these animals. Egyptian rousette bats (Rousettus aegyptiacus) are the natural reservoir hosts of Marburg virus (MARV). In contrast to humans, these bats do not become sick when infected with MARV. A striking difference to the human genome is that Egyptian rousettes have an expanded repertoire of IFNW genes. To probe the biological implications of this expansion, we synthesized IFN-ω4 and IFN-ω9 proteins and tested their antiviral activity in Egyptian rousette cells. Both IFN-ω4 and IFN-ω9 showed antiviral activity against RNA viruses, including MARV, with IFN-ω9 being more efficient than IFN-ω4. Using RNA-Seq, we examined the transcriptional response induced by each protein. Although the sets of genes induced by the two IFNs were largely overlapping, IFN-ω9 induced a more rapid and intense response than did IFN-ω4. About 13% of genes induced by IFN-ω treatment are not found in the Interferome or other ISG databases, indicating that they may be uniquely IFN-responsive in this bat."
2020-03-16 | GSE145761 | GEO
Project description:Bats harbor high-impact zoonotic viruses in absence of clinical disease, which has been recently associated with unique features of their immune system. They seem to restrict inflammation and possibly limit disease manifestation to a minimum. In-depth characterization of cellular immunity in bats is yet largely missing, and imprinting of age and development on immune cell compartments remains unexplored. We employed single-cell transcriptomics and established immunostaining panels to investigate the immune cell populations peripheral blood for juvenile and adult Egyptian Rousette bats (ERB).
2022-07-21 | GSE183925 | GEO
Project description:NGS (enriched and shotgun) data for 2 individual Egyptian mummies from the 12th Dynasty. Mummies provided by Manchester Museum and originally collected from middle Egypt in 1907. The aim was to look at kinship relationships (maternal and paternal) between them.
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