Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1306349 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Bispecific T-cell engager (BiTE)-based cancer therapies that activate the cytotoxic T cells of a patient’s own immune system have gained momentum with the recent FDA approval of Blinatumomab for treating B cell malignancies. However, this approach has had limited success in targeting solid tumors. We have reported the development of BiTE-sialidase fusion proteins that enhance tumor cell susceptibility to BiTE-mediated cytolysis by T cells via targeted desialylation at the BiTE-induced T cell-tumor cell interface. Targeted desialylation results in better immunological synapse formation, T-cell activation and effector function. As a result, BiTE-sialidase fusion proteins show remarkably increased efficacy in inducing T-cell-dependent tumor cell cytolysis in response to target antigens compared to the parent BiTE molecules alone. This enhanced function is seen both in vitro and in in vivo xenograft and syngeneic solid tumor mouse models. Our findings highlight BiTE-sialidase fusion proteins as promising candidates for the development of next-generation bispecific T-cell engaging molecules for cancer immunotherapy. This transcriptomic dataset documents the effect of BiTE-sialidase vs uncojugated BiTE on T cells including the upregulation of effector associated genes.
2024-06-05 | GSE245991 | GEO
Project description:Proteomic data from moose fistulated rumen; metagenomic and viral sequencing performed; metabolic pathways reconstructed
2018-07-03 | PXD008667 | Pride
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:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
2016-08-22 | PXD003791 | Pride
Project description:We applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the change of mouse gut microbiota composition and function.
2019-11-09 | GSE140149 | GEO
Project description:Purpose: To analyze the expression of two different CD19 isoforms during BiTE treatment, and to further determine cell lineage specific molecules before and after BiTE treatment Methods: For transcriptome sequencing, we isolated patient's bone marrow samples, quality of total RNA was evaluated by Agilent 2100. RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB,USA). RNA sequencing process and the data acquisition were finished on Novogene Experimental Department according to the manufacturer’s protocol. Reads were aligned to hg38 reference genome. Relative abundance of CD19 and other gene transcripts were mapped and estimated at both gene and transcript level (FPKM) by feature Counts. Results: The expression of CD19 isoform with exon 2 deletion was found at diagnosis before BiTE therapy. The patient did not achieve remission after BiTE treatment, and the expression of CD19 antigen turned negative by flow cytometry detection. But the expression ratio of exon 2 deleted CD19 was not increased, and the flow cytometry phenotype and transcriptome sequencing confirmed that no linage switching occurred, which suggested the expression of CD19 isoform caused by exon alternative splicing and lineage switching was not the driving mechanism of CD19 epitope loss in this patient. Immune escape could not be prevented by targeting alternative exons. This patient achieved complete remission by sequential infusions of our own developed CD22 CAR-T and CD19 CAR-T after disease progression Conclusions: transcriptome sequencing confirmed that no linage switching occurred in this patient, which suggested the expression of CD19 isoform caused by exon alternative splicing and lineage switching was not the driving mechanism of CD19 epitope loss in this patient.
2022-11-01 | GSE140279 | GEO