Ontology highlight
ABSTRACT:
PROVIDER: PRJNA578354 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metagenomic sequencing of mice with different treatments: Mice were randomly divided into donor control group (Donor + MRS), constipation model group (STC + MRS), or a Lactobacillus acidophilus treated group (STC + La): A humanized mouse model was established by intragastric administration of fecal bacterial liquid from healthy donors or STC patients on alternate days, followed by continuous administration of Lactobacillus acidophilus in treatment group. Finally, the feces of each group of mice were collected, and the intestinal microbial communities of the mice were analyzed through metagenomic sequencing. 16S rRNA sequencing of mice before and after the use antibiotics: Before and after treating the mice with antibiotics, the mice's feces were collected for 16s rRNA sequencing respectively.
2026-03-11 | E-MTAB-16505 | biostudies-arrayexpress
Project description:Interventions: Case (colorectal cancer) group:a newly diagnosed colorectal cancer( CRC ) by colonoscopy and pathology;Control group:Clinically healthy volunteers with no symptoms or history of intestinal disease(e.g. colonic adenomatous polyps, CRC or inflammatory bowel disease)
Primary outcome(s): composition of gut microbiota;intestinal microbial phytase activity;16s rRNA metagenomic sequencing;diet surveys;phytic acid intake
Study Design: Case-Control study
| 2667847 | ecrin-mdr-crc
Project description:Combining single-cell and spatial transcriptomics for mapping different intestinal segments is still relatively absented, and the subtypes of intestinal stromal cells and their downstream signling also remain obscure. Our study provides a comprehensive view of 18 identified cell types across five mouse intestinal segments using single-cell RNA sequencing (scRNA-seq). Integrating scRNA-seq with spatial transcriptomics reveals gene profiles along both segmental and crypt-villus spatial dimensions, including cell characteristics, interactions, signaling networks, extracellular matrix contributions, and functional coordination. Not only the different subtypes of intestinal immune cells were analyzed, but also a subtype of Pdgfra-high stromal cells, Gnai1+ stromal cells, was identified. These cells can support intestinal morphology and regulate the activities of goblet cells, Paneth cells, and intestinal stem cells via the activation of c-Jun and Wnt signaling. Thus, we have compiled a publicly available single-cell and spatial transcriptomics resource covering five intestinal segments to facilitate further research, particularly on stromal cell populations and intestinal microenvironment homeostasis.
2025-09-27 | GSE278251 | GEO
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:In this data set we aimed to interrogate the milestones of human functional gut development from 13-20 weeks post gestation for proximal intestinal segments and 15-35 weeks gestation for distal intestinal segments
2023-11-24 | GSE247523 | GEO
Project description:The early interaction of Salmonella enterica serovar typhimurium DT104 with intact small intestinal mucosa was studied in a Small Intestinal Segment Perfusion (SISP) model. Intestinal segments were infected with or without Salmonella. Scrapings from jejunal segments were collected after perfusion for 0, 2, 4, or 8 hours. Details of the SISP experiment are described in: Niewold TA, Veldhuizen EJ, van der Meulen J, Haagsman HP, de Wit AA, Smits MA, Tersteeg MH, Hulst MM. Using the Operon 13K pig oligonucleotide array differences in host gene expression were recorded between infected and uninfected segments within a single pig (isogenic comparisons), and between identical treated segments collected from 3 individual SISP pigs, all responding markedly different to infection with Salmonella (inter-animal comparisons).
2013-04-17 | GSE41630 | GEO
Project description:Primary outcome(s): Metagenomic analysis and Metabolome analysis of Intestinal flora before, 2weeks, 1months, 3months, 6months, 12months
| 2636430 | ecrin-mdr-crc