Accession

PRJNA781853

Title

In-vitro response pattern of mesenteric lymph node (MLN) cells to specific gut commensal microbes

Relevance

ModelOrganism

Data types

Transcriptome or Gene expression

Sample scope

Multiisolate

Organism

Mus musculus [Taxonomy ID: 10090]

Description

Gut microbiota plays a significant role in shaping gut and systematic immune and huge strain- and species- dependent differences exit. Using in-vitro MLN co-culture models, we want to initially uncover these differences. MLN cells were isolated from C57BL/6 mice and co-cultured with bacterial cells with or without anti-CD3 and anti-CD28 antibodies for three days. After that, IL-10 in cell supernatant was measured and RNA was extracted using Trizol reagent. RNA-seq was performed on Illumina Hiseq X ten. Raw sequenced data were filtered by fastp and clean data were mapped to reference genome (Mus_musculus, GRCm39). Data processing adopted featurecounts in subread, abundance_estimates_to_matirx.pl in Trinity, DEseq and ClusterProfiler. We found that all bacterial species activated the innate immunity response. However, only Akkermansia muciniphila and Clostridium butyricum had cognate T cell antigen and activated adaptive immunity responses even without stimulus. Overall design: mRNA profiles of MLN cells isolated from C57BL/6 mice and colcultured with specifc gut microbes or stimulus in vitro for three days

Publication

PubMed ID	Article title	Journal name	DOI	Year
36356718

External link

Link description

Organization

Food Biotechnology, School of Food Science and Technology, Jiangnan University

Data Source

NCBI

Project Data

Resource name	Description
Experiment (11) show	-
SRX13171823	GSM5695744: L1HFA060349: MLN cells co-cultured with Clostridium butyricum rep1; Mus musculus; RNA-Seq
SRX13171821	GSM5695742: L1HEK190244: MLN cells co-cultured with Akkermansia muciniphila AH39 rep1; Mus musculus; RNA-Seq
SRX13171825	GSM5695746: L1HFA060351: MLN cells co-cultured with Clostridium butyricum rep3; Mus musculus; RNA-Seq
SRX13171826	GSM5695747: L1HFA060356: MLN cells co-cultured with Bifidobacterium bifidum and anti-CD3, anti-CD28 antibodies rep1; Mus musculus; RNA-Seq
SRX13171824	GSM5695745: L1HFA060350: MLN cells co-cultured with Clostridium butyricum rep2; Mus musculus; RNA-Seq
SRX13171828	GSM5695749: L1HFA060358: MLN cells co-cultured with Bifidobacterium bifidum and anti-CD3, anti-CD28 antibodies rep3; Mus musculus; RNA-Seq
SRX13171829	GSM5695750: L1HFA060359: MLN cells co-cultured with anti-CD3, anti-CD28 antibodies rep1; Mus musculus; RNA-Seq
SRX13171827	GSM5695748: L1HFA060357: MLN cells co-cultured with Bifidobacterium bifidum and anti-CD3, anti-CD28 antibodies rep2; Mus musculus; RNA-Seq
SRX13171831	GSM5695752: L1HFA060361: MLN cells co-cultured with anti-CD3, anti-CD28 antibodies rep3; Mus musculus; RNA-Seq
SRX13171830	GSM5695751: L1HFA060360: MLN cells co-cultured with anti-CD3, anti-CD28 antibodies rep2; Mus musculus; RNA-Seq
SRX13171822	GSM5695743: L1HEK190246: MLN cells co-cultured with Akkermansia muciniphila AH39 rep2; Mus musculus; RNA-Seq