Comment[GEAAccession]	E-GEAD-901
MAGE-TAB Version	1.1
Investigation Title	Epigenetic reprogramming of moDCs by Bifidobacterium priming.
Experiment Description	The gut commensal microbiota play a crucial role in regulating systemic innate immunity, contributing to infection defense and homeostasis maintenance. However, the specific members of the intestinal microbiota that play critical roles remain unclear. Here, we demonstrate that gut commensal bifidobacteria have the potential to induce innate immune tolerance in monocyte-derived dendritic cells (moDCs) of healthy adults. We found that the abundance of gut-resident Bifidobacterium was negatively correlated with the inflammatory responses of moDCs to four different bacterial species. Furthermore, we showed that priming of monocytes by Bifidobacterium induced transcriptome and epigenetic reprogramming, thereby suppressing inflammatory responses upon secondary bacterial stimulation. These findings provide insights into how gut commensal bifidobacteria contribute to immune homeostasis through the induction of innate immune tolerance, and highlight potential therapeutic strategies for managing excessive inflammation. Raw files for human/patient samples were not submitted to GEA due to concerns about submitting personally identifiable sequence data for open access.
Experimental Design	case control design	replicate design
Experimental Factor Name	priming
Experimental Factor Type	priming
Person Last Name	Kaneko	Odamaki	Ishihara	Nishimura
Person First Name	Hiroki	Toshitaka	Sayaka	Tatsuki
Person Affiliation	Innovative Research Institute, Morinaga Milk Industry Co Ltd			
Person Roles	submitter	submitter	submitter	submitter
Public Release Date	2026-05-19
Protocol Name	P-GEAD-3520	P-GEAD-3521	P-GEAD-3522	P-GEAD-3523	P-GEAD-3524	P-GEAD-3525
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	Monocytes were primed with B. longum-, B. pseudocatenulatum- bacterial lysate supernatant or were kept in RPMI as the contro (n=2 or 3). Following 24 hours incubation, cells were washed twice and further differentiated into moDCs for an additional 6 days.cells were collected on day 6.	RNA-seq was performed by Takarabio. Total RNA was extracted from cells via NucleoSpin RNA XS (Macherey-Nagel) according to the manufacturer's instructions. The RNA purity, concentration, and integrity were evaluated with an Agilent TapeStation or BioAnalyzer (Agilent Technologies).	nucleic acid library construction protocol: RNA libraries were prepared using a SMART-Seq mRNA LP kit (takarabio) and Nextera XT DNA Library Prep Kit (Illumina).	nucleic acid sequencing protocol: The indexed libraries were subjected to sequencing on an Illumina NovaSeq X Plus (2 x 150 bp).	dummy	processed data files format and content: RNA-seq_data_raw counts contain geneID, Gene name, counts for each sample. genome build: GRCh38 (GENCODE, relese 39). software information: NovaSeq X Plus Control Software v1.2.0, bcl2fastq2 v2.20, DRAGEN Bio-IT Platform v4.3.6.
SDRF File	E-GEAD-901.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-11
Comment[AEExperimentType]	microRNA profiling by array
Comment[BioProject]	PRJDB19955
Comment[Last Update Date]	2026-05-19