ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/006/SRR13360906/SRR13360906.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/013/SRR13360913/SRR13360913.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/005/SRR13360905/SRR13360905.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/015/SRR13360915/SRR13360915.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/008/SRR13360908/SRR13360908.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/014/SRR13360914/SRR13360914.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/010/SRR13360910/SRR13360910.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/007/SRR13360907/SRR13360907.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/009/SRR13360909/SRR13360909.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/011/SRR13360911/SRR13360911.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR133/012/SRR13360912/SRR13360912.fastq.gzprimaryOK200GenomicsExperimental Immunology, Molecular Infection Biology, Helmholtz Centre for Infection Researchhttps://www.ebi.ac.uk/ena/browser/view/PRJNA689792Mus musculuscDCs home from the periphery into the thymus. In order to determine the phenotypic and functional changes introduced by the thymic microenvironment to these thymus-homing cDCs, RNA-based next generation sequencing (RNAseq) was performed with splenic (sp-DC) and thymic conventional DCs (t-DCs) re-isolated from RTOCs after two days of culture. Methods: RTOCs were generated from single-cell suspensions of thymi isolated from E14.5 to E16.5 fetuses of Foxp3hCD2 reporter mice (BALB/c background), and sp‑DCs or t‑DCs sorted from 4-8 weeks old female CD45.1xBALB/c mice were introduced. After two days of culture, 1‑2x103 cDCs were re-isolated from RTOCs as CD45.1+Lin-CD11chi by FACS, and total RNA for transcriptional profiling by low-input RNAseq was isolated. Total RNA from sp-DC and t-DCs isolated ex vivo from 4-8 weeks old female CD45.1xBALB/c mice was used as control. RNAseq was performed on an Illumina HiSeq2500 system. Differential gene expression between the four different conditions was computed from the read counts. Results: The number of differentially expressed genes between ex vivo isolated sp-DC and t-DC was drastically reduced comparing sp-DCs and t-DCs re-isolated from RTOCs. This finding implies that the thymic microenvironment within an RTOC modulates the gene expression in sp‑DCs, conferring a transcriptomic profile that more closely resembled the one from t‑DCs. Conclusion: The thymic microenvironment modulates the transcriptome of thymus-homing peripheral cDCs. Overall design: RNAseq of sp-DC and t-DCs re-isolated from RTOCs two days after introduction, comparison to ex vivo isolated sp-DC and t-DCxref:PubMed:34748687ENAfalseTranscriptome analysis of conventional dendritic cells (cDCs) introduced into the thymic microenvironment of re-aggregated thymic organ cultures (RTOCs)Transcriptome analysis of conventional dendritic cells (cDCs) introduced into the thymic microenvironment of re-aggregated thymic organ cultures (RTOCs)2025-09-242021-03-02PRJNA689792GSE1642801009034748687