Computational protocol: Classical dendritic cells are required for dietary antigen-mediated peripheral regulatory T cell and tolerance induction

Similar protocols

Protocol publication

[…] RNA from sorted cell pellets was extracted and column-purified using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems). Genomic DNA was removed by on-column digest with DNAse I (Qiagen), according to the PicoPure RNA Isolation kit manual. RNA libraries were prepared using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech Laboratories) and sequenced using 50 base pair paired end reading on a HiSeq 2500 instrument (Illumina). The reads were aligned using the STAR version 2.3.0 software that permits unique alignments to Mouse Ensembl genes. Differential expression was determined by use of the Cufflinks software with default settings. Heat maps were generated by comparing the expression profile CD11b+ and CD103+CD11b− DCs, or of OT-II cells cultured with CD11b+ and CD103+CD11b− DCs. Gene clusters were determined using Gene Set Enrichment Analysis (GSEA v2.2.2) software. PCA was performed using R software. […]

Pipeline specifications

Software tools STAR, Cufflinks, GSEA
Application RNA-seq analysis
Organisms Mus musculus
Diseases Carcinoma, Renal Cell, Adenomatous Polyposis Coli