Regulatory T cells from colonic lamina propria [RNA-Seq]

The colonic lamina propria contains a distinct population of Foxp3+ T regulatory cells (Tregs) that modulate responses to commensal microbes. Analysis of gene expression revealed that the transcriptome of colonic Tregs is distinct from splenic and other tissue Tregs. Rorgamma and Helios in colonic Tregs mark distinct populations: Rorgamma+ Helios- or Rorgamma-Helios+ Tregs. We uncovered an unanticipated role for Rorgamma, a transcription factor generally considered to be antagonistic to Foxp3. Rorgamma in colonic Tregs accounts for a small but specific part of the colon-specific Treg signature. Nrp1- Tregs were sorted from Foxp3-cre.Rorcfl/fl mice, which have a Treg-selective deletion of Rorc, or paired WT littermates. For low-input RNAseq, 1,000 TCRb+CD4+YFP(Foxp3)+Nrp1- cells were double-sorted into Trizol, RNA extracted and reverse-transcribed using ArrayScript (Ambion). To reduce variability at least three replicates were generated.