Project description:To determine the activation patterns of ILC2s and associated ILC2-intrinsic functional molecules triggered by the high fiber diet, we administered either a control or high fiber diet in WT mice and performed RNA sequencing of FACS-sorted ILC2s from mouse colons. RNAseq libraries were prepared from 1,000 sorted colonic lamina propria ILC2s (CD45+Lin-CD90.2+CD127+KLRG1+) by the Epigenomics Core at WCM using the Clontech SMARTer® Ultra® Low Input RNA Kit V4 (Clontech Laboratories). Libraries were sequenced on an Illumina HiSeq 2500, generating 50 bp single-end reads. Two samples from two control diet-fed WT SPF mice and two samples from two high fiber diet-fed WT SPF mice were used.
Project description:To investigate the comprehensive mRNA expression profile of ILC2s from IPF patients, we performed bulk RNA-sequencing analysis of ILC2s sorted from IPF patients and healthy controls.
Project description:To investigate the transcriptional regulation of Xbp1s in ILC2s, sorted large intestinal ILC2s from mice were used for CUT&Tag sequencing to analyze the target of Xbp1s.
Project description:RNA sequencing was performed for the toyocamycin- or vehicle-treated ILC2s sorted from the large intestine of C57BL/6 mice (n = 3 per group).
Project description:To investigate the effect of NAD+ metabolism on ILC2s function, sorted ILC2s from the gut were treated with NAMPT inhibitor FK866 for bulk RNA sequcecing.
Project description:Transcriptomes of ILC2s sorted as KLRG1+CD127+CD90+Lin-CD45+ cells from mesenteric lymph nodes of non-treated mice were analyzed. The mice were part of the experiments described in PMID: 29496881 and were sequenced together with samples submitted in GSE108884.
Project description: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. Rorγ and Helios in colonic Tregs mark distinct populations: Rorγ+Helios- or Rorγ-Helios+ Tregs. We uncovered an unanticipated role for Rorγ, a transcription factor generally considered to be antagonistic to Foxp3. Rorγ 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.
Project description: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. Rorγ and Helios in colonic Tregs mark distinct populations: Rorγ+Helios- or Rorγ-Helios+ Tregs. We uncovered an unanticipated role for Rorγ, a transcription factor generally considered to be antagonistic to Foxp3. Rorγ in colonic Tregs accounts for a small but specific part of the colon-specific Treg signature. (1) Total colonic and splenic Foxp3+ Treg comparison: Lymphocytes were isolated from colonic lamina propria and spleens of Foxp3-ires-GFP mice, where GFP reports Foxp3 expression. TCRb+CD4+GFP+ cells were double sorted into Trizol. (2) Colonic Rorγ+ and Rorγ- Treg comparison: Foxp3-ires-Thy1.1 reporter mice were crossed to Rorc-GFP reporter mice to generate mice that report both Foxp3 and Rorγ expression. Rorγ+Foxp3+ Tregs (TCRb+CD4+Thy1.1+GFP+) and Rorγ-Foxp3+ Tregs (TCRb+CD4+Thy1.1+GFP-) from colonic lamina propria were double sorted into Trizol.To reduce variability and increase cell number, cells from multiple mice were pooled for sorting and at least three replicates were generated for all groups. RNA from 1.5-3.0 x104 cells was amplified, labeled and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays.