DOI: 10.5061/dryad.crjdfn35n
title: Data from: Gastrointestinal gd T cells reveal upregulated T-cell transcripts and signaling pathways during peanut oral immunotherapy

description: Oral immunotherapy (OIT) has been successful in desensitizing patients to
 offending food allergens, although identification of tissue-resident T
 cell subsets and cognate pathways leading to desensitization has been
 challenging. The T cells are a major T-cell subset of mucosal
 intraepithelial lymphocytes (IELs) and play a significant role in tissue
 homeostasis and repair. Studies in mouse models suggested a regulatory
 role of gd T cells in food allergy (FA). Also, peripheral gd T cells from
 patients analyzed over 24 weeks of peanut OIT were shown to undergo
 dynamic changes in expression profiles, implicating pathways involved in
 immune homeostasis. To our knowledge, the role of gd T cells in the
 intestinal mucosa of FA patients during immunotherapy has not been
 examined.  To this end, we investigated whether gd T cells in the
 gastrointestinal (GI) tract are modulated during peanut OIT. We
 hypothesized that GI-resident gd T cells in FA patients would increase
 during the course of peanut OIT and reveal transcripts and pathways
 relevant to the mechanisms of peanut desensitization.
description: # Gastrointestinal gd T cells reveal upregulated T-cell transcripts and
 signaling pathways during peanut oral immunotherapy
 [https://doi.org/10.5061/dryad.crjdfn35n](https://doi.org/10.5061/dryad.crjdfn35n) ## Description of the data and file structure Supplementary File 1 : Differentially expressed genes predicted in sorted gdT cells RNAseq dataset. Each sheet includes DE genes predicted by comparing RNAseq dataset from two timepoints. Supplementary File 2 : Pathways enriched from differentially expressed genes in gdT cells RNAseq dataset, using pathfindR. Supplementary File 3 : Differentially expressed genes predicted in Bulk RNAseq dataset. Each sheet includes DE genes predicted by comparing RNAseq dataset from two timepoints. Supplementary Figure S1: (A) KEGG hsa04330 Notch signaling pathway, (B) KEGG hsa04540 Gap junction pathway, (C) KEGG hsa04662 B cell receptor signaling pathway, (D) KEGG hsa04350 TGF-b pathway. Transcripts identified to be differentially expressed in sorted gd T cells at baseline compared to week 104 featuring per pathway are highlighted. (green = downregulated at week 104 and red = upregulated transcripts at week104). Supplementary Figure S2: (A) Volcano plots representing DE transcripts among bulk biopsy-derived RNA-Seq dataset from autologous samples (n=6) at indicated time points. Red = significant DE transcripts with absolute log2(Fold Change) &gt; 1, and q&lt; 0.3; Blue = transcripts with absolute log2(Fold Change) &lt; 1, but FDR-adjusted P-value &lt;0.3; Grey = transcripts with no significant change in expression. (B) Heatmap depicting 33 DE transcripts across indicated time-points in RNA-Seq from bulk biopsy-derived RNA in autologous samples (clustering method = linkage) The supplementary dataset contains four files: 1. Supplementary_File1.xlsx: This file contains differential gene expression profile in gd T cells, for the comparison all three comparisons- [Sheet 1] : baseline versus Week-52; [Sheet 2] Baseline versus Week-104; [Sheet 3] Week-52 versus Week-104. Headers are described below. 2. Supplementary_File2.xlsx: This file contains list of KEGG pathways significantly enriched from deferentially expressed transcripts from each comparison- [Sheet 1] : baseline versus Week-52; [Sheet 2] Baseline versus Week-104; [Sheet 3] Week-52 versus Week-104. Headers are described below. 3. Supplementary_File3.xlsx: his file contains differential gene expression profile in bulk cell population, for the comparison all three comparisons- [Sheet 1] : baseline versus Week-52; [Sheet 2] Baseline versus Week-104; [Sheet 3] Week-52 versus Week-104. Headers are described below. 4. Supplementary_Figures.pdf: Supplementary figures referred in the main manuscript. This file contains two supplementary figures S1 & S2. Figure legends are described at the bottom of figures. \================================ Variable or Column header description: \================================ 1. **Transcript**: NCBI Gene ID of transcript for which differential expression was enumerated. 2. **log2FC**: Fold Change observed for a transcript in a given comparison. 3. **Df**: Statistical degree of freedom 4. **AIC**: Akaike information criterion (AIC) is an estimator of prediction error and relative quality of statistical models 5. **LRT**: Likelihood-Ratio Test 6. **LRT_pvalue**: P-value significance of Likelihood-Ratio Test 7. **FDR_Padj**: FDR adjusted P-value 8. **KEGGID**: KEGG pathway ID 9. **pathway**: Name of KEGG pathway 10. **FoldEnrichment**: Enrichment score for a given pathway enriched. 11. **Group**: Groups that were compared for pathway enrichment analysis. 12. **lowest.p.value**: Lowest P-value observed for a given KEGG pathway.