Data from: Gastrointestinal gd T cells reveal upregulated T-cell transcripts and signaling pathways during peanut oral immunotherapy

# 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) > 1, and q< 0.3; Blue = transcripts with absolute log2(Fold Change) < 1, but FDR-adjusted P-value <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.