Dataset in support of the University of Southampton Doctoral thesis 'Role of IL-33 on human mast cell responses to rhinovirus infection in asthma'

Abstract

This dataset contains: MC RNASeq Count files • Individual Count files for each sample, used for producing data for Chapter 5 of my thesis. • 42 samples. • 6 conditions = Control, UVRV Control (MOI 5), RV (MOI 5), Control + IL33 (10ng/ml), UVRV (MOI 5) + IL33 (10ng/ml), RV (MOI 5) + IL33 (10ng/ml), all at 6 hours. 7 replicates. 2 batches, n=1-3 and n=4-7, from 2 defrosted batches of LAD2 MCs. Counts were aligned to GRCh38.99 human reference genome. • 'Counts_table_collated.txt' is a table of all of the individual count files put into one table. • 'Counts_table_applied_batch_effect_combat_log2cpm.txt' is the collated table, where log2 was applied to counts and batch effect was accounted for using the combat package. This was the counts table used for all further bioinformatics analysis. Thesis Chapter 6 Validation Figures Files • 'Chapter_6_Results_PRISM_Graphs.pzfx' - All the figures for Chapter 6 with statistics. Thesis Chapter 5 RNASeq Analysis Figures Files • Images, PRISM files, and Excel data that corresponds to the figures used for Chapter 5. • 'Counts Input for Heatmaps' contains tables used for inputting data into Morpheus to create the heatmaps. • 'Counts_table_applied_batch_effect_combat_log2pcm.txt' is the Counts table used for all analysis. This is the collated counts in one table, applied log2, and corrected for batch effect using Combat. • 'Counts_table_collated.txt' is the collated counts in one table, without any corrections. CSVs of differentially expressed genes identified per comparison in Chapter 5 Results • Differentially expressed genes (DEGs) were defined as genes that had a fold change of over 1.5 and a FDR-adjusted p value of less than 0.05. • 'FC1.5_C.IL33vC.csv' contains list of 2,001 DEGs when comparing Control v Control+IL33 • 'FC1.5_RVvUV.csv' contains list of 135 DEGs when comparing UVRV v RV • 'FC1.5_UV.IL33vUV.csv' contains list of 1938 DEGs when comparing UVRV v UVRV+IL33 • 'FC1.5_RV.IL33vUV.csv' contains list of 2564 DEGs when comparing UVRV v RV+IL33 • 'FC1.5_UVvC.csv' contains list of 0 DEGs when comparing Control v UVRV Thesis Chapter 4 Optimisation Results Figures Files • 'Figures for Chapter 4.pzfx' is the GraphPad PRISM file containing all figures produced for Chapter 4. Please note that figure numbers in this file does not correspond directly to Thesis figure numbers. Please see 'Information accompanying Figures for Chapter 4.docx' • 'Accompanying statistics for Chapter 4 figures.pzfx' is the GraphPad PRISM file that contains all the statistics calculations for all the figures from 'Figures for Chapter 4.pzfx'. Please note that figure numbers in this file does not correspond directly to Thesis figure numbers. Please see 'Information accompanying Figures for Chapter 4.docx' • 'Information accompanying Figures for Chapter 4.docx' is a table that details which figure number in the Thesis corresponds to the Figures and Statistics produced in the above PRISM files. Thesis Chapter 3 BMMCs Analysis Figures Files • 'Figures for Chapter 3 - 3-1 to 3-13.pptx' is a powerpoint of figures used in this chapter. • 'Figures 3-4, A-B Tables - workbook for clustvis.xlsx' - contains data for Figures 3-4, alongside data input to create the heatmaps in clustvis for this chapter. • 'DEG_WT.IgE.csv' - is the list of 772 differentially expressed genes when comparing WT unstimulated vs WT IgE/Ag. • 'DEG_ST2KO.WT.csv' - is the list of 2 differentially expressed genes when comparing WT unstimulated vs ST2KO unstimulated. • 'DEG_ST2KO.WT.IgE.csv' - is the list of 2 differentially expressed genes when comparing WT IgE/Ag vs ST2KO IgE/Ag. • 'DEG_ST2KO.IgE.csv' - is the list of 782 differentially expressed genes when comparing ST2KO unstimulated vs ST2KO IgE/Ag. • 'DEG_WT.IL33.csv' - is the list of 781 differentially expressed genes when comparing WT unstimulated vs WT IL33. • 'DEG_ST2KO.IL33.csv' - is the list of 0 differentially expressed genes when comparing ST2KO unstimulated vs ST2KO IL33.

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