READ ME File For 'Dataset supporting doctoral thesis "Investigating a Role for Activity-Regulated Cytoskeleton-Associated Protein in the Mast Cell Response to Hydrogen Peroxide and Rhinovirus Infection"' Dataset DOI: 10.5258/SOTON/D3524 ReadMe Author: Anna Willis, University of Southampton, ORCID ID https://orcid.org/0000-0002-4675-9536 This dataset supports the thesis entitled "Investigating a Role for Activity-Regulated Cytoskeleton-Associated Protein in the Mast Cell Response to Hydrogen Peroxide and Rhinovirus Infection" AWARDED BY: University of Southampton DATE OF AWARD: 2025 Date of data collection: 01/10/2020 - 01/08/2024 Information about geographic location of data collection: Brooke Laboratory, South Academic Block, Southampton General Hospital Licence: CC-BY Related projects/Funders: Funded by the MRC DTP Received a grant from the MRC DTP Flexible Supplement Fund Form (High Cost) This dataset contains: Chapter_3_Data.zip Chapter_4_Data.zip Chapter_5_Data.zip Zipped folders for chapters 3, 4 and 5, each containing subfolders with raw data for each figure, an Excel sheet showing processing of raw data for each figure (where applicable) and a Graphpad PRISM file showing data and statistical tests for each final figure (where applicable). Excel and PRISM files show experiment labels (e.g. Ex1A, Ex2B) that link to raw data Appendix_Data.zip Raw data (qPCR CFX file and western blot images), an Excel sheet showing processing of raw data for each figure and a Graphpad PRISM file showing data and statistical tests. Methodological and further information for Chapters 3-5 and Appendix data - RT-qPCR data was collected in .pcrd files which were opened and analysed with the BioRad CFX manager software, where thresholds were set and Ct values were taken and processed in the provided Excel spreadsheets. - Unedited western blot images are provided. Image J software was used to calculate density of bands, where the 'mean gray value' of bands were taken and processed in the provided Excel spreadsheets. - Unedited agarose gel electrophoresis images and fluorescent/light microscope images are also provided. Chapter_6_7_Data.zip (Aug 2024) The "Counts" folder contains raw count data and counts per million (CPM) from RNA-Sequencing data in csv files, separated into HeLa cell and mast cell data. "Chapter 6 Figures and DEGs" and "Chapter 7 Figures and DEGs" each contain .jpg or .svg files for figures included in the thesis, as well as .csv files of differentially expressed genes (DEGs) for each comparison which were used for downstream analysis. Methodological information: 12 conditions, 5 replicated of each: WT LAD2 mast cells (M), GFP-overexpressing HeLa cells (G) and ARC-overexpressing HeLa cells (A) were either: Treated with H2O2 (2 mM, 1h) then recovered for 3h or 9h (mast cells or HeLa cells respectively). Media control (C) or H2O2 treatment (HT) Infected with RV16 (MOI 1) for 1h while rocking, washed, then incubated for a further 24h. UV-irradiated control (UV) or RV16 (RV) Total RNA was collected from these cells, which was sent to NovoGene for RNA-sequencing. Library preparation (polyA enrichment, mRNA fragmentation, reverse transcription), sequencing (Illumina Novaseq 6000, paired-end 150-nucleotide read length (PE150), read depth of 20 million), pseudoalignment of resultant FASTQ raw reads to the human GRCh38 transcriptome using kallisto. Raw counts data from two publicly available RNA-sequencing datasets were used Murphy, et al. 2022: GSE206680 found at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206680 Tao, et al. 2022: GSE193164 founnd at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193164