Data and code for Junction-Specific Cryptic Exon RT-qPCR

This dataset, including raw experimental data, uncropped Western blot images, and accompanying analysis code, supports the findings of the manuscript "Junction-Specific Cryptic Exon RT-qPCR Quantifies Sub-percent Nuclear TDP-43 Loss in Cells and ALS Cortex" by Koide et al. The study focuses on the development and validation of an ultrasensitive RT-qPCR assay for quantifying cryptic exon (CE) splicing, a molecular hallmark of TDP-43 dysfunction in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The novel assay employs a junction-specific primer design targeting STMN2 CE, which significantly enhances sensitivity and dynamic range compared to conventional methods by eliminating pre-mRNA co-amplification. This repository contains: Raw_Ct_value.xlsx: An Excel file containing the raw cycle threshold (Ct) values from all RT-qPCR experiments performed in cultured cells (SH-SY5Y, HEK293T) and post-mortem human ALS motor cortex and control tissues. This sheet serves as the primary source for qPCR quantification. Raw data CSV files (within a Rawdata): CSV files derived from Raw_Ct_value.xlsx or other primary sources, formatted for direct input into the R analysis script. These files contain data used to quantify the expression of STMN2 CE, other TDP-43 responsive CEs, alternative splicing events, and reference genes, and form the basis for generating figures and tables. Uncropped Western Blot Images: Original, uncropped images for all Western blots presented in the manuscript (e.g., Figure 3B). These images provide the full context for the presented cropped blots, ensuring transparency in data presentation. R Markdown file (.Rmd): The R Markdown script used for all statistical analyses, data processing, and figure generation presented in the manuscript. This code allows for the full reproduction of the analyses and figures from the provided CSV data files. PDF report generated from the R Markdown file (.pdf): This document ("Raw Data and Analysis Code for: Junction-Specific Cryptic Exon RT-qPCR Quantifies Sub-percent Nuclear TDP-43 Loss in Cells and ALS Cortex.pdf") details the R code, package versions used, and sequentially shows the code execution and resulting figures and statistical outputs, corresponding to each figure in the main manuscript. The aim of sharing this comprehensive dataset and code is to ensure full transparency and reproducibility of our research findings, and to enable further investigation and utilization by the scientific community. Keywords: TDP-43, Cryptic Exon, STMN2, RT-qPCR, Western Blot, Amyotrophic Lateral Sclerosis, ALS, Frontotemporal Dementia, FTD, Biomarker, Neurodegeneration, Raw Data, R code, Reproducibility.