Best ChatGPT prompts for Medical Scientists, Except Epidemiologists

Given a specific disease-associated gene variant, design a CRISPR-Cas9 gene editing protocol to correct the mutation, including the selection of appropriate guide RNAs, donor templates, and sequencing primers. Assume a human embryonic kidney cell line as the target cells and consider the potential off-target effects. Provide a detailed experimental workflow, including the preparation of reagents, cell culture conditions, and sequencing analysis parameters.

Develop a bioinformatics pipeline to analyze a dataset of paired-end RNA-seq reads from a tumor sample, including quality control, adapter trimming, mapping to a reference genome, and differential gene expression analysis. Assume a minimum of 10 million reads per sample and consider the impact of sequencing depth on detection of low-abundance transcripts. Provide a detailed list of required software tools, parameters, and output files.

Design an experiment to optimize the cell culture conditions for differentiating human induced pluripotent stem cells into functional neurons, including the evaluation of various growth factors, small molecules, and culture media compositions. Assume a 96-well plate format and consider the impact of cell density, seeding efficiency, and culture duration on differentiation efficiency. Provide a detailed experimental plan, including the preparation of reagents, cell seeding protocols, and immunocytochemistry staining procedures.

Given a failed protein purification experiment, troubleshoot the potential causes of the failure, including issues with protein expression, cell lysis, chromatography conditions, and buffer composition. Assume a recombinant protein expressed in E. coli and consider the impact of protein aggregation, proteolytic degradation, and contamination on purification efficiency. Provide a detailed list of potential causes, recommended troubleshooting steps, and optimized protocols for protein purification.