Dictionary

Fundamental Concepts

Term	Definition
Genomics	The study of genomes, focusing on the structure, function, evolution, and mapping of all genetic material within an organism.
Sequencing	Determining the precise order of nucleotides in a DNA or RNA sequence is crucial for understanding genetic variation.
Multiplexing	Sequencing multiple genetic material samples simultaneously, each labelled for efficient post-sequencing analysis.
Genomics Multiplexing	Applying multiplexing techniques to genomics to enhance the efficiency of sequencing multiple samples together.
Genomics Demultiplexing	Separating and identifying individual samples after a multiplexed sequencing run for independent analysis.

Molecular Biology

Term	Definition
DNA, RNA, mRNA	DNA is the genetic blueprint; RNA translates DNA messages; mRNA carries specific gene information from DNA for protein synthesis.
Unique Molecular Identifier (UMI)	Short sequences added to each DNA molecule before amplification to precisely quantify original molecules and correct sequencing errors.
Proteins	Complex molecules made of amino acids, essential for performing vital cellular functions.
Primer Index	A unique sequence of DNA added to a sample before sequencing, allowing for the identification and differentiation of samples in a multiplexed experiment.

Laboratory Techniques & Tools

Term	Definition
CEL-Seq2	A method for single-cell RNA sequencing that precisely measures gene expression in individual cells.
FACS (Fluorescence-Activated Cell Sorting)	A specialised flow cytometry technique for sorting cells based on their fluorescence characteristics.
Well	A single compartment or space in a well-plate used to hold samples for experiments.
Well-plate	A plate with multiple "wells" used in labs to hold samples for various experiments, available in configurations like 96 or 384 wells.
Well barcode	A unique code for each well in a well plate, allowing for the tracking of specific samples or reactions.
Plate barcode	A unique identifier for an entire plate, facilitating the management of all contained samples.
Minibulk	A method where hundreds of cells, instead of just one, are loaded into a well to increase efficiency and reduce costs.

Data Analysis & Software

Term	Definition
FCS file	A file format for storing flow cytometry data, encompassing information from such experiments.
FlowJo	A software application used to analyse flow cytometry data, aiding in managing and interpreting complex datasets.
ScPipe	A software package for processing single-cell RNA sequencing data, focusing on demultiplexing, mapping, and quality control.
Shiny	A web application framework for R, used to build interactive web applications for data analysis and visualisation directly from R.
FCSparser	A Python package used for reading and converting FCS files into CSV format, facilitating flow cytometry data analysis.
Channel Values	The measured fluorescence intensity values for each cell or particle in a flow cytometry experiment are used to identify and quantify specific properties of the sample.
Scatter Channel	A channel in flow cytometry that measures light scattering properties of cells or particles, indicating size and internal complexity.
Fluoro Channel	A channel in flow cytometry used to detect fluorescence emitted by cells or particles, often used to determine the presence of specific markers or proteins.
FlowKit	A software library for analyzing flow cytometry data, offering functionalities for data transformation and visualization, similar to FlowJo but designed for use in programming environments.
Linear Transformation	A mathematical operation applied in data analysis to scale data linearly, often used in normalizing flow cytometry measurements for comparability.
Logical Transformation	A data transformation technique that applies logical operations to modify or categorize data based on specific criteria, commonly used in flow cytometry data analysis to differentiate cell populations.