Process of measuring the activity of thousands of genes simultaneously

Understanding cellular function

Identifying gene regulatory networks

Characterizing cell line differences

Diverse cell lines for comparison

Homogenous cell lines for baseline studies

Standardization of growth conditions

Control of environmental factors

Biological replicates for reliability

Technical replicates for precision

Timely collection of cells

Avoiding stress or changes in gene expression

Use of high-quality RNA extraction kits

Ensuring RNA integrity

Spectrophotometry

Agarose gel electrophoresis

Hybridization-based gene expression profiling

Use of gene-specific probes

RNA sequencing (RNA-seq)

Transcriptome-wide coverage

Quantification of spot intensities

Background subtraction

Conversion of raw sequencing data into reads

Quality control of sequencing reads

Correction for technical biases

Standardization of data across samples

Removal of low-quality data points

Exclusion of non-informative genes

Identification of genes with significant changes in expression

Use of statistical tests (e.g., t-test, ANOVA)

Grouping of genes based on expression patterns

Classification of cell lines based on gene expression

Functional categorization of differentially expressed genes

Identification of enriched pathways

Use of qPCR or Western blotting

Replication of findings in independent experiments

Identification of genes associated with disease states

Characterization of gene expression changes in response to drug treatment

Elucidation of gene expression changes in disease models

Handling large datasets

Data storage and analysis software

Accounting for inherent differences between cell lines

Minimizing errors from sample preparation and data acquisition

Compliance with regulations for cell line usage