biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsKim Dong Keontranscription profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15599Gene expression profiles of SW480 and SW620 cells were used for differential expression analysis. DEGs between SW480 and SW620 cells were analyzed using an integrated statistical frameworkbiostudies-arrayexpressScaning - After hybridization and staining, HumanHT-12 v4 BeadChips were scanned using the Illumina BeadStation 500X platform according to the manufacturer’s instructions. The scanner was operated with default PMT (photomultiplier tube) settings, and high-resolution images were collected for each array.Raw intensity data were extracted from scanned images using Illumina GenomeStudio software (version 2011.1). Data were subjected to background correction and initial quality control according to Illumina’s default settings. Detection p-values were generated for each probe, and data were exported as normalized signal intensity files for downstream analysis.Labeling - For Illumina HumanHT-12 v4 Expression BeadChip analysis, 500 ng of high-quality total RNA was amplified and biotin-labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions. The cRNA was purified and quantified prior to hybridization.Sample Collection - Cells were seeded in six-well plates and allowed to adhere overnight. At 70–80% confluence, cells were harvested directly for RNA extraction without drug treatment. Cell pellets were washed twice with cold PBS, collected by centrifugation, snap-frozen in liquid nitrogen, and stored at –80 °C until RNA isolation.Nucleic Acid Extraction - Total RNA was extracted using TRIzol according to the manufacturer’s instructions. RNA quality and integrity were assessed by Agilent 2100 Bioanalyzer, and samples with RNA integrity number (RIN) ≥ 8.0 were used for downstream processing.Hybridization - Labeled cRNA (750 ng) was hybridized to HumanHT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA) at 58 °C for 16–18 hours in a hybridization oven. After hybridization, BeadChips were washed, blocked, and stained with streptavidin-Cy3 according to Illumina’s standard protocol. Arrays were scanned using the Illumina BeadStation 500X system, and raw intensity data were extracted using GenomeStudio v2011.1 software (Illumina).Growth Protocol - W480 and SW620 colon cancer cell lines were cultured in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin at 37°C in a humidified atmosphere with 5% CO2.MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsKim Dong KeonfalseMicroarray of human colon cancer cell line SW480 and SW620Gene expression profiles of SW480 and SW620 cells were used for differential expression analysis. DEGs between SW480 and SW620 cells were analyzed using an integrated statistical framework2026-09-10T00:00:00Z2026-09-10T01:02:13.522Z2025-09-17T22:05:11.686ZE-MTAB-15599EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0003789EFO_0005518EFO_0003815