biostudies-arrayexpressRGCC Central Europe GmbHHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16637Human cancer cell lines are frequently used in controlled culture systems to investigate cancer biology. However, extended cultivation can introduce genomic and transcriptional instability. The cell line HCT-116 is a well characterized and widely used model for colorectal cancer. To assess transcriptome stability over time and characterize passage‑dependent gene expression changes, HCT‑116 cells were cultured for 25 consecutive passages (~16 weeks). Cells were harvested at passages 1, 5, 10, 15, 20, and 25, and total RNA was extracted for genome‑wide expression analysis. Microarray‑based transcriptome profiling was performed using the SurePrint G3 Human Gene Expression 8x60K v3 platform (Agilent, G4851C), and arrays were scanned with the InnoScan 910 system (Innopsys). Three biological replicates were included for each selected passage. Differential expression analysis was conducted to compare transcriptomic changes across passages and to identify potential shifts associated with prolonged in vitro cultivation.biostudies-arrayexpressScaning - The prepared microarray chip was scanned by the microarray scanner InnoScan910 (Innopsys). InnoScan910 controlling and raw data extraction was performed via the Mapix software (Innopsys).Sample Collection - RNA was isolated from cultivated HCT-116 cells at 70% confluency.Nucleic Acid Extraction - RNA was isolated via RNeasy Mini kit (Qiagen) with an additional on-column DNase I (Qiagen) digest according to the manufacturer’s instructions.Growth Protocol - HCT‑116 cells were cultured for 25 consecutive passages (~16 weeks). Cells were harvested at passages 1, 5, 10, 15, 20, and 25, and total RNA was extracted.Hybridization - Labeled cRNA was purified by using the RNeasy Mini kit (Qiagen) without on-column DNase digest. 600 ng purified cRNA was fragmented according to the Gene Expression Hybridization Kit (Agilent, 5188-5242) and transferred to Gasket slides (Agilent, G2534-60014). The microarray chip SurePrint G3 human gene expression 8x60k v3 (Agilent, G4851C) was added to Gasket slide to form the hybridization sandwich which was fixed via the hybridization chamber (Agient, G2534A) and subsequently incubated at 65°C for 17 h while rotation. Unbound cRNA was removed using the Gene Expression Wash Buffer Kit (Agilent, 5188-5327).Labeling - 200 ng of total RNA were reversely transcribed to cDNA, further transcribed to cRNA and labelled with Cyanin 3-CTP via the Low Input Quick Amp Labelling Kit (Agilent, 5190-2305).MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsData Transformation - Raw intensities were log2-transformed, background corrected using the normexp method with an offset of 50 and quantile normalized. Microarray probes were filtered for protein-coding genes and for genes expressed in at least one sample group.UnknownTranscriptomicsGenomicsProteomicstranscription profiling by arrayHomo sapiensLong-term cultivation shifts transcriptomic profile of HCT-116 cellsGudrun Marquardt, Theresa Wießner-Kroh, Stefan Rubner and Ioannis PapasotiriouRGCC Central Europe GmbHfalseMicroarray analysis of HCT‑116 cells during in vitro culture over timeHuman cancer cell lines are frequently used in controlled culture systems to investigate cancer biology. However, extended cultivation can introduce genomic and transcriptional instability. The cell line HCT-116 is a well characterized and widely used model for colorectal cancer. To assess transcriptome stability over time and characterize passage‑dependent gene expression changes, HCT‑116 cells were cultured for 25 consecutive passages (~16 weeks). Cells were harvested at passages 1, 5, 10, 15, 20, and 25, and total RNA was extracted for genome‑wide expression analysis. Microarray‑based transcriptome profiling was performed using the SurePrint G3 Human Gene Expression 8x60K v3 platform (Agilent, G4851C), and arrays were scanned with the InnoScan 910 system (Innopsys). Three biological replicates were included for each selected passage. Differential expression analysis was conducted to compare transcriptomic changes across passages and to identify potential shifts associated with prolonged in vitro cultivation.2026-04-07T00:00:00Z2026-04-07T10:32:10.466Z2026-02-11T11:27:03.016ZE-MTAB-16637EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0003789EFO_0005518EFO_0003816EFO_0003815