RNA-seq of human cancer cell lines HCT116, T47D and A549 in 3D collagen I microenvironments compared to 2D cell culture
The behavior of cancer cells strongly relies on the properties of the extracellular microenvironment. The aim was to compare the whole transcriptome of three non-invasive cancer cell lines, HCT-116, A549 and T-47D, embedded in collagen I matrices in a time-dependent manner to standard two-dimensional cell culture. For this purpose, human cancer cell lines (HCT-116, A549 and T-47D) were cultured in their recommended media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C, 5% CO2 and 95% humidity. Cells were regularly tested negative for mycoplasma and authenticated by STR analysis. For 2D culture, cells were grown to 70–90% confluency and RNA was isolated. For 3D culture, single cells were embedded in 2.5 mg/mL collagen I matrices, which was polymerized at 37 °C, and cultured in medium. After 3, 5, 7, and 10 days, cells were released by collagenase IV digestion for RNA isolation.
The behavior of cancer cells strongly relies on the properties of the extracellular microenvironment. The aim was to compare the whole transcriptome of three non-invasive cancer cell lines, HCT-116, A549 and T-47D, embedded in collagen I matrices in a time-dependent manner to standard two-dimensional cell culture. For this purpose, human cancer cell lines (HCT-116, A549 and T-47D) were cultured in their recommended media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C, 5% CO2 and 95% humidity. Cells were regularly tested negative for mycoplasma and authenticated by STR analysis. For 2D culture, cells were grown to 70–90% confluency and RNA was isolated. For 3D culture, single cells were embedded in 2.5 mg/mL collagen I matrices, which was polymerized at 37 °C, and cultured in medium. After 3, 5, 7, and 10 days, cells were released by collagenase IV digestion for RNA isolation.