biostudies-arrayexpressRGCC Central Europe GmbHHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17224Intensive usage of cancer cell lines as cellular model system in cancer research caused the generation of variant subtypes during the last decades. This study focused on the human leukemic THP-1 cell line as a monocyte model. THP-1 cells from two different depositors were differentiated into various immune states. Additionally primary immune cells were differentiated into various immune states in order to be a comparative dataset.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 THP-1 cells, primary monocytes and respective M0, M1 and M2 differentiation states.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 - THP-1 cells were purchased from German Collection of Microorganism and Cell Cultures (DSMZ, Braunschweig Germany) and European Collection of Authenticated Cell Cultures (ECACC, Salisbury United Kingdom). Cells were maintained in RPMI 1640 medium (Thermo Fisher Scientific, 42401042) supplemented with 10 % heat-inactivated fetal bovine serum (Thermo Fisher Scientific, A5256801), 1 % (v/v) penicillin/streptomycin (Thermo Fisher Scientific,15140122), 1 % (v/v) L-glutamine (Thermo Fisher Scientific, 25030024), 1 % (v/v) sodium pyruvate (Thermo Fisher Scientific, 11360039) and 0.01 % (v/v) ß-mercaptoethanol (Thermo Fisher Scientific, 31350010). Cells were cultured at 37 °C and 5 % CO2 in a humid environment. Mycoplasma tests were regularly performed during cultivation using TransDetect® PCR Mycoplasma Detection Kit (Biotrend, FM311-01). Cells were verified by short tandem repeat (STR) analysis (Eurofins, Germany). Cell number has been determined using automated brightfield cell counting (Countess, Thermo Fisher Scientific). For THP-1 differentiation, cells were seeded with a density of 120,000 cells/cm² into different culture flasks containing media supplemented with 150 nM PMA (Sigma Aldrich, P8139) and incubated for 48 h. Cells were washed three times with RPMI media without FBS. Afterwards cells were rested for 24 h in culture media to generate M0 macrophages. For further polarization cells were incubated for 72 h with RPMI containing 50 ng/mL interleukin 4 (IL-4, Biolegend, 574006) and IL-13 (Biolegend, 571106) for M2 macrophages, or 100 pg/mL lipopolysaccharid (LPS, Sigma Aldrich, L6529) and 50 ng/mL interferon-γ (IFN-γ, Biolegend, 570204) for M1 macrophages.Nucleic Acid Extraction - Cells were lysed using 1 mL QIAzol Reagent (Qiagen). 200 µL chloroform (Roth) per mL QIAzol were added, followed by homogenization of the suspension and centrifugation at 4°C, 12000 x g for 15 min. The aqueous phase was merged with 1 volume cold isopropanol (Roth) and RNA was precipitated at - 20°C for 3 days. Precipitated RNA was pelleted at 4°C, washed three times with ice cold 75% ethanol (ITW Reagents). Afterwards, the pellet was dried and dissolved in RNase-free H2O.Growth Protocol - RNA was isolated from primary monocytes, isolated from fresh Leukopaks from healthy adult donors purchased from Grifols Bio Supplies Inc. First, peripheral blood mononuclear cells (PBMCs) were isolated using the StraightFrom Leukopak PBMC Isolation Kit (Miltenyi, 130-123-456) in combination with the MultiMACS-Cell24-Separator-Plus. Monocytes were isolated with a positive selection using CD14 MicroBeads (Miltenyi, 130-050-201) and were differentiated using a standard protocol from Promocell. Here, cells were seeded at 120,000 cells/cm² in an appropriate cell culture flask with Monocyte Attachment media (Promocell, C-28051). Cells were incubated at 37 °C and 5 % CO2 in a humid environment for 1.5 h. For further differentiation, media was changed to M1 macrophage generation media XF (Promocell, C-28055) or to M2 macrophage generation media XF (Promocell, C-28056) for 7 days and final polarization for 48 h.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.MetabolomicsUnknownTranscriptomicsGenomicsProteomicstranscription profiling by arrayHomo sapiensComparison of THP-1 subtypes reveals differences on transcriptomic and protein expression level throughout their immunological differentiationRGCC Central Europe GmbHSabine Klatt, Gudrun Marquardt, Miriam Faxel, Stefan Rubner and Ioannis PapasotirioufalseMicroarray of differentiation states of primary monocytes and THP-1 cells (from two depositors)Intensive usage of cancer cell lines as cellular model system in cancer research caused the generation of variant subtypes during the last decades. This study focused on the human leukemic THP-1 cell line as a monocyte model. THP-1 cells from two different depositors were differentiated into various immune states. Additionally primary immune cells were differentiated into various immune states in order to be a comparative dataset.2026-07-24T00:00:00Z2026-07-24T07:02:11.189Z2026-06-25T13:49:24.609ZE-MTAB-17224EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0003789EFO_0005518EFO_0003816EFO_0003815