{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Jana Kuhn"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16794"],"description":["Cu is an essential trace element for the human body, and moreover, increasingly used in industry and clinical applications due to many favorable characteristics of this transition metal. In this context, it has been shown that CuO NP are more toxic than, e.g., CuO MP or ionic copper. Nevertheless, detailed mechanistic studies comparing cellular effects in different organ-relevant models are scarce. For example, transcriptomic profiling of cells exposed to CuO NPs has been conducted only in murine lung cells. Hence, we exposed BEAS-2B (lung) cells to subcytotoxic concentrations of both CuO NP and ionic copper in the form of CuCl2 for 24 h, and HepG2 (liver) cells to subcytotoxic concentrations of ionic Cu for 24 h. The aim was to compare both the relevance of the type of copper compound used and the differences between different cell lines exposed to copper. Briefly, cells were cultivated under submerged conditions for 24 h and exposed to the respective copper compounds for 24 h. Afterwards, cell pellets were obtained, and samples were transcribed into RNA.  Samples were then sent to NovoGene Munich to perform RNA-sequencing. Changes in gene expression of cells treated with copper were then analyzed in comparison to untreated controls."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - Cells were exposed to 0-40 µg/mL total Cu for 24 h. Cu exposure was performed using either CuO NP or CuCl2 in BEAS-2B cells, and with CuCl2 in HepG2 cells.","Sample Collection - Both cell lines were first washed with warm PBS. BEAS-2B cells were then treated with 700 µL Accutase(R) for 3 min in a humidified incubator, and cell suspension was transferred to a 1.5 mL microtube. HepG2 cells were treated with 0.25 % trypsin-EDTA in PBS for 3 min in a humidified incubator and reaction was stoppped with 700 µL DMEM clel culture medium supplemented with 10 % FBS. Cell suspension was then also transferred to a 1.5 mL microcentrifugation tube. For both cell lines, cell suspensions were centrifuged at 300 g at 4 °C for 5 min, and the cell pellet was washed with cold PBS three times.","Sequencing - Illumina NovaSeq sequencer with PE150","Growth Protocol - 4.5×10^5 cells were seeded in 6-well plates for 24 h in a humidified incubator. For BEAS-2B cells, wells were previously treated with a 1:1:1 mixture of 10 µg/mL fibronectin, 30 µg/mL collagen, and 10 µg/mL bovine serum albumin for 30 min at 37°C.","Library Construction - Samples were sent to NovoGene Munich. An mRNA-Sequencing was applied using Illumina RNA-Sequencing with poly-A capture and reverse transcription of mRNA into cDNA.","Nucleic Acid Extraction - The NucleoSpin RNA Plus kit from Marchery Nagel (Germany) was used and manufacturer's instructions were followed."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","organisation","MAGE-TAB Files"],"pubmed_authors":["Hanna Karlsson","Jana Kuhn","Andrea Hartwig","Anda Gliga"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of human bronchial cells (BEAS-2B) treated with 4-40 µg/mL Cu by CuO NP and ionic Cu, and human hepatoblastoma cells (HepG2) treated with 4-40 µg/mL ionic Cu compared to untreated controls","description":"Cu is an essential trace element for the human body, and moreover, increasingly used in industry and clinical applications due to many favorable characteristics of this transition metal. In this context, it has been shown that CuO NP are more toxic than, e.g., CuO MP or ionic copper. Nevertheless, detailed mechanistic studies comparing cellular effects in different organ-relevant models are scarce. For example, transcriptomic profiling of cells exposed to CuO NPs has been conducted only in murine lung cells. Hence, we exposed BEAS-2B (lung) cells to subcytotoxic concentrations of both CuO NP and ionic copper in the form of CuCl2 for 24 h, and HepG2 (liver) cells to subcytotoxic concentrations of ionic Cu for 24 h. The aim was to compare both the relevance of the type of copper compound used and the differences between different cell lines exposed to copper. Briefly, cells were cultivated under submerged conditions for 24 h and exposed to the respective copper compounds for 24 h. Afterwards, cell pellets were obtained, and samples were transcribed into RNA.  Samples were then sent to NovoGene Munich to perform RNA-sequencing. Changes in gene expression of cells treated with copper were then analyzed in comparison to untreated controls.","dates":{"release":"2026-05-24T00:00:00Z","modification":"2026-05-26T17:04:59.657Z","creation":"2026-03-23T08:51:08.97Z"},"accession":"E-MTAB-16794","cross_references":{"ENA":["ERP191149"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}