{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Anda Gliga"],"organism":["Homo sapiens"],"software":["Count matrix were created using HTseq version 0.6.1 on bam files with duplicates included","Tophat v 2.0.4"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-6321"],"description":["Human bronchial lung cells (BEAS-2B) were treated for 6 weeks with low doses (1 µg/mL) of Ag nanoparticles (10 nm citrate coated). At the end of the exposure control and treated samples were submitted for RNA-Seq analysis (Hiseq2500). The overall goal of this experiment was to gain an in-depth understanding of the transcriptomic changes induced by low-dose, long-term exposure of  human lung cells to Ag nanoparticles and to generate hypotheses related to their mechanisms of toxicity."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - For the long-term exposure, BEAS-2B were seeded in 6 well-plates (5000 cells/cm2, 2 mL cell medium per well) and allowed to attach for approx. 2 h. Thereafter, cells were exposed to 1 µg/mL Ag10 (approx. 0.2 µg/cm2) in triplicates. Cells were split (trypsinization), counted, reseeded twice a week (5000 cells/ cm2, 2 mL cell medium per well) and re-exposed to the Ag nanoparticles.","Library Construction - Stranded mRNA-seq (Illumina TruSeq RNA HT with polyA-selection","Growth Protocol - BEAS-2B cells (European Collection of Cell Cultures) were cultured in bronchial epithelial cell growth medium (BEGM, Lonza) supplemented with BEGM bullet-kit (Lonza: recombinant epidermal growth factor (EGF), hydrocortisone, insulin, bovine pituitary extract, GA-1000 (Gentamicin Sulfate and Amphotericin-B), retinoic acid, transferrin, triiodothyronine and epinephrine). Cells were cultured in flasks and plates pre-coated with: 0.01 mg/mL fibronectin, 0.03 mg/mL bovine collagen type I, 0.01 mg/mL bovine serum albumin and 0.2% penicillin-streptomycin in BEGM additive free medium for 1-2 h prior to the seeding. Cells were maintained in a humidified atmosphere at 37˚C, 5% CO2 and sub-cultured at 80% confluency.","Sequencing - Illumina HiSeq 2500","Nucleic Acid Extraction - For RNA extraction, the cells were washed after exposure and total RNA was extracted using the RNeasy Mini Columns (Qiagen) according to the manufacturer’s instructions, including the purification step with DNase I treatment."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Count matrix were created using HTseq version 0.6.1 on bam files with duplicates included","Sequence Alignment - Tophat v. 2.0.4 were used to map to human genome version GRCh37"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500"],"pubmed_abstract":["Despite a considerable focus on the adverse effects of silver nanoparticles (AgNPs) in recent years, studies on the potential long-term effects of AgNPs are scarce. The aim of this study was to explore the effects of AgNPs following repeated low-dose, long-term exposure of human bronchial epithelial cells. To this end, the human BEAS-2B cell line was exposed to 1 µg/mL AgNPs (10 nm) for 6 weeks followed by RNA-sequencing (RNA-Seq) as well as genome-wide DNA methylation analysis. The transcriptomics analysis showed that a substantial number of genes (1717) were differentially expressed following AgNP exposure whereas only marginal effects on DNA methylation were observed. Downstream analysis of the transcriptomics data identified several affected pathways including the 'fibrosis' and 'epithelial-mesenchymal transition' (EMT) pathway. Subsequently, functional validation studies were performed using AgNPs of two different sizes (10 nm and 75 nm). Both NPs increased collagen deposition, indicative of fibrosis, and induced EMT, as evidenced by an increased invasion index, anchorage independent cell growth, as well as cadherin switching. In conclusion, using a combination of RNA-Seq and functional assays, our study revealed that repeated low-dose, long-term exposure of human BEAS-2B cells to AgNPs is pro-fibrotic, induces EMT and cell transformation."],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells."],"pubmed_authors":["Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL.","Anda Gliga"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of BEAS-2B cells treated with low doses of Ag nanoparticles for 6 weeks","description":"Human bronchial lung cells (BEAS-2B) were treated for 6 weeks with low doses (1 µg/mL) of Ag nanoparticles (10 nm citrate coated). At the end of the exposure control and treated samples were submitted for RNA-Seq analysis (Hiseq2500). The overall goal of this experiment was to gain an in-depth understanding of the transcriptomic changes induced by low-dose, long-term exposure of  human lung cells to Ag nanoparticles and to generate hypotheses related to their mechanisms of toxicity.","dates":{"release":"2018-04-30T00:00:00Z","modification":"2026-03-13T17:20:11.96Z","creation":"2022-02-03T13:36:02.303Z"},"accession":"E-MTAB-6321","cross_references":{"pubmed":["29703973"],"ENA":["ERP105806"],"Biostudies":["E-MTAB-6331"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"],"doi":["10.1038/s41598-018-25085-5"]}}