dc.contributor | Morić, Ivana | |
dc.contributor | Đorđević, Valentina | |
dc.creator | Milivojević Dimitrijević, Nevena | |
dc.creator | Ivanović, Miloš | |
dc.creator | Živić, Andreja | |
dc.creator | Ljujić, Biljana | |
dc.creator | Gazdić Janković, Marina | |
dc.creator | Prosenc Zmrzljak, Uršula | |
dc.creator | Mirić, Ana | |
dc.creator | Đorđević, Valentina | |
dc.creator | Puač, Feđa | |
dc.creator | Živanović, Marko | |
dc.creator | Filipović, Nenad | |
dc.date.accessioned | 2024-07-24T21:56:50Z | |
dc.date.available | 2024-07-24T21:56:50Z | |
dc.date.issued | 2024 | |
dc.identifier.uri | 978-86-82679-16-5 | |
dc.identifier.uri | www.belbi.bg.ac.rs | |
dc.identifier.uri | https://imagine.imgge.bg.ac.rs/handle/123456789/2456 | |
dc.description.abstract | Transcriptome profiling at the single cell level is crucial for understanding complex
biological systems and molecular mechanisms. We wanted to unravel the influence
of polystyrene nanoparticles on peripheral blood mononuclear cells (PBMCs), using
microfluidic technology. A total of 4 single-cell sequencing libraries were analyzed (one
control and three different treatments). Thousands of individual cells per sample are
Barcoded separately to index the transcriptome of each cell individually. Raw sequencing
data were analyzed with the Cell Ranger software and visualized using Loupe Browser
software. Set of analysis pipelines processes Chromium Single Gene Expression data
to align reads, generate Feature Barcode matrices, and perform clustering and gene
expression analysis. Each element of the matrix is the number of UMIs (Unique Molecular
Identifier) associated with a feature (row) and a barcode (column). Principal component
analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) algorithms on
single-cell sequencing samples were carried out. The expressed cells were clustered
during which typical cell marker genes were used for annotation. Genes showing adjusted
p-value < 0.05 and |log2 (fold change) | > 0.5 were considered to be marker genes. Loupe
Browser was used for visualization of clusters and analysis of the single-cell data. In this
way, gene markers for individual cell types obtained by single-cell sequencing represent a
good model for the analysis of biological events. | sr |
dc.language.iso | en | sr |
dc.publisher | Belgrade : Institute of Molecular Genetics and Genetic Engineering | sr |
dc.relation | info:eu-repo/grantAgreement/MESTD/inst-2020/200378/RS// | sr |
dc.relation | info:eu-repo/grantAgreement/MESTD/inst-2020/200111/RS// | sr |
dc.rights | openAccess | sr |
dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0/ | |
dc.source | 5th Belgrade Bioinformatics Conference | sr |
dc.subject | bioinformatics | sr |
dc.subject | single cell | sr |
dc.subject | sequencing | sr |
dc.subject | scRNA-seq | sr |
dc.subject | microfluidic | sr |
dc.title | Deciphering the effects of nanosized polystyrene particles | sr |
dc.type | article | sr |
dc.rights.license | BY-NC-ND | sr |
dc.citation.epage | 61 | |
dc.citation.spage | 61 | |
dc.description.other | Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024. | sr |
dc.identifier.fulltext | https://imagine.imgge.bg.ac.rs/bitstream/id/845705/BelBi2024-Book-of-Abstracts_1-16,77,141-142.pdf | |
dc.identifier.rcub | https://hdl.handle.net/21.15107/rcub_imagine_2456 | |
dc.type.version | publishedVersion | sr |