TY  - CONF
AU  - Milivojević, Nevena
AU  - Prosenc Zmrzljak, Uršula
AU  - Ljujić, Biljana
AU  - Đorđević, Valentina
AU  - Gazdić Janković, Marina
AU  - Živanović, Marko
AU  - Puač, Feđa
AU  - Ivanović, Miloš
AU  - Filipović, Nenad
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1986
AB  - Whole 3’ transcriptome profiling at the single cell level opens up new abilities for researchers to
answer complex questions. Thousands of individual cells per sample are Barcoded separately to
index the transcriptome of each cell individually. It is done by partitioning thousands of cells into
nanoliter-scale Gel Beads-in-emulsion (GEMs), where cells are delivered at a limiting dilution, such
that the majority (~90-99%) of generated GEMs contain no cell. The 16 bp 10x Barcode and 12 bp
UMI are encoded in Read 1, while the poly(dT) primers are used in this protocol for generating Single
Cell 3’ Gene Expression libraries. After GEM generation, copartitioned cells are lysed and reverse
transcription (RT) was performed after which all cDNA from single cell share a common Barcode.
Full-length cDNA was amplified via PCR to generate sufficient mass for library construction. This is
followed by enzymatic fragmentation and size selection to optimize the cDNA amplicon size. Library
construction was finished via End Repair, A-tailing, Adaptor Ligation, and PCR. P5, P7, i7 and i5
sample index, and TruSeq Read 2 (read 2 primer sequence) were added. TruSeq Read 1 and TruSeq
Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. The library
prepared in this way, containing the P5 and P7 primers, is ready for Illumina amplification.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Single cell 3’ transcriptome profiling
EP  - 45
SP  - 45
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1986
ER  - 

@conference{
author = "Milivojević, Nevena and Prosenc Zmrzljak, Uršula and Ljujić, Biljana and Đorđević, Valentina and Gazdić Janković, Marina and Živanović, Marko and Puač, Feđa and Ivanović, Miloš and Filipović, Nenad",
year = "2023",
abstract = "Whole 3’ transcriptome profiling at the single cell level opens up new abilities for researchers to
answer complex questions. Thousands of individual cells per sample are Barcoded separately to
index the transcriptome of each cell individually. It is done by partitioning thousands of cells into
nanoliter-scale Gel Beads-in-emulsion (GEMs), where cells are delivered at a limiting dilution, such
that the majority (~90-99%) of generated GEMs contain no cell. The 16 bp 10x Barcode and 12 bp
UMI are encoded in Read 1, while the poly(dT) primers are used in this protocol for generating Single
Cell 3’ Gene Expression libraries. After GEM generation, copartitioned cells are lysed and reverse
transcription (RT) was performed after which all cDNA from single cell share a common Barcode.
Full-length cDNA was amplified via PCR to generate sufficient mass for library construction. This is
followed by enzymatic fragmentation and size selection to optimize the cDNA amplicon size. Library
construction was finished via End Repair, A-tailing, Adaptor Ligation, and PCR. P5, P7, i7 and i5
sample index, and TruSeq Read 2 (read 2 primer sequence) were added. TruSeq Read 1 and TruSeq
Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. The library
prepared in this way, containing the P5 and P7 primers, is ready for Illumina amplification.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Single cell 3’ transcriptome profiling",
pages = "45-45",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1986"
}

Milivojević, N., Prosenc Zmrzljak, U., Ljujić, B., Đorđević, V., Gazdić Janković, M., Živanović, M., Puač, F., Ivanović, M.,& Filipović, N.. (2023). Single cell 3’ transcriptome profiling. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 45-45.
https://hdl.handle.net/21.15107/rcub_imagine_1986

Milivojević N, Prosenc Zmrzljak U, Ljujić B, Đorđević V, Gazdić Janković M, Živanović M, Puač F, Ivanović M, Filipović N. Single cell 3’ transcriptome profiling. in 4th Belgrade Bioinformatics Conference. 2023;4:45-45.
https://hdl.handle.net/21.15107/rcub_imagine_1986 .

Milivojević, Nevena, Prosenc Zmrzljak, Uršula, Ljujić, Biljana, Đorđević, Valentina, Gazdić Janković, Marina, Živanović, Marko, Puač, Feđa, Ivanović, Miloš, Filipović, Nenad, "Single cell 3’ transcriptome profiling" in 4th Belgrade Bioinformatics Conference, 4 (2023):45-45,
https://hdl.handle.net/21.15107/rcub_imagine_1986 .

TY  - CONF
AU  - Virijević, Katarina
AU  - Živanović, Marko
AU  - Gazdić Janković, Marina
AU  - Ramović Hamzagić, Amra
AU  - Milivojević, Nevena
AU  - Pecić, Katarina
AU  - Šeklić, Dragana
AU  - Jovanović, Milena
AU  - Kastratović, Nikolina
AU  - Mirić, Ana
AU  - Đukić, Tijana
AU  - Petrović, Ivica
AU  - Jurišić, Vladimir
AU  - Ljujić, Biljana
AU  - Filipović, Nenad
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2010
AB  - Biomedicine is a multidisciplinary branch of science that requires a clear approach to the
study and analysis of various life processes necessary for a deeper understanding of
human health. This research focuses on the use of numerical simulations with the aim of an
improved comprehension of cancer viability and apoptosis during treatment with commercial
chemotherapeutic agents. In recent times, the usage of numerical models was successfully
applied to predict the behavior of tumors. This study includes a wide range of numerical results
that have been obtained by examining cell viability in real-time, determining the type of cell
death and the genetic factors that control these processes. The results of the in vitro test were
used to develop a numerical model that provides a new perspective on the proposed problem.
In this study, colon, and breast cancer cell lines (HCT-116 and MDA-MB-231), as well as healthy
lung fibroblast cell line (MRC-5) were treated with commercial chemotherapeutic agents. The
obtained results showed a decrease in viability and the occurrence of predominantly late
apoptosis upon treatment, as well as a strong correlation between parameters. A mathematical
model was developed and used to gain a better understanding of the investigated processes.
This method can accurately simulate the behavior of cancer cells and reliably predict their
growth.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Numerical and Biological Modeling Approach in the Analysis of the Cancer Viability and Apoptosis
EP  - 70
SP  - 70
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2010
ER  - 

@conference{
author = "Virijević, Katarina and Živanović, Marko and Gazdić Janković, Marina and Ramović Hamzagić, Amra and Milivojević, Nevena and Pecić, Katarina and Šeklić, Dragana and Jovanović, Milena and Kastratović, Nikolina and Mirić, Ana and Đukić, Tijana and Petrović, Ivica and Jurišić, Vladimir and Ljujić, Biljana and Filipović, Nenad",
year = "2023",
abstract = "Biomedicine is a multidisciplinary branch of science that requires a clear approach to the
study and analysis of various life processes necessary for a deeper understanding of
human health. This research focuses on the use of numerical simulations with the aim of an
improved comprehension of cancer viability and apoptosis during treatment with commercial
chemotherapeutic agents. In recent times, the usage of numerical models was successfully
applied to predict the behavior of tumors. This study includes a wide range of numerical results
that have been obtained by examining cell viability in real-time, determining the type of cell
death and the genetic factors that control these processes. The results of the in vitro test were
used to develop a numerical model that provides a new perspective on the proposed problem.
In this study, colon, and breast cancer cell lines (HCT-116 and MDA-MB-231), as well as healthy
lung fibroblast cell line (MRC-5) were treated with commercial chemotherapeutic agents. The
obtained results showed a decrease in viability and the occurrence of predominantly late
apoptosis upon treatment, as well as a strong correlation between parameters. A mathematical
model was developed and used to gain a better understanding of the investigated processes.
This method can accurately simulate the behavior of cancer cells and reliably predict their
growth.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Numerical and Biological Modeling Approach in the Analysis of the Cancer Viability and Apoptosis",
pages = "70-70",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2010"
}

Virijević, K., Živanović, M., Gazdić Janković, M., Ramović Hamzagić, A., Milivojević, N., Pecić, K., Šeklić, D., Jovanović, M., Kastratović, N., Mirić, A., Đukić, T., Petrović, I., Jurišić, V., Ljujić, B.,& Filipović, N.. (2023). Numerical and Biological Modeling Approach in the Analysis of the Cancer Viability and Apoptosis. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 70-70.
https://hdl.handle.net/21.15107/rcub_imagine_2010

Virijević K, Živanović M, Gazdić Janković M, Ramović Hamzagić A, Milivojević N, Pecić K, Šeklić D, Jovanović M, Kastratović N, Mirić A, Đukić T, Petrović I, Jurišić V, Ljujić B, Filipović N. Numerical and Biological Modeling Approach in the Analysis of the Cancer Viability and Apoptosis. in 4th Belgrade Bioinformatics Conference. 2023;4:70-70.
https://hdl.handle.net/21.15107/rcub_imagine_2010 .

Virijević, Katarina, Živanović, Marko, Gazdić Janković, Marina, Ramović Hamzagić, Amra, Milivojević, Nevena, Pecić, Katarina, Šeklić, Dragana, Jovanović, Milena, Kastratović, Nikolina, Mirić, Ana, Đukić, Tijana, Petrović, Ivica, Jurišić, Vladimir, Ljujić, Biljana, Filipović, Nenad, "Numerical and Biological Modeling Approach in the Analysis of the Cancer Viability and Apoptosis" in 4th Belgrade Bioinformatics Conference, 4 (2023):70-70,
https://hdl.handle.net/21.15107/rcub_imagine_2010 .