{"id":2797,"date":"2023-06-13T01:08:23","date_gmt":"2023-06-13T00:08:23","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&p=2797"},"modified":"2023-06-14T18:37:24","modified_gmt":"2023-06-14T17:37:24","slug":"single-cell-3-transcriptome-profiling","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/single-cell-3-transcriptome-profiling\/","title":{"rendered":"Single cell 3` transcriptome profiling"},"content":{"rendered":"\n

Nevena Milivojevi\u01071*<\/sup>, Ur\u0161ula Prosenc Zmrzljak2<\/sup>, Biljana Ljuji\u01073<\/sup>, Valentina \u0110or\u0111evi\u01074<\/sup>, Marina Gazdi\u0107 Jankovi\u01073<\/sup>, Marko \u017divanovi\u01071,5<\/sup>, Fe\u0111a Pua\u010d6<\/sup>, Milo\u0161 Ivanovi\u01077<\/sup>, and Nenad Filipovi\u01075,8<\/sup><\/p>\n\n\n\n

1<\/sup>Institute for Information Technologies, University of Kragujevac, Jovana Cviji\u0107a bb, 34000 Kragujevac, Serbia <\/p>\n\n\n\n

2<\/sup>BIA Separations CRO Laboratory, Teslova ulica 30, 1000 Ljubljana, Slovenia<\/p>\n\n\n\n

3<\/sup>Faculty of Medical Sciences, University of Kragujevac, Svetozara Markovi\u0107a 69, 34000 Kragujevac, Serbia<\/p>\n\n\n\n

4<\/sup>Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia<\/p>\n\n\n\n

5<\/sup>BioIRC – Bioengineering Research and Development Center, University of Kragujevac, Prvoslava Stojanovi\u0107a 6, 34000 Kragujevac, Serbia<\/p>\n\n\n\n

6<\/sup>Labena d.o.o. Serbia, Bulevar Zorana \u0110in\u0111i\u0107a 123G, 11070 Belgrade, Serbia<\/p>\n\n\n\n

7<\/sup>Faculty of Science, University of Kragujevac, Radoja Domanovi\u0107a 12, 34000 Kragujevac, Serbia<\/p>\n\n\n\n

8<\/sup>Faculty of Engineering, University of Kragujevac, Sestre Janji\u0107 6, 34000 Kragujevac, Serbia<\/p>\n\n\n\n

nevena_milivojevic [at] live.com<\/p>\n\n\n\n

Abstract<\/strong><\/p>\n\n\n\n

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\u02b9 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.<\/p>\n\n\n\n

Keywords:<\/strong> single-cell analysis, mRNA, bioinformatics, transcriptome, sequencing <\/p>\n\n\n\n

Acknowledgement:<\/strong> This research is funded by Labena Slovenia 10xGenomics Grant Challenge (Project title: Deciphering the effects of nanosized polystyrene particles using lab-on-chip technology and transcriptome profile). This research was supported by Labena Serbia, the Ministry of Science, Technological Development and Innovation of the Republic of Serbia, contract number 451-03-47\/2023-01\/200378 (Institute for Information Technologies Kragujevac, University of Kragujevac), 451-03-47\/2023-01\/200111 (Faculty of Medical Sciences, University of Kragujevac), as well as Junior projects of Faculty of Medical Sciences, University of Kragujevac JP 25\/19, JP 05\/20, JP 06\/20 and JP 24\/20. This work is supported by the European Union\u2019s Horizon 2020 research and innovation program under grant agreement No 952603 (SGABU). This article reflects only the author\u2019s view. The Commission is not responsible for any use that may be made of the information it contains.<\/p>\n","protected":false},"excerpt":{"rendered":"

Nevena Milivojevi\u01071*<\/sup>, Ur\u0161ula Prosenc Zmrzljak2<\/sup>, Biljana Ljuji\u01073<\/sup>, Valentina \u0110or\u0111evi\u01074<\/sup>, Marina Gazdi\u0107 Jankovi\u01073<\/sup>, Marko \u017divanovi\u01071,5<\/sup>, Fe\u0111a Pua\u010d6<\/sup>, Milo\u0161 Ivanovi\u01077<\/sup>, and Nenad Filipovi\u01075,8<\/sup><\/p>\n

1<\/sup>Institute for Information Technologies, University of Kragujevac, Jovana Cviji\u0107a bb, 34000 Kragujevac, Serbia <\/p>\n

2<\/sup>BIA Separations CRO Laboratory, Teslova ulica 30, 1000 Ljubljana, Slovenia<\/p>\n

3<\/sup>Faculty of Medical Sciences, University of Kragujevac, Svetozara Markovi\u0107a 69, 34000 Kragujevac, Serbia<\/p>\n

4<\/sup>Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia<\/p>\n

5<\/sup>BioIRC – Bioengineering Research and Development Center, University of Kragujevac, Prvoslava Stojanovi\u0107a 6, 34000 Kragujevac, Serbia<\/p>\n

6<\/sup>Labena d.o.o. Serbia, Bulevar Zorana \u0110in\u0111i\u0107a 123G, 11070 Belgrade, Serbia<\/p>\n

7<\/sup>Faculty of Science, University of Kragujevac, Radoja Domanovi\u0107a 12, 34000 Kragujevac, Serbia<\/p>\n

8<\/sup>Faculty of Engineering, University of Kragujevac, Sestre Janji\u0107 6, 34000 Kragujevac, Serbia<\/p>\n

Continue reading<\/span><\/i><\/a> <\/p>\n","protected":false},"author":162,"featured_media":0,"template":"","categories":[18],"tags":[],"yoast_head":"\nSingle cell 3` transcriptome profiling - BelBi 2023<\/title>\n<meta name=\"robots\" content=\"noindex, follow\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Single cell 3` transcriptome profiling - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"Nevena Milivojevi\u01071*, Ur\u0161ula Prosenc Zmrzljak2, Biljana Ljuji\u01073, Valentina \u0110or\u0111evi\u01074, Marina Gazdi\u0107 Jankovi\u01073, Marko \u017divanovi\u01071,5, Fe\u0111a Pua\u010d6, Milo\u0161 Ivanovi\u01077, and Nenad Filipovi\u01075,81Institute for Information Technologies, University of Kragujevac, Jovana Cviji\u0107a bb, 34000 Kragujevac, Serbia 2BIA Separations CRO Laboratory, Teslova ulica 30, 1000 Ljubljana, Slovenia3Faculty of Medical Sciences, University of Kragujevac, Svetozara Markovi\u0107a 69, 34000 Kragujevac, Serbia4Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia5BioIRC - Bioengineering Research and Development Center, University of Kragujevac, Prvoslava Stojanovi\u0107a 6, 34000 Kragujevac, Serbia6Labena d.o.o. 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