Oliver Morell (s204116) Morell1123
André Rosengaard Jørgensen (s183451) whelixw
Antonios Otapasidis (s232996) s232996
Konstantinos Lyroudis (s232994) LyroudisK
Georgios Retsinias (s233079) GeorgiosR
We investigated two studies on comparative RNA-seq of coding RNA on a mouse cancer cell line and 18 human cancer cell lines.
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install.packages("quarto")
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install.packages("tidyverse")
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install.packages("viridis")
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install.packages("ggridges")
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install.packages("VennDiagram")
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install.packages("broom")
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install.packages("ggrepel")
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install.packages("RColorBrewer")
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install.packages("cowplot")
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install.packages("scales")
Mouse data sets
In a study focusing on mouse melanoma cell line B16-F10, 12 samples were examined to understand the impact of different compounds---dimethyl sulfoxide (DMSO), WNT3a, and G007-LK on the RNA-seq profile of coding RNA. Each compound was applied in triplicates, and the RNA sequencing, performed via Illumina HiSeq 2500. The cell line B16-F10C was treated with specific concentrations of the compounds, serving as negative controls or actively targeting pathways related to cancer.
Cell line: B16-F10C
Compounds treated with:
| DMSO | G007-LK | WNT3a | G007-LK + WNT3a | |
|---|---|---|---|---|
| Concentration | 0.01% | 1μM | 0.5 μg/ml | 1μM + 0.5 μg/ml |
Human data sets
The two data sets concerning human RNA-seq were derived from the study "Human melanoma cell lines treated with G007-LK"". During this experiment 18 human melanoma cell lines derived from skin were treated with the compound GOO7-LK with the purpose of detecting its effect on the RNA-seq profile of the cells. Three pooled technical replicates from a panel of the 18 human melanoma cell lines were treated with dimethyl sulfoxide (DMSO) or G007-LK for 24 hours
Cell lines: A-375, FEMX-I, FEMX-V, LOX-IMVI, MeWo, SK-MEL-28, WM115, WM1341B, WM1366, WM1382, WM239A, WM266.4, WM35, WM451Lu, WM793B, WM852, WM9, WM983B
Compounds treated with:
| DMSO | G007-LK | |
|---|---|---|
| Concentration | 0.01% | 1μM |
The four data sets were retrieved from from EBI-EMBL website (https://www.ebi.ac.uk/biostudies/arrayexpress/studies) and uploaded to another repo of Group 24 from where the URLs are provided for data loading. In this way, our team makes sure that the data sets will be available even if changes occur to the original source.
Study on human cell lines Accession Number: E-MTAB-8438
Study on mouse cell line Accession Number: E-MTAB-8101
Waaler, Jo, et al. "Tankyrase Inhibition Sensitizes Melanoma to PD-1 Immune Checkpoint Blockade in Syngeneic Mouse Models." Communications Biology, vol. 3, no. 1, 24 Apr. 2020, https://doi.org/10.1038%2Fs42003-020-0916-2 Accessed 25 Nov. 2023.
Link to our presentation: https://raw.githack.com/rforbiodatascience23/group_24_project/main/doc/presentation.html