RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. General Sequencing Statistics
2.2. Presence of Specific Mutations in the Investigated Cell Lines
2.3. Global Gene Expression Patterns of the Investigated Cell Lines
2.4. Expression Levels of Specific Genes in the Investigated Cell Lines
3. Discussion
4. Materials and Methods
4.1. Characterized Hepatobiliary Cancer Cell Lines, Contamination Testing, and RNA Extraction and Sequencing
4.2. Quality Control, Pre-Processing, and Statistical Analysis of RNA Sequencing Data
4.3. External Data Used for the Exemplary Applications
4.4. Validation of Gene Expression Results
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Cell Line | Gene | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Proportion of Primary GBC Tumours in MSK-IMPACT with One or More Mutations | |||||||||||||||||||||||||||||||||||||||||
Type | Name | TP53 | ATM | SMAD4 | ARID1A | ARID1B | CTNNB1 | KEAP1 | NF1 | NOTCH3 | PTPRD | ||||||||||||||||||||||||||||||
44% | 33% | 28% | 22% | 11% | 11% | 11% | 11% | 11% | 11% | ||||||||||||||||||||||||||||||||
A | B | C | D | A | B | C | D | A | B | C | D | A | B | C | D | A | B | C | D | A | B | C | D | A | B | C | D | A | B | C | D | A | B | C | D | A | B | C | D | ||
GBC | G-415 | ||||||||||||||||||||||||||||||||||||||||
GB-d1 | x | ||||||||||||||||||||||||||||||||||||||||
Mz-Cha-1 | x | ||||||||||||||||||||||||||||||||||||||||
NOZ | x | ||||||||||||||||||||||||||||||||||||||||
OCUG-1 | x | ||||||||||||||||||||||||||||||||||||||||
OZ | |||||||||||||||||||||||||||||||||||||||||
SNU308 | x | x | x | x | x | x | |||||||||||||||||||||||||||||||||||
TGBC1 | x | x | x | x | x | x | |||||||||||||||||||||||||||||||||||
TGBC2 | x | ||||||||||||||||||||||||||||||||||||||||
YoMi | x | x | |||||||||||||||||||||||||||||||||||||||
HCC | Hep3B | x | x | ||||||||||||||||||||||||||||||||||||||
HepG2 | x | x | |||||||||||||||||||||||||||||||||||||||
HHT4 | |||||||||||||||||||||||||||||||||||||||||
HLE | x | x | x | x | |||||||||||||||||||||||||||||||||||||
HLF | x | ||||||||||||||||||||||||||||||||||||||||
HuH1 | x | x | x | x | x | x | x | ||||||||||||||||||||||||||||||||||
HuH6 | x | x | x | x | x | x | |||||||||||||||||||||||||||||||||||
HuH7 | x | x | x | x | x | x | x | x | |||||||||||||||||||||||||||||||||
CCA | EGI-1 | x | x | x | |||||||||||||||||||||||||||||||||||||
HuCCT1 | x | x | x | ||||||||||||||||||||||||||||||||||||||
KMCH | x | ||||||||||||||||||||||||||||||||||||||||
SNU478 | x | x | |||||||||||||||||||||||||||||||||||||||
TFK-1 | x |
Gene-Specific Median TPM Expression Value | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Name | TP53 | TERT | ARID2 | EGFR | CCND1 | CCND3 | ERBB3 | KMT2D | KMT2C | TET1 | TET2 | TET3 | |
Median TPM | 4.95 | 0.04 | 0.67 | 1.45 | 45.04 | 1.73 | 33.08 | 6.16 | 0.68 | 0.04 | 0.42 | 0.42 | |
5th percentile–95th percentile | 2.34–7.55 | −0.1–0.17 | 0.44–0.89 | 0.71–2.19 | 6.02–84.06 | 0.79–2.66 | 30.23–34.71 | 3.49–8.82 | 0.42–0.94 | −0.04–0.11 | 0.17–0.9 | 0.37–0.9 | |
RNA Sequencing | GB-d1 | 14.09 | 1.59 | 1.78 | 16.76 | 184.35 | 2.88 | 39.69 | 34.67 | 1.27 | 0.05 | 1.22 | 1.43 |
Mz-Cha-1 | 29.98 | 0.14 | 1.37 | 13.55 | 100.15 | 5.06 | 57.79 | 41.35 | 3.43 | 0.04 | 0.59 | 2.19 | |
NOZ | 3.90 | 0.30 | 0.59 | 7.32 | 151.95 | 3.15 | 1.98 | 21.87 | 1.49 | 0.06 | 0.26 | 1.03 | |
OCUG-1 | 25.41 | 2.01 | 0.64 | 21.78 | 30.05 | 2.91 | 31.73 | 10.56 | 3.85 | 0.10 | 0.57 | 0.56 | |
OZ | 39.80 | 0.36 | 1.84 | 19.97 | 149.99 | 2.85 | 198.17 | 69.93 | 3.18 | 0.06 | 1.12 | 4.59 | |
SNU308 | 41.07 | 0.16 | - | 21.38 | 201.48 | 1.67 | 35.15 | 56.81 | 2.62 | 0.11 | 1.93 | 2.51 | |
TGBC1 | 1.62 | 3.67 | 0.79 | 4.19 | 81.09 | 2.26 | 31 | 20.34 | 2.22 | 0.26 | 0.53 | 1.19 | |
TGBC2 | 1.50 | 9.54 | 0.51 | 6.35 | 106.40 | 7.28 | 3.16 | 19.03 | 1.53 | 0.11 | 0.80 | 1.58 | |
YoMi | 4.71 | 0.30 | 3.20 | 24.72 | 256.11 | 6.54 | 284.89 | 66.87 | 5.01 | - | 2.20 | 8.11 | |
small RNA Sequencing | GB-d1 | 2.07 | 0.45 | 5.25 | 49.02 | 83.05 | 2.53 | 9.65 | 37.48 | 3.35 | 0.58 | 2.13 | 10.45 |
Mz-Cha-1 | 2.58 | 0.14 | 5.06 | 37.27 | 39.53 | 2.33 | 15.43 | 39.12 | 10.45 | 1.07 | 1.39 | 9.86 | |
NOZ | 0.79 | - | 3.82 | 28.94 | 94.33 | 3.19 | 0.34 | 26.37 | 5.09 | 1.27 | 0.71 | 8.12 | |
OCUG-1 | 8.61 | 2.66 | 3.64 | 122.31 | 27.62 | 11.73 | 18.83 | 37.79 | 24.93 | 5.39 | 3.74 | 3.67 | |
OZ | 7.29 | 0.31 | 9.89 | 53.12 | 132.32 | 5.01 | 25.38 | 54.95 | 8.71 | 0.71 | 2.25 | 47.57 | |
SNU308 | 2.10 | 0.23 | 0.20 | 17.52 | 51.47 | 1.21 | 2.61 | 23.03 | 2.87 | - | 0.81 | 5.73 | |
TGBC1 | 1.06 | 2.99 | 3.94 | 26.63 | 75.96 | 4.78 | 12.90 | 57.30 | 12.75 | 9.97 | 1.62 | 14.45 | |
TGBC2 | 0.70 | 6.54 | 2.86 | 16.29 | 60.75 | 6.23 | 0.58 | 34.57 | 3.86 | 0.53 | 0.53 | 10.22 | |
YoMi | 1.03 | 0.43 | 10.73 | 30.21 | 150.31 | 13.48 | 68.40 | 52.66 | 15.80 | 0.86 | 2.93 | 30.39 | |
% concordance | 33 | 78 | 44 | 100 | 44 | 67 | 22 | 100 | 100 | 11 | 56 | 89 |
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Share and Cite
Scherer, D.; Dávila López, M.; Goeppert, B.; Abrahamsson, S.; González Silos, R.; Nova, I.; Marcelain, K.; Roa, J.C.; Ibberson, D.; Umu, S.U.; et al. RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling. Cancers 2020, 12, 2510. https://doi.org/10.3390/cancers12092510
Scherer D, Dávila López M, Goeppert B, Abrahamsson S, González Silos R, Nova I, Marcelain K, Roa JC, Ibberson D, Umu SU, et al. RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling. Cancers. 2020; 12(9):2510. https://doi.org/10.3390/cancers12092510
Chicago/Turabian StyleScherer, Dominique, Marcela Dávila López, Benjamin Goeppert, Sanna Abrahamsson, Rosa González Silos, Igor Nova, Katherine Marcelain, Juan C. Roa, David Ibberson, Sinan U. Umu, and et al. 2020. "RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling" Cancers 12, no. 9: 2510. https://doi.org/10.3390/cancers12092510