Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
Abstract
:1. Introduction
2. Results and Discussion
2.1. Correlation of RNA-Seq and cDNA Microarrays
2.2. Analysis of the Loss of SOX Genes with RNA-Seq
2.3. Analysis of Further Genes through Transcriptome Analysis
2.4. Discussion of Possible Causes of Gene Loss
2.5. Analysis of Mechanically Sheared RNA-Seq Datasets
3. Materials and Methods
3.1. Cell Lines and Culture Conditions
3.2. Protein Analysis (Western Blotting)
3.3. Analysis of Gene Expression with Quantitative Real-Time PCR (qRT-PCR)
3.4. Transcriptome Analysis with cDNA Microarrays
3.5. Transcriptome Analysis with Total RNA-Seq
3.6. Analysis of the RNA
3.7. Statistical Analysis
3.8. Accession Numbers
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primer | Forward Primer 5′-3′ | Reverse Primer 5′-3′ | Product Size in bp | Melting Peak in °C |
---|---|---|---|---|
GAPDH | TGGGGAAGGTGAAGGTCGGA | TTGATGACAAGCTTCCCGTTC | 207 | 83 |
GAPDH | GGCTCTCCAGAACATCATCCCTGC | GGGTGTCGCTGTTGAAGTCAGAGG | 269 | 88 |
SOX21 | GGAGAACCCCAAGATGCACA | CCGGGAAGGCGAACTTGT | 202 | 89 |
SOX2 | GAACCAGCGCATGGACAGTT | AGCCGTTCATGTAGGTCTGC | 199 | 91 |
SOX3 | GATAAGCCTACCCTTCCCGC | GTGTCCCTACGGGGTTCTTG | 196 | 92 |
SOX4 | CAGCAAACCAACAATGCCGA | GATCTGCGACCACACCATGA | 209 | 93 |
SOX11 | GAGGGCGAATTCATGGCTTG | ATTTTCCAGCGCTTGCCCAG | 199 | 89 |
YAP1 | CCCTCGTTTTGCCATGAACC | ACCATCCTGCTCCAGTGTTG | 286 | 88 |
TAZ | TGGACCAAGTACATGAACCACC | AAATTCTGCTCCTCGGCACA | 278 | 88 |
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Rachinger, N.; Fischer, S.; Böhme, I.; Linck-Paulus, L.; Kuphal, S.; Kappelmann-Fenzl, M.; Bosserhoff, A.K. Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR. Int. J. Mol. Sci. 2021, 22, 9349. https://doi.org/10.3390/ijms22179349
Rachinger N, Fischer S, Böhme I, Linck-Paulus L, Kuphal S, Kappelmann-Fenzl M, Bosserhoff AK. Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR. International Journal of Molecular Sciences. 2021; 22(17):9349. https://doi.org/10.3390/ijms22179349
Chicago/Turabian StyleRachinger, Nicole, Stefan Fischer, Ines Böhme, Lisa Linck-Paulus, Silke Kuphal, Melanie Kappelmann-Fenzl, and Anja K. Bosserhoff. 2021. "Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR" International Journal of Molecular Sciences 22, no. 17: 9349. https://doi.org/10.3390/ijms22179349