tRNA fragments 2015

Please cite:

Telonis, AG, Loher, P, Honda, S, Jing, Y, Palazzo, J, Kirino, Y, Rigoutsos, I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015;6 (28):24797-822. doi: 10.18632/oncotarget.4695. PubMed PMID:26325506 PubMed Central PMC4694795.

The following links below allow you to download the data matrices used for the analysis in the paper:

1. LCL (Lymphoblastoid cell line) dataset, comprised from 482 samples originating from subjects from 5 different populations (CEU, FIN, GBR, TSI, YRI), originally described in [2]. Click the button below to download.
   Download LCL dataset
   892 Downloads


2. BRCA (Breast Cancer) dataset, comprised from 311 samples (16 normal and 294 tumor), originally described in [3]. Click the button below to download.
   Download BRCA dataset
   891 Downloads


3. Argonaute HITS-CLIP-seq dataset from 3 breast cancer model cell lines, each one analyzed in triplicate, originally described in [4]. Click the button below to download.
   Download Ago dataset
   882 Downloads

References

1. Telonis, AG, Loher, P, Honda, S, Jing, Y, Palazzo, J, Kirino, Y, Rigoutsos, I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015;6 (28):24797-822. doi: 10.18632/oncotarget.4695. PubMed PMID:26325506 PubMed Central PMC4694795.
2. Pillai, MM, Gillen, AE, Yamamoto, TM, Kline, E, Brown, J, Flory, K, Hesselberth, JR, Kabos, P. HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer. Breast Cancer Res Treat. 2014;146 (1):85-97. doi: 10.1007/s10549-014-3004-9. PubMed PMID:24906430 PubMed Central PMC4115274.
3. Lappalainen, T, Sammeth, M, Friedländer, MR, 't Hoen, PA, Monlong, J, Rivas, MA, Gonzàlez-Porta, M, Kurbatova, N, Griebel, T, Ferreira, PG, Barann, M, Wieland, T, Greger, L, van Iterson, M, Almlöf, J, Ribeca, P, Pulyakhina, I, Esser, D, Giger, T, Tikhonov, A, Sultan, M, Bertier, G, MacArthur, DG, Lek, M, Lizano, E, Buermans, HP, Padioleau, I, Schwarzmayr, T, Karlberg, O, Ongen, H, Kilpinen, H, Beltran, S, Gut, M, Kahlem, K, Amstislavskiy, V, Stegle, O, Pirinen, M, Montgomery, SB, Donnelly, P, McCarthy, MI, Flicek, P, Strom, TM, Geuvadis Consortium, Lehrach, H, Schreiber, S, Sudbrak, R, Carracedo, A, Antonarakis, SE, Häsler, R, Syvänen, AC, van Ommen, GJ, Brazma, A, Meitinger, T, Rosenstiel, P, Guigó, R, Gut, IG, Estivill, X, Dermitzakis, ET. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501 (7468):506-11. doi: 10.1038/nature12531. PubMed PMID:24037378 PubMed Central PMC3918453.
4. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490 (7418):61-70. doi: 10.1038/nature11412. PubMed PMID:23000897 PubMed Central PMC3465532.

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