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Somatic mutations and cell id linked by transcriptome genotyping


Sperling, A.S., Gibson, C.J. and Ebert, B.L. Genetics of myelodysplastic syndrome: from clonal hematopoiesis to secondary leukemia. Nat. Rev. Most cancers 17, 5-19 (2017).


Landau, D.A. et al. The evolving panorama of power lymphocytic leukemia handled with ibrutinib is a focused remedy. Nat. Widespread. eight, 2185 (2017).


Burger, J.A. et al. Clonal evolution in sufferers with power lymphocytic leukemia creating resistance to BTK inhibition. Nat. Widespread. 7, 11589 (2016).


Landau, D.A. et al. Evolution and influence of subclonal mutations in power lymphocytic leukemia. Cell 152, 714-726 (2013).


Landau, D.A. et al. Mutations resulting in the LLC and their development in development and relapse. Nature 526, 525-530 (2015).


Nangalia, J. et al. Somatic mutations of CALR in myeloproliferative neoplasms with non-mutated JAK2. N. Engl. J. Med. 369, 2391-2405 (2013).


Klampfl, T. et al. Somatic mutations of calreticulin in myeloproliferative neoplasms. N. Engl. J. Med. 369, 2379-2390 (2013).


Giustacchini, A. et al. The unicellular transcriptomic reveals the distinct molecular signatures of stem cells in power myeloid leukemia. Nat. Med. 23, 692-702 (2017).


Cheow, L. F. et al. Unicellular multimodal profiling reveals mobile epigenetic heterogeneity. Nat. Strategies 13, 833-836 (2016).


Macosko, E. Z. et al. Expression profile extremely parallel to the genome scale of particular person cells utilizing nanoliter droplets. Cell 161, 1202-1214 (2015).


Klein, A.M. et al. Droplet barcode for the single-cell transcriptome utilized to embryonic stem cells. Cell 161, 1187-1201 (2015).


Elf, S. et al. Mutant calreticulin requires each its mutant C-terminal finish and its thrombopoietin receptor for oncogenic transformation. Most cancers Discov. 6, 368-381 (2016).


Defour, J.P., Chachoua, I., Pecquet, C. and Constantinescu, S. N. Oncogenic activation of the MPL / thrombopoietin receptor by 17 mutations at W515: implications for myeloproliferative neoplasms. Leukemia 30, 1214-1216 (2016).


Kollmann, Okay. et al. A brand new signaling display screen demonstrates that CALR mutations activate important MAPK signaling and facilitate the differentiation of megakaryocytes. Leukemia 31, 934-944 (2017).


Marty, C. et al. Mutants of calreticulin in mice induce MPL-dependent thrombocytosis with frequent development to myelofibrosis. Blood 127, 1317-1324 (2016).


Nivarthi, H. et al. The thrombopoietin receptor is required for the oncogenic perform of CALR mutants. Leukemia 30, 1759-1763 (2016).


Satija, R., Farrell, J.A., Gennert, D., Schier, A.F. and Regev, A. Spatial reconstitution of single-gene expression information. Nat. Biotechnol. 33, 495-502 (2015).


Stuart, T. et al. Full integration of single-cell information. Cell 177, 1888-1902 (2019).


Lopez, R., Regier, J., Cole, M.B., Jordan, M.I. and Yosef, N. Deep generative modeling for the unicellular transcriptomic. Nat. Strategies 15, 1053-1058 (2018).


Trapnell, C. et al. The dynamics and regulators of choices in regards to the destiny of cells are revealed by the pseudotemporal order of single cells. Nat. Biotechnol. 32, 381-386 (2014).


Farrell, J.A. et al. Monocellular reconstruction of developmental trajectories throughout zebrafish embryogenesis. Science 360, eaar313 (2018).


Chen, E. et al. The distinct scientific phenotypes related to JAK2V617F replicate STAT1 differential signaling. Most cancers Cell 18, 524-535 (2010).


Rampal, R. et al. Built-in genomic evaluation illustrates the central position of JAK – STAT pathway activation within the pathogenesis of myeloproliferative neoplasm. Blood 123, e123 to e133 (2014).


Tirosh, I. et al. Dissect the multicellular ecosystem of metastatic melanoma by unicellular RNA-seq. Science 352, 189-196 (2016).


Georgantas, R. W. III et al. A microarray and serial evaluation of gene expression analyzes determine identified and novel transcripts overexpressed in hematopoietic stem cells. Most cancers Res. 64, 4434-4441 (2004).


Velten, L. et al. The dedication of the hematopoietic stem cell line to people is a steady course of. Nat. Cell Biol. 19, 271-281 (2017).


Hetz, C. and Papa, F. R. The unfolded protein response and management of cell destiny. Mol. Cell 69, 169-181 (2018).


Pronier, E. et al. Concentrating on the CALR interactome in myeloproliferative neoplasms. JCI Perception three, e122703 (2018).


Lau, W.W., Hannah, R., Inexperienced, A.R. and Göttgens, B. The JAK-STAT signaling pathway is differentially activated in ETR sufferers constructive for the CALR-positive gene in comparison with the constructive JAK2V617F ETJ affected person. Blood 125, 1679-1681 (2015).


Shivarov, V., Ivanova, M. & Tiu, R. V. Mutated calreticulin retains the structurally disordered C-terminus that may not bind to Ca2 +: some mechanistic and therapeutic implications. Blood Most cancers, J. four, e185 (2014).


Zini, R. et al. The CALR mutational standing identifies totally different subtypes of important thrombocythemia illnesses with distinct expression patterns. Blood Most cancers, J. 7, 638 (2017).


Wu, J. et al. ATF6α optimizes long-term endoplasmic reticulum perform to guard cells from power stress. Dev. Cell 13, 351-364 (2007).


van Galen, P. et al. The unfolded protein response governs the integrity of the hematopoietic stem cell pool underneath stress. Nature 510, 268-272 (2014).


Lee, A.H., Iwakoshi, N.N. and Glimcher, L.H. XBP-1 regulate a subset of resident endoplasmic reticulum chaperone genes within the unfolded protein response. Mol. Cell. Biol. 23, 7448-7459 (2003).


Cubillos-Ruiz, J.R. et al. The ER XBP1 stress sensor controls anti-tumor immunity by disrupting dendritic cell homeostasis. Cell 161, 1527-1538 (2015).


Yoshida, H., Matsui, T., A. Yamamoto, A. Okada, T. and Okay. Mori, Okay. The mRNA of XBP1 is induced by ATF6 and spliced ​​by IRE1 in response to ER stress to supply an especially lively transcription issue. Cell 107, 881-891 (2001).


Luo, J.L., Kamata, H. and Karin, M.IKK / NF-κB Signaling: balancing life and loss of life – a brand new strategy to most cancers remedy. J. Clin. Make investments. 115, 2625-2632 (2005).


Stein, S.J. and Baldwin, A. S. Deletion of the NF-KB p65 / RelA subunit within the hematopoietic compartment results in abnormalities in hematopoietic stem cell perform. Blood 121, 5015-5024 (2013).


Abu-Zeinah, G. et al. Myeloproliferative neoplasm (MPN) driver mutations are enriched throughout hematopoietic stem cell differentiation in patterns correlated with scientific phenotype and response to remedy. Blood 132, 4317 (2018).


Castro-Malaspina, H., Rabellino, E.M., Yen, A., Nachman, R.L. & Moore, MA. Stimulation by human megakaryocytes of the proliferation of bone marrow fibroblasts. Blood 57, 781-787 (1981).


Ciurea, S. O. et al. Pivotal contributions of megakaryocytes to the biology of idiopathic myelofibrosis. Blood 110, 986-993 (2007).


Terui, T. et al. The manufacturing of remodeling development issue beta in acute megakaryoblastic leukemia and its attainable implications in myelofibrosis. Blood 75, 1540-1548 (1990).


Obeng, E.A. et al. Physiological expression of Sf3b1
Okay700E causes alteration of erythropoiesis, aberrant splicing and sensitivity to therapeutic modulation of the splice osome. Most cancers Cell 30, 404-417 (2016).


Saikia, M. et al. Sequencing of multiplexed amplicons and simultaneous transcriptome profiling in single cells. Nat. Strategies 16, 59-62 (2019).


Hill, A.J. et al. On the design of single-cell molecular screens based mostly on CRISPR. Nat. Strategies 15, 271-274 (2018).


Kleppe, M. et al. The twin concentrating on of oncogenic activation and inflammatory signaling will increase the therapeutic efficacy in myeloproliferative neoplasms. Most cancers Cell 33, 785-787 (2018).


Mu, P. et al. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53 and RB1 poor prostate cancers. Science 355, 84-88 (2017).


Suva, M.L. et al. Rebuild and reprogram the tumor propagation potential of glioblastoma-like stem cells. Cell 157, 580-594 (2014).


Geyer, J. T. et al. Persistent oligomonocytic myelomonocytic leukemia (power myelomonocytic leukemia with out absolute monocytosis) has a clinico-pathological and mutational profile just like that of classical power myelomonocytic leukemia. Mod. Pathol. 30, 1213-1222 (2017).


Butler, A., Hoffman, P., Smibert, P., Papalexi, E. and Satija, R. Integration of unicellular transcriptomic information underneath totally different situations, applied sciences and species. Nat. Biotechnol. 36, 411-420 (2018).


Bolker, B.M. et al. Generalized Linear Combined Fashions: A Sensible Information to Ecology and Evolution. Traits Ecol. Evol. 24, 127-135 (2009).


Liaw, A. & Wiener, M. Classification and regression by randomForest. R Information 2, 18-22 (2002).


Reinius, B. & Sandberg, R. Monallelic random expression of autosomal genes: stochastic transcription and allelic stage regulation. Nat. Rev. Broom. 16, 653-664 (2015).


Zheng, G. X. Y. et al. Massively parallel digital transcription profile of particular person cells. Nat. Widespread. eight, 14049 (2017).


Ntranos, V., Yi, L., Melsted, P. and Pachter, L. A Discriminant Studying Strategy for the Evaluation of Differential Expression for Monocellular RNA. Nat. Strategies 16, 163-166 (2019).


Reimand, J. et al. g: Profiler – an internet server for the practical interpretation of gene lists (replace 2016). Nucleic Acids Res. 44, W83 – W89 (2016).


Rhee, J.Okay., Lee, S., Park, W. Y., Kim, Y.H. and Kim, T.M. An allelic imbalance of somatic mutations in most cancers genomes and transcriptomes. Sci. Rep. 7, 1653 (2017).


Li, H. et al. The format of sequence / map alignment and SAMtools. Bioinformatics 25, 2078-2079 (2009).


Forbes, S.A. et al. COSMIC: Somatic most cancers genetics with excessive decision. Nucleic Acids Res. 45, D777 to D783 (2017).


Vogelstein, B. et al. Landscapes of the most cancers genome. Science 339, 1546-1558 (2013).


Bailey, M.H. et al. Full characterization of the genes and mutations of the most cancers driver. Cell 174, 1034-1035 (2018).


Durinck, S., Spellman, P. T., Birney, E. & Huber, W. Mapping identifiers for integrating genomic information units to the R / Biomonductor biomaRt package deal. Nat. Protocols four, 1184-1191 (2009).


Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094-3100 (2018).

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