Page 95 - 2021_10-Haematologica-web

BLUEPRINT hematopoietic transcriptomes atlas
5. Kapranov P, Cawley SE, Drenkow J, et al. Large-scale transcriptional activity in chro- mosomes 21 and 22. Science. 2002; 296(5569):916-919.
6. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008;24(3):133-141.
7. Pertea M, Pertea GM, Antonescu CM, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290-295.
8. Adams D, Altucci L, Antonarakis SE, et al. BLUEPRINT to decode the epigenetic signa- ture written in blood. Nat Biotechnol. 2012; 30(3):224-226.
9. Stunnenberg HG; International Human Epigenome Consortium, Hirst M. The International Human Epigenome Consortium: a blueprint for scientific collab- oration and discovery. Cell. 2016;1 67(5):1145-1149.
10. Chen L, Kostadima M, Martens JHA, et al. Transcriptional diversity during lineage commitment of human blood progenitors. Science. 2014;345(6204):1251033.
11. Chen L, Ge B, Casale FP, et al. Genetic driv- ers of epigenetic and transcriptional varia- tion in human immune cells. Cell. 2016;167(5):1398-1414.
12. Turro E, Su SY, Goncalves A, et al. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol. 2011;12(2):R13.
13. Turro E, Astle WJ, Tavare S. Flexible analysis of RNA-seq data using mixed effects mod- els. Bioinformatics. 2014;30(2):180-188.
14. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient align- ment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
15. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-2079.
16. Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562-578.
17. Harrow J, Frankish A, Gonzalez JM, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22(9):1760-1774.
18. Rosenbloom KR, Armstrong J, Barber GP, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015;43 (Database issue):D670-681.
19. Lawrence M, Huber W, Pages H, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9(8):e1003118.
20. Wang L, Park HJ, Dasari S, et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41(6):e74.
21.Yanai I, Benjamin H, Shmoish M, et al. Genome-wide midrange transcription pro- files reveal expression level relationships in human tissue specification. Bioinformatics. 2005;21(5):650-659.
22.Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in verte- brate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034-1050.
23. Genotype-Tissue Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013;45(6):580-585.
24. Mele M, Ferreira PG, Reverter F, et al. Human genomics. The human transcrip- tome across tissues and individuals. Science. 2015;348(6235):660-665.
2007;29(3):288-299.
39.Dobin A, Davis CA, Schlesinger F, et al.
STAR: ultrafast universal RNA-seq aligner.
Bioinformatics. 2013;29(1):15-21.
40. O'Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids
Res. 2016;44(D1):D733-745.
41. Li Z, Huang C, Bao C, et al. Exon-intron cir-
cular RNAs regulate transcription in the
nucleus. Nat Struct Mol Biol. 2015;22(3):256- human mitochondrial transcriptome. Cell. 264.
25. Mercer TR, Neph S, Dinger ME, et al. The
2011;146(4):645-658.
26. Kozomara A, Griffiths-Jones S. miRBase:
annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(Database issue):D68-73.
27. Ru Y, Kechris KJ, Tabakoff B, et al. The multiMiR R package and database: integra- tion of microRNA-target interactions along with their disease and drug associations. Nucleic Acids Res. 2014;42(17):e133.
28. Das A, Ganesh K, Khanna S, Sen CK, Roy S. Engulfment of apoptotic cells by macrophages: a role of microRNA-21 in the resolution of wound inflammation. J Immunol. 2014;192(3):1120-1129.
29.Wang Z, Brandt S, Medeiros A, et al. MicroRNA 21 is a homeostatic regulator of macrophage polarization and prevents prostaglandin E2-mediated M2 generation. PLoS One. 2015;10(2):e0115855.
30. Yu HR, Hsu TY, Huang HC, et al. Comparison of the functional microRNA expression in immune cell subsets of neonates and adults. Front Immunol. 2016; 7:615.
31. Ghisi M, Corradin A, Basso K, et al. Modulation of microRNA expression in human T-cell development: targeting of NOTCH3 by miR-150. Blood. 2011; 117(26):7053-7062.
32.Opalinska JB, Bersenev A, Zhang Z, et al. MicroRNA expression in maturing murine megakaryocytes. Blood. 2010;116(23):e128- 138.
33. Ple H, Landry P, Benham A, et al. The reper- toire and features of human platelet microRNAs. PLoS One. 2012;7(12):e50746.
34. Bazzini AA, Lee MT, Giraldez AJ. Ribosome profiling shows that miR-430 reduces trans- lation before causing mRNA decay in zebrafish. Science. 2012;336(6078):233-237.
35. Cheng J, Kapranov P, Drenkow J, et al. Transcriptional maps of 10 human chromo- somes at 5-nucleotide resolution. Science. 2005;308(5725):1149-1154.
36. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447(7146):799-816.
37. Flynn RA, Chang HY. Long noncoding RNAs in cell-fate programming and repro- gramming. Cell Stem Cell. 2014;14(6):752- 761.
38. Taft RJ, Pheasant M, Mattick JS. The rela- tionship between non-protein-coding DNA and eukaryotic complexity. Bioessays.
42. Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013; 495(7441):384-388.
43.Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333-338.
44. Westholm JO, Miura P, Olson S, et al. Genome-wide analysis of Drosophila circu- lar RNAs reveals their structural and sequence properties and age-dependent neu- ral accumulation. Cell Rep. 2014;9(5):1966- 1980.
45. Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 2015; 16:4.
46. Zhang XO, Dong R, Zhang Y, et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26(9):1277-1287.
47. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental duplications: organi- zation and impact within the current human genome project assembly. Genome Res. 2001;11(6):1005-1017.
48. Starke S, Jost I, Rossbach O, et al. Exon cir- cularization requires canonical splice signals. Cell Rep. 2015;10(1):103-111.
49. Glazar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014;20(11):1666-1670.
50. Rybak-Wolf A, Stottmeister C, Glazar P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58(5):870-885.
51. Alhasan AA, Izuogu OG, Al-Balool HH, et al. Circular RNA enrichment in platelets is a signature of transcriptome degradation. Blood. 2016;127(9):e1-e11.
52. Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. circRNA biogenesis competes with pre- mRNA splicing. Mol Cell. 2014;56(1):55-66.
53. Schwarzer A, Emmrich S, Schmidt F, et al. The non-coding RNA landscape of human hematopoiesis and leukemia. Nat Commun. 2017;8(1):218.
54. Alvarez-Dominguez JR, Lodish HF. Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis. Blood. 2017;130(18):1965- 1975.
55. Lorenzi L, Chiu H-S, Cobos FA, et al. The RNA Atlas, a single nucleotide resolution map of the human transcriptome. bioRxiv. 2019 Oct 17. [Epub ahead of print].
haematologica | 2021; 106(10)
2623