Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes

Jin Zhang; Malachi Griffith; Christopher A. Miller; Obi L. Griffith; David H. Spencer; Jason R. Walker; Vincent Magrini; Sean D. McGrath; Amy Ly; Nichole M. Helton; Maria Trissal; Daniel C. Link; Ha X. Dang; David E. Larson; Shashikant Kulkarni; Matthew G. Cordes; Catrina C. Fronick; Robert S. Fulton; Jeffery M. Klco; Elaine R. Mardis; Timothy J. Ley; Richard K. Wilson; Christopher A. Maher

doi:10.1016/j.exphem.2017.07.008

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes

Jin Zhang, Malachi Griffith, Christopher A. Miller, Obi L. Griffith, David H. Spencer, Jason R. Walker, Vincent Magrini, Sean D. McGrath, Amy Ly, Nichole M. Helton, Maria Trissal, Daniel C. Link, Ha X. Dang, David E. Larson, Shashikant Kulkarni, Matthew G. Cordes, Catrina C. Fronick, Robert S. Fulton, Jeffery M. Klco, Elaine R. MardisTimothy J. Ley, Richard K. Wilson, Christopher A. Maher

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10 Scopus citations

Abstract

To detect diverse and novel RNA species comprehensively, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA-based analyses.

Original language	English
Pages (from-to)	19-33
Number of pages	15
Journal	Experimental Hematology
Volume	55
DOIs	https://doi.org/10.1016/j.exphem.2017.07.008
State	Published - Nov 2017

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Zhang, J., Griffith, M., Miller, C. A., Griffith, O. L., Spencer, D. H., Walker, J. R., Magrini, V., McGrath, S. D., Ly, A., Helton, N. M., Trissal, M., Link, D. C., Dang, H. X., Larson, D. E., Kulkarni, S., Cordes, M. G., Fronick, C. C., Fulton, R. S., Klco, J. M., ... Maher, C. A. (2017). Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. Experimental Hematology, 55, 19-33. https://doi.org/10.1016/j.exphem.2017.07.008

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title = "Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes",

abstract = "To detect diverse and novel RNA species comprehensively, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA-based analyses.",

author = "Jin Zhang and Malachi Griffith and Miller, {Christopher A.} and Griffith, {Obi L.} and Spencer, {David H.} and Walker, {Jason R.} and Vincent Magrini and McGrath, {Sean D.} and Amy Ly and Helton, {Nichole M.} and Maria Trissal and Link, {Daniel C.} and Dang, {Ha X.} and Larson, {David E.} and Shashikant Kulkarni and Cordes, {Matthew G.} and Fronick, {Catrina C.} and Fulton, {Robert S.} and Klco, {Jeffery M.} and Mardis, {Elaine R.} and Ley, {Timothy J.} and Wilson, {Richard K.} and Maher, {Christopher A.}",

note = "Publisher Copyright: {\textcopyright} 2017 ISEH – Society for Hematology and Stem Cells",

year = "2017",

month = nov,

doi = "10.1016/j.exphem.2017.07.008",

language = "English",

volume = "55",

pages = "19--33",

journal = "Experimental Hematology",

issn = "0301-472X",

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Zhang, J , Griffith, M , Miller, CA , Griffith, OL , Spencer, DH, Walker, JR, Magrini, V, McGrath, SD, Ly, A, Helton, NM, Trissal, M, Link, DC, Dang, HX, Larson, DE, Kulkarni, S, Cordes, MG, Fronick, CC, Fulton, RS, Klco, JM, Mardis, ER, Ley, TJ, Wilson, RK & Maher, CA 2017, 'Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes', Experimental Hematology, vol. 55, pp. 19-33. https://doi.org/10.1016/j.exphem.2017.07.008

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T1 - Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes

AU - Zhang, Jin

AU - Griffith, Malachi

AU - Miller, Christopher A.

AU - Griffith, Obi L.

AU - Spencer, David H.

AU - Walker, Jason R.

AU - Magrini, Vincent

AU - McGrath, Sean D.

AU - Ly, Amy

AU - Helton, Nichole M.

AU - Trissal, Maria

AU - Link, Daniel C.

AU - Dang, Ha X.

AU - Larson, David E.

AU - Kulkarni, Shashikant

AU - Cordes, Matthew G.

AU - Fronick, Catrina C.

AU - Fulton, Robert S.

AU - Klco, Jeffery M.

AU - Mardis, Elaine R.

AU - Ley, Timothy J.

AU - Wilson, Richard K.

AU - Maher, Christopher A.

PY - 2017/11

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N2 - To detect diverse and novel RNA species comprehensively, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA-based analyses.

AB - To detect diverse and novel RNA species comprehensively, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA-based analyses.

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EP - 33

JO - Experimental Hematology

JF - Experimental Hematology

ER -

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes

Abstract

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