@article{3ec74eb03a47445a9eb6181367dde715,
title = "Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas",
abstract = "Transcriptional profiling of hematopoietic cell subpopulations has helped to characterize the developmental stages of the hematopoietic system and the molecular bases of malignant and non-malignant blood diseases. Previously, only the genes targeted by expression microarrays could be profiled genome-wide. High-throughput RNA sequencing, however, encompasses a broader repertoire of RNA molecules, without restriction to previously annotated genes. We analyzed the BLUEPRINT consortium RNA-sequencing data for mature hematopoietic cell types. The data comprised 90 total RNA-sequencing samples, each composed of one of 27 cell types, and 32 small RNA-sequencing samples, each composed of one of 11 cell types. We estimated gene and isoform expression levels for each cell type using existing annotations from Ensembl. We then used guided transcriptome assembly to discover unannotated transcripts. We identified hundreds of novel non-coding RNA genes and showed that the majority have cell type-dependent expression. We also characterized the expression of circular RNA and found that these are also cell type-specific. These analyses refine the active transcriptional landscape of mature hematopoietic cells, highlight abundant genes and transcriptional isoforms for each blood cell type, and provide a valuable resource for researchers of hematologic development and diseases. Finally, we made the data accessible via a web-based interface: https://blueprint.haem.cam.ac.uk/bloodatlas/.",
author = "Luigi Grassi and Izuogu, {Osagie G.} and Jorge, {Natasha A.N.} and Denis Seyres and Mariona Bustamante and Frances Burden and Samantha Farrow and Neda Farahi and Martin, {Fergal J.} and Adam Frankish and Mudge, {Jonathan M.} and Myrto Kostadima and Romina Petersen and Lambourne, {John J.} and Sophia Rowlston and Enca Martin-Rendon and Laura Clarke and Kate Downes and Xavier Estivill and Paul Flicek and Martens, {Joost H.A.} and Yaspo, {Marie Laure} and Stunnenberg, {Hendrik G.} and Ouwehand, {Willem H.} and Fabio Passetti and Ernest Turro and Mattia Frontini",
note = "Funding Information: The work was funded by a grant from the European Commission 7th Framework Program (FP7/2007-2013, grant 282510, BLUEPRINT) to XE, PF, JHAM, MY, HGS and WHO. WHO is an NIHR senior investigator and receives funding from Bristol-Myers Squibb, the British Heart Foundation, the Medical Research Council and the NIHR. OGI, FJM, AF, JMM, LC and PF are funded by the Wellcome Trust (WT108749/Z/15/Z) with additional funding for specific project components such as GENCODE from the National Human Genome Research Institute of the National Institutes of Health (2U41HG007234). The content of this manuscript is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. KD is a HSST trainee supported by NHS Health Education England. NF is funded by the NIHR Cambridge Biomedical Research Centre. FP is supported by the Funda{\c c}{\~a}o Carlos Chagas Filho de Amparo {\`a} Pesquisado Estado do Rio de Janeiro (FAPERJ; E-26/203.229/2016). NANJ is a recipient of a scholarship from the Coordena{\c c}{\~a}o de Aperfei{\c c}oamento de Pessoal de N{\'i}vel Superior - Brasil (CAPES; Finance Code 001). The work by DS was supported in part by an Isaac Newton fellowship to MF. MF is supported by the British Heart Foundation (FS/18/53/33863). Publisher Copyright: {\textcopyright} 2021 Ferrata Storti Foundation",
year = "2021",
month = oct,
doi = "10.3324/haematol.2019.238147",
language = "English",
volume = "106",
pages = "2613--2623",
journal = "Haematologica",
issn = "0390-6078",
publisher = "Ferrata Storti Foundation",
number = "10",
}