Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas.
Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas.
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BLUEPRINT造血转录组图谱中的细胞类型特异性新型长非编码RNA和环状RNA。
DOI：
10.3324/haematol.2019.238147
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发表时间：
2021-10-01
期刊：
影响因子：
10.1
通讯作者：
Frontini M
中科院分区：
文献类型：
--
作者：
Grassi L;Izuogu OG;Jorge NAN;Seyres D;Bustamante M;Burden F;Farrow S;Farahi N;Martin FJ;Frankish A;Mudge JM;Kostadima M;Petersen R;Lambourne JJ;Rowlston S;Martin-Rendon E;Clarke L;Downes K;Estivill X;Flicek P;Martens JHA;Yaspo ML;Stunnenberg HG;Ouwehand WH;Passetti F;Turro E;Frontini M
造血细胞亚群的转录谱分析有助于表征造血系统的发育阶段以及恶性和非恶性血液疾病的分子基础。以前，只有表达微阵列靶向的基因可以进行全基因组分析。然而，高通量RNA测序涵盖了更广泛的RNA分子库，而不限于先前注释的基因。我们分析了成熟造血细胞类型的BLUEPRINT联盟RNA测序数据。数据包括90个总RNA测序样品，每个样品由27种细胞类型中的一种组成，以及32个小RNA测序样品，每个样品由11种细胞类型中的一种组成。我们使用Ensembl的现有注释估计了每种细胞类型的基因和亚型表达水平。然后，我们使用引导转录组组装来发现未注释的转录本。我们鉴定了数百个新的非编码RNA基因，并表明大多数具有细胞类型依赖性表达。我们还表征了环状RNA的表达，并发现这些也是细胞类型特异性的。这些分析完善了成熟造血细胞的活跃转录景观，突出了每种血细胞类型的丰富基因和转录亚型，并为血液发育和疾病的研究人员提供了宝贵的资源。最后，我们通过一个基于Web的界面访问数据：https://blueprint.haem.cam.ac.uk/bloodatlas/。
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/.
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影响因子：
30.5
作者：
Laurenti E;Doulatov S;Zandi S;Plumb I;Chen J;April C;Fan JB;Dick JE
通讯作者：
Dick JE
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
56.9
作者：
Cheng, J;Kapranov, P;Gingeras, TR
通讯作者：
Gingeras, TR
DOI：
10.1126/science.1251033
发表时间：
2014-09-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Chen L;Kostadima M;Martens JHA;Canu G;Garcia SP;Turro E;Downes K;Macaulay IC;Bielczyk-Maczynska E;Coe S;Farrow S;Poudel P;Burden F;Jansen SBG;Astle WJ;Attwood A;Bariana T;de Bono B;Breschi A;Chambers JC;Consortium B;Choudry FA;Clarke L;Coupland P;van der Ent M;Erber WN;Jansen JH;Favier R;Fenech ME;Foad N;Freson K;van Geet C;Gomez K;Guigo R;Hampshire D;Kelly AM;Kerstens HHD;Kooner JS;Laffan M;Lentaigne C;Labalette C;Martin T;Meacham S;Mumford A;Nürnberg S;Palumbo E;van der Reijden BA;Richardson D;Sammut SJ;Slodkowicz G;Tamuri AU;Vasquez L;Voss K;Watt S;Westbury S;Flicek P;Loos R;Goldman N;Bertone P;Read RJ;Richardson S;Cvejic A;Soranzo N;Ouwehand WH;Stunnenberg HG;Frontini M;Rendon A
通讯作者：
Rendon A
影响因子：
23.9
作者：
Flynn, Ryan A.;Chang, Howard Y.
通讯作者：
Chang, Howard Y.