Generation of an isoform-level transcriptome atlas of macrophage activation.
Generation of an isoform-level transcriptome atlas of macrophage activation.
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DOI：
10.1016/j.jbc.2021.100784
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发表时间：
2021-01
期刊：
影响因子：
--
通讯作者：
Vollmers C
中科院分区：
文献类型：
--
作者：
Vollmers AC;Mekonen HE;Campos S;Carpenter S;Vollmers C
RNA-seq通常用于测量响应于细胞扰动的基因表达变化。在一些扰动后上调或下调的基因被指定为感兴趣的基因，然后选择它们表达最多的同种型用于后续实验。然而，由于需要将RNA分子片段化，RNA-seq捕获基因亚型及其表达模式的能力有限。这种异构体特异性数据的缺乏意味着将基于不完整的、非组织特异性的或不提供关于表达水平的关键信息的注释数据库来选择异构体。因此，少数或不存在的异构体可能被选择用于随访，导致宝贵的资源和时间的损失。因此，非常需要全面鉴定基因同种型沿着其相应的表达水平。使用基于长读纳米孔的R2 C2方法，该方法不使RNA分子片段化，我们生成了巨噬细胞活化的同种型水平转录组图谱，其鉴定了原代人单核细胞衍生的巨噬细胞中的全长同种型。巨噬细胞是关键的先天性免疫细胞，对于通过病原体相关分子模式与toll样受体的结合识别病原体至关重要，最终引发宿主防御途径。我们表征了静息和toll样受体激活的单核细胞源性巨噬细胞中大多数中度至高度表达基因的亚型，鉴定了不同条件下差异表达的亚型，并通过RT-qPCR验证了这些亚型。我们将这些数据编译到UCSC基因组浏览器（https：//genome.ucsc.edu/s/vollmers/IAMA）中的用户友好数据门户中。我们的图谱代表了先天免疫研究的宝贵资源，为原代人类巨噬细胞提供了前所未有的同种型信息。
RNA-seq is routinely used to measure gene expression changes in response to cell perturbation. Genes upregulated or downregulated following some perturbation are designated as genes of interest, and their most expressed isoform(s) would then be selected for follow-up experimentation. However, because of its need to fragment RNA molecules, RNA-seq is limited in its ability to capture gene isoforms and their expression patterns. This lack of isoform-specific data means that isoforms would be selected based on annotation databases that are incomplete, not tissue specific, or do not provide key information on expression levels. As a result, minority or nonexistent isoforms might be selected for follow-up, leading to loss in valuable resources and time. There is therefore a great need to comprehensively identify gene isoforms along with their corresponding levels of expression. Using the long-read nanopore-based R2C2 method, which does not fragment RNA molecules, we generated an Isoform-level transcriptome Atlas of Macrophage Activation that identifies full-length isoforms in primary human monocyte-derived macrophages. Macrophages are critical innate immune cells important for recognizing pathogens through binding of pathogen-associated molecular patterns to toll-like receptors, culminating in the initiation of host defense pathways. We characterized isoforms for most moderately-to-highly expressed genes in resting and toll-like receptor–activated monocyte-derived macrophages, identified isoforms differentially expressed between conditions, and validated these isoforms by RT-qPCR. We compiled these data into a user-friendly data portal within the UCSC Genome Browser (https://genome.ucsc.edu/s/vollmers/IAMA). Our atlas represents a valuable resource for innate immune research, providing unprecedented isoform information for primary human macrophages.
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影响因子：
64.8
作者：
Harris CR;Millman KJ;van der Walt SJ;Gommers R;Virtanen P;Cournapeau D;Wieser E;Taylor J;Berg S;Smith NJ;Kern R;Picus M;Hoyer S;van Kerkwijk MH;Brett M;Haldane A;Del Río JF;Wiebe M;Peterson P;Gérard-Marchant P;Sheppard K;Reddy T;Weckesser W;Abbasi H;Gohlke C;Oliphant TE
通讯作者：
Oliphant TE
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
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
DOI：
10.1126/science.1240925
发表时间：
2013-08-16
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Carpenter S;Aiello D;Atianand MK;Ricci EP;Gandhi P;Hall LL;Byron M;Monks B;Henry-Bezy M;Lawrence JB;O'Neill LA;Moore MJ;Caffrey DR;Fitzgerald KA
通讯作者：
Fitzgerald KA
影响因子：
7
作者：
Cole, Charles;Byrne, Ashley;Vollmers, Christopher
通讯作者：
Vollmers, Christopher