Transcriptional Atlas of Human Brain Development

人脑发育转录图谱

• 批准号: 7941722
• 负责人: JAMES A KNOWLES
• 金额: $ 394.65万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7941722
• 关键词: Address; Adolescent Development; Affect; Age; Alternative Splicing; Amygdaloid structure; Area; Atlases; Brain; Brain Diseases; Brain region; Cells; Cerebellum; Collaborations; Communication; Communities; Complex; Corpus striatum structure; DNA; DNA Fingerprinting; Data; Detection; Development; Disease; Female; Funding; Gender; Gene Expression; Generations; Genes; Genetic Risk; Genetic Transcription; Genetic Variation; Goals; Hippocampus (Brain); Human; Inferior; Informatics; Knowledge; Laboratories; Length; Life; Maps; Measures; Medial; Mental disorders; Methylation; Modeling; National Institute of Mental Health; Neurosciences Research; Occipital lobe; Online Systems; Pattern; Poly(A)+ RNA; Prefrontal Cortex; RNA; Reading; Research; Research Infrastructure; Resources; Rest; Risk; Sampling; Scientist; Small RNA; Specificity; Technology; Temporal Lobe; Time; Tissues; Transcript; United States National Institutes of Health; Ventral Striatum; area striata; design; follow-up; frontal lobe; male; meetings; nonhuman primate; novel; postnatal; prenatal; programs; public health relevance; repository; response; skills

DESCRIPTION (provided by applicant): We will create a transcriptional atlas of the developing human brain, including novel transcripts and regional expression patterns that can be followed up subsequently with histochemical mapping for cellular specificity. These data will be made available to the research community at-large via an easy-to-use, web-based informatics framework. To accomplish these goals, we will purify RNA and DNA from 3 male and 3 female post-mortem brains at the approximate ages of 25 weeks, 2 months, 1year, 2.5 years, 7 years, 13 -19 years and 20-30 years. For the 25 week brains, we will sample Dorsolateral Prefrontal Cortex (DLPFC), Orbital Frontal Cortex (OFC), Inferior Temporal Cortex (ITC) and Hippocampus (HIP). The rest of the time points will add Occipital Cortex (OC), cerebellum (CB) and striatum (STR), for a total of 276 brain samples. We will profile DNA from these 276 samples with 1 million SNPs (Human1MDuo array) and will determine methylation patterns with an Illumina Infinium array. RNA from these 276 samples will be used to determine regional expression pattern, identify novel genes and alternative transcripts using RNA-Seq. Each poly-A RNA sample will be sequenced with 45 million reads to provide detection at 1 copy/cell (15%). 30 million of these reads will be 72 bp X 2 paired-end and 15 million reads will be 150+125 bp paired-end to provide the maximal information on alternative splicing. We will also sequence small RNA molecules from each sample using 15 million 36 bp strand specific single-end reads. The RNA-Seq data will be analyzed with GenomeStudio (Illumina, Inc.), ERANGE3, NextGENe" (Softgenetics Inc.), TransSeq (USC) and novel programs we will develop, to identify novel genes and determine the levels of transcription, allelic expression and alternative splicing of all genes. We will then compare these measures of transcription across brain regions, developmental ages and gender. We will also perform RNA-Seq with 5,000 bp read lengths using a third generation DNA sequencer (G3), in collaboration with Life Technologies, Inc, to confirm or refine our alternative splicing models. An automated RNA-Seq analysis workflow that is portable to other laboratories will be developed and an easy-to-use, web-based informatics framework for communication of these data to other scientists will be designed and implemented. PUBLIC HEALTH RELEVANCE: Mental disorders are increasingly recognized as brain disorders that have their origins during development. While these developmental brain disorders occur in people at genetic risk, relatively little is known about how specific risk genes or gene variants affect brain development. We will determine the expression patterns of genes in particular brain regions at particular points in development. This information is essential for understanding how genetic variation affects normal and abnormal brain development, potentially giving rise to mental disorders.

描述（由申请人提供）：我们将创建一个发展中的人脑的转录图集，包括新的转录本和区域表达模式，随后可以使用组织化学映射进行细胞特异性的组织化学映射。这些数据将通过易于使用的，基于网络的信息学框架提供给研究社区。为了实现这些目标，我们将在25周，2个月，1岁，2.5岁，7年7年零13-19岁和20-30岁的大约25周，2个月，1岁，2个月，2个月，2个月，2个月，2个月，1年，25个月，2个月，2个月中净化RNA和DNA。在25周的大脑中，我们将采样背外侧前额叶皮层（DLPFC），轨道额叶皮层（OFC），下颞皮层（ITC）和海马（HIP）。其余时间点将增加枕皮层（OC），小脑（CB）和纹状体（Str），总共276个脑样品。我们将以100万个SNP（Human1MDUO阵列）的形式从这276个样品中介绍DNA，并将用Illumina Infinium Array确定甲基化模式。这些276个样品的RNA将用于确定区域表达模式，使用RNA-Seq鉴定新的基因和替代转录本。每个Poly-A RNA样品将用4500万个读取进行测序，以1拷贝/细胞（15％）提供检测。其中有3000万次读取为72 bp x 2配对，1500万读的读数将为150+125 bp配对端，以提供有关替代剪接的最大信息。我们还将使用1500万36 bp链特异性单端读数对每个样品的小RNA分子进行序列。 RNA-SEQ数据将通过Genomestudio（Illumina，Inc。），Erange3，NextGene”（SoftGenetics Inc.），TransSeq（USC）（USC）和我们将开发的新型程序进行分析，以识别新颖的基因并确定转录的水平，并确定所有基因的跨性别型和跨性别的脑图。使用第三代DNA测序仪（G3）与Life Technologies，Inc合作确认或完善我们的替代剪接模型的RNA-seq读取长度。 公共卫生相关性：越来越多的精神障碍被认为是在发育过程中起源的脑疾病。尽管这些发育性脑部疾病发生在处于遗传风险的人中，但对特定风险基因或基因变异的影响相对较少。我们将确定在发育中特定点的特定大脑区域中基因的表达模式。该信息对于理解遗传变异如何影响正常和异常的脑发育，可能引起精神障碍。

项目成果

The Allen Brain Atlas as a Resource for Teaching Undergraduate Neuroscience.

• 发表时间: 2018
• 期刊: Journal of undergraduate neuroscience education : JUNE : a publication of FUN, Faculty for Undergraduate Neuroscience
• 作者: Terri L. Gilbert

Effect of RNA integrity on uniquely mapped reads in RNA-Seq.

• DOI: 10.1186/1756-0500-7-753
• 发表时间: 2014-10-23
• 期刊: BMC research notes
• 影响因子: 1.8
• 作者: Chen EA;Souaiaia T;Herstein JS;Evgrafov OV;Spitsyna VN;Rebolini DF;Knowles JA
• 通讯作者: Knowles JA

Loss-of-Function Mutations in KIF15 Underlying a Braddock-Carey Genocopy.

Braddock-Carey 基因拷贝中 KIF15 的功能缺失突变。

• DOI: 10.1002/humu.23188
• 发表时间: 2017
• 期刊: Human mutation
• 影响因子: 3.9
• 作者: Sleiman,PatrickMA;March,Michael;Nguyen,Kenny;Tian,Lifeng;Pellegrino,Renata;Hou,Cuiping;Dridi,Walid;Sager,Mohamed;Housawi,YousefH;Hakonarson,Hakon
• 通讯作者: Hakonarson,Hakon