Higher Precision Human and Mouse Transcriptomes

更高精度的人类和小鼠转录组

• 批准号: 10241205
• 负责人: Seyed Ali Mortazavi
• 金额: $ 288.87万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-02-01 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10241205
• 关键词: Adult; Affect; Aging; Alzheimer' s Disease; Amino Acid Sequence; Architecture; Biological; Cell Line; Cell Nucleus; Cell model; Cells; Chromatin; Code; Cognitive; Combinatorics; Companions; Complex; Cytoplasm; Data; Data Analyses; Data Set; Dementia; Dendrites; Dimensions; Disease; Encyclopedia of DNA Elements; Exons; Fetal Tissues; Generations; Genes; Genetic Transcription; Genetic Translation; Genome; Haplotypes; Health; Human; Human Genome; Hybrids; Individual; Ion Channel; Length; Life; Life Cycle Stages; Maps; Measurement; Measures; Messenger RNA; MicroRNAs; Mission; Modernization; Modification; Molecular; Mus; National Human Genome Research Institute; Output; Phase; Phenotype; Play; Production; Property; Protein Isoforms; Proteins; RNA; RNA Precursors; RNA Sequences; RNA Splicing; RNA analysis; RNA-Protein Interaction; Regulatory Element; Role; Sampling; Series; Site; Source; Specific qualifier value; Structure; Technology; Tissue Sample; Tissues; Transcript; Translating; Untranslated RNA; aged; base; cell type; extracellular; human data; human tissue; in vivo; mRNA Stability; nanopore; new technology; polyadenylated messenger RNA; sequencing platform; single molecule; single-cell RNA sequencing; transcriptome; transcriptome sequencing; transcriptomics

PROJECT SUMMARY/ABSTRACT with changes for year5 extension (underlined) It is said that if the genome represents the set of things that the cell could say, then the transcriptome represents the set of things that the cell is saying right now. The transcriptome is the primary read-out of the genome and is composed mainly of mRNAs, long noncoding RNAs, and microRNAs. At all stages of life, in health and in disease, differences in the transcriptome causally define and distinguish each cell type and cell state. The mission of the ENCODE Consortium is to discover, map and define all genes and their regulatory elements. RNA-Seq data and the resulting transcriptomes have therefore been a prominent component of prior phases of ENCODE, and our groups have contributed over 350 released poly(A) mRNA and microRNA datasets for the project. Valuable and high quality as those data are, new technologies will allow us to produce a new generation of transcriptomes that are much more information rich and definitive. Specifically, they resolve the multiple different cell types that comprise complex tissues and they resolve the multiple molecular isoforms. They document long-range single molecule splicing and end processing and we provide companion quantification of microRNAs, plus discovery of their often-undocumented precursor RNAs. Finally, we map RNA secondary structure across the transcriptome in vivo. We propose to complete contributing at least 200 higher precision long-read transcriptomes and companion measurement types, and their integrated analysis. We also add short- read ribo-minus RNA-seq across the NHGRI approved consortium biosamples. A portion of this study focuses on aging humans and mice, a whole life cycle stage that has not previously been studied in ENCODE. The corresponding disease component contrasts cognitively normal with Alzheimer’s dementia.

项目摘要/摘要，包括第5年延期的变化（下划线）

项目成果

TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts.

• DOI: 10.1093/bioinformatics/bty483
• 发表时间: 2019-01-15
• 期刊: Bioinformatics (Oxford, England)
• 作者: Wyman D;Mortazavi A
• 通讯作者: Mortazavi A

Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types.

• DOI: 10.1101/gr.275723.121
• 发表时间: 2022-03
• 期刊: Genome research
• 影响因子: 7
• 作者: Moore JE;Zhang XO;Elhajjajy SI;Fan K;Pratt HE;Reese F;Mortazavi A;Weng Z
• 通讯作者: Weng Z

RNAget: an API to securely retrieve RNA quantifications.

RNAGET：API可安全检索RNA定量。

• DOI: 10.1093/bioinformatics/btad126
• 发表时间: 2023-04-03
• 期刊: Bioinformatics (Oxford, England)

Chemical Approaches To Analyzing RNA Structure Transcriptome-Wide.

• DOI: 10.1002/cbic.202000340
• 发表时间: 2021-04-06
• 期刊: Chembiochem : a European journal of chemical biology
• 作者: England WE;Garfio CM;Spitale RC
• 通讯作者: Spitale RC

Swan: a library for the analysis and visualization of long-read transcriptomes.

• DOI: 10.1093/bioinformatics/btaa836
• 发表时间: 2021-06-09
• 期刊: Bioinformatics (Oxford, England)
• 作者: Reese F;Mortazavi A
• 通讯作者: Mortazavi A