Anatomical and gene expression resource for Macrostomum lignano

Macrostomum lignano 的解剖和基因表达资源

基本信息

批准号：
10926476
负责人：
Erin Davies
金额：
$ 36.41万
依托单位：
DIVISION OF BASIC SCIENCES - NCI
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10926476
关键词：
Address Adult Agreement Algorithms Anatomy Animals Atlases Behavior Bioinformatics CCR Cell Lineage Cells Data Data Set Development Dissociation Dyes Embryonic Development Female Fluorescence-Activated Cell Sorting Gene Expression Genes Genetic Transcription Germ Cells Heterogeneity Homeostasis In Situ Hybridization Internships Laboratories Lead Morphology Natural regeneration Nuclear Oregon Platyhelminths Pluripotent Stem Cells Postdoctoral Fellow Postembryonic Preparation Protocols documentation Regulation Reporting Reproductive system Resources Sampling Scientist Sexual Maturation Specific qualifier value Stains System Technology Time Tissue-Specific Gene Expression Tissues Treatment Protocols Universities Work analysis pipeline cell fate specification cell type comparative differential expression digital germline stem cells irradiation male marine programs regenerative research facility single-cell RNA sequencing statistical service transcriptome sequencing

项目摘要

The Macrostomum lignano (Mlig) postembryonic anatomical atlas is a collaborative team effort. Dr. Matthew Voas has optimized cell dissociation, vital nuclear dye staining, and fluorescence activated cell sorting protocols required for sample preparation, and he is producing pilot 10x scRNA-Seq data sets in conjunction with Dr. Sevilay Turan and Dr. Bao Tran's team at the CCR Sequencing Facility at the NCI-Frederick Advanced Technology Research Facility. Postdoctoral Scientist Dr. Xintao Fan has determined the developmental time points, from hatchling to sexually mature adult, that are most biologically impactful for sequencing, and he determined the irradiation treatment regimen necessary for complete elimination of adult pluripotent stem cells and germ cells. University of Oregon Masters intern Laura Paez Baena developed a scRNA-Seq analysis pipeline tailored to Mlig expression data. Laura was the lead bioinformatic analyst for the project but her May 2023 departure means we are now working out new collaborative agreements with NCI Statistical Services staff for our analysis needs. Data sets have been acquired and we are moving on to analysis of our data. In We will work to create an interactive Shiny app that integrates digital and spatial gene expression data for differentially expressed genes defining anatomical entities captured in our analysis.

大型Lignano（MLIG）后胚后解剖图集是一项协作团队的努力。 Matthew Voas博士已经优化了样品制备所需的细胞分离，重要的核染料染色和荧光激活的细胞分类协议，并且他正在与Sevilay Turan博士和Bao Tran博士的CCR测序机构在Nci-Frederick-Frederick Intervellock Intervelloys Researchsity的CCR测序机构中生产10倍SCRNA-SCRNA-SEQ数据集。博士后科学家Xintao Fan博士确定了从孵化到性成熟的成年人的发育时间点，这些时间点对测序具有最大的影响，他确定了完全消除成人多能干细胞和生殖细胞所需的辐射治疗方案。俄勒冈大学大师赛实习生劳拉·佩恩·巴纳（Laura Paez Baena）开发了针对MLIG表达数据量身定制的SCRNA-SEQ分析管道。劳拉（Laura）是该项目的主要生物信息学分析师，但她2023年5月的出发者意味着我们现在正在与NCI统计服务人员达成新的合作协议，以满足我们的分析需求。数据集已被获取，我们正在继续分析数据集。我们将努力创建一个交互式闪亮的应用程序，该应用程序集成了定义分析中捕获的解剖实体的差异表达基因的数字和空间基因表达数据。