Ivy Glioblastoma Atlas Project (RNA-Seq)

The Ivy Glioblastoma Atlas Project (Ivy GAP) is a detailed anatomically based transcriptomic atlas of human glioblastoma tumors. As collaborators, the Ivy Foundation funded the Allen Institute and the Swedish Neuroscience Institute to design and create the atlas. The Paul G. Allen Family Foundation also supported the project. This resource consists of a viewer interface that resolves the manually- and machine-annotated histologic images (H&E and RNA in situ hybridization) at 0.5 µm/pixel, a transcriptome browser to view and mine the anatomically-based RNA-Seq samples, an application programming interface, help documentation that describes the methods and how to use the resource, as well as SNP array data and the supporting longitudinal clinical information and MRI time course data. The resource is made available to the public without charge as part of the Ivy GAP (http://glioblastoma.alleninstitute.org/) via the Allen Institute data portal (http://www.brain-map.org), the Ivy GAP Clinical and Genomic Database (http://ivygap.org/) via the Swedish Neuroscience Institute (http://www.swedish.org/services/neuroscience-institute), and The Cancer Imaging Archive (https://wiki.cancerimagingarchive.net/display/Public/Ivy+GAP). The Ivy GAP processed data at GEO includes normalized RNA-Seq FPKM files used for analysis in "An anatomic transcriptional atlas of glioblastoma,” which is under review. Other processed data files as well as sample and donor meta-data and QC metrics are available at http://glioblastoma.alleninstitute.org/static/download.html. The raw RNA-Seq and SNP array data will be submitted to dbGaP.

艾维胶质母细胞瘤图谱项目（Ivy GAP）是一款基于解剖结构的详细人类胶质母细胞瘤肿瘤转录组图谱。作为项目合作资助方，艾维基金会资助艾伦研究所（Allen Institute）与瑞典神经科学研究所（Swedish Neuroscience Institute）设计并打造该图谱，保罗·G·艾伦家族基金会（Paul G. Allen Family Foundation）亦对本项目提供了支持。该资源包含以下组成部分：可将手动与机器标注的组织学图像（苏木精-伊红染色（Hematoxylin and Eosin，H&E）与RNA原位杂交（RNA in situ hybridization））以0.5微米/像素的分辨率进行展示的可视化界面、用于查看与挖掘基于解剖结构的RNA测序（RNA-Seq）样本的转录组浏览器、一套应用程序编程接口、详细说明研究方法与资源使用规范的帮助文档，此外还包含单核苷酸多态性阵列（SNP array）数据、配套的纵向临床信息与磁共振成像（MRI）时间序列数据。该资源可免费向公众开放，作为Ivy GAP官方站点（http://glioblastoma.alleninstitute.org/）的组成部分，可通过艾伦研究所数据门户（http://www.brain-map.org）访问；同时可通过瑞典神经科学研究所（http://www.swedish.org/services/neuroscience-institute）旗下的Ivy GAP临床与基因组数据库（http://ivygap.org/）获取；此外还可通过癌症影像档案库（The Cancer Imaging Archive，https://wiki.cancerimagingarchive.net/display/Public/Ivy+GAP）获取相关资源。已在基因表达综合数据库（Gene Expression Omnibus，GEO）上架的Ivy GAP处理后数据，包含用于《胶质母细胞瘤解剖转录组图谱》（该论文目前处于审稿阶段）分析所用的标准化RNA测序每千碱基百万片段数（FPKM）文件。其余处理后数据文件、样本与供体元数据以及质量控制（QC）指标，均可通过http://glioblastoma.alleninstitute.org/static/download.html获取。原始RNA测序与单核苷酸多态性阵列数据将提交至数据库基因型与表型档案（dbGaP）。

搜集汇总

背景与挑战

背景概述

该数据集是Ivy胶质母细胞瘤图谱项目的一部分，专注于人类胶质母细胞瘤的解剖学转录组分析，基于RNA-Seq技术构建。它提供了详细的转录组数据、SNP阵列、临床信息和MRI时间序列数据，可通过Allen研究所等公共门户免费访问，用于支持胶质母细胞瘤的研究。数据集包含14个样本，发布于2022年，属于公开资源。