Introduction to Land Content

From Array Suite Wiki

(Difference between revisions)
Jump to: navigation, search
(DiseaseLand collection)
(OncoLand collection)
Line 21: Line 21:
 
* [[CellLine Pfizer B37|Pfizer Cell Line Profiling]]
 
* [[CellLine Pfizer B37|Pfizer Cell Line Profiling]]
 
* [[Introduction to Sanger Land Content|SANGER]]
 
* [[Introduction to Sanger Land Content|SANGER]]
 +
* CellLine Sanger*
 +
* CellLine Genentech*
  
 
===Oncology Project Collections===
 
===Oncology Project Collections===
Line 36: Line 38:
 
* [[Introduction to expO Land Content|expO]]
 
* [[Introduction to expO Land Content|expO]]
 
* Genentech SCLC
 
* Genentech SCLC
* [[Introduction to GENIE Land Content|GENIE]]
+
* [[Introduction to GENIE Land Content|GENIE]]*
 
* [[Introduction to ICGC Land Content|ICGC]]
 
* [[Introduction to ICGC Land Content|ICGC]]
 +
* mCRPC*
 +
* MET500*
 
* METABRIC
 
* METABRIC
 
* [[Introduction to TARGET Land Content|TARGET]]
 
* [[Introduction to TARGET Land Content|TARGET]]
 
* [[Introduction to TCGA Land Content|TCGA]]
 
* [[Introduction to TCGA Land Content|TCGA]]
 +
 +
'* Certain Lands contain restricted data, so cannot be distributed to general users. If you are interested in accessing a restricted Land, QIAGEN can submit a co-application for access with your organization, and provide access to the processed data and curated metadata generated as part of the project.
  
 
==DiseaseLand collection==
 
==DiseaseLand collection==

Revision as of 09:36, 12 August 2019


Contents

Overview

OmicSoft Land technology is a revolutionary method to store and explore -Omic data, a central data hub to gather public disease-related data to enable discovery. OmicSoft continually adds data to our Land collections, which can be explored using the Array Studio interface or R API.

Land content is organized by disease focus, and each Land within a collection serves as a repository for thousands of -Omic samples.

Body Map collection

The Body Map collection profiles gene expression in "normal" tissues by microarray and RNA-seq. The Body Map collection is available for subscribers to OncoLand and DiseaseLand.

  • GTEx
  • Blueprint
  • HPA

OncoLand collection

Cell Line Expression Data

Oncology Project Collections

Oncology Consortium Data

'* Certain Lands contain restricted data, so cannot be distributed to general users. If you are interested in accessing a restricted Land, QIAGEN can submit a co-application for access with your organization, and provide access to the processed data and curated metadata generated as part of the project.

DiseaseLand collection

Disease-Focused Studies

  • Human Disease (formerly known as ImmunoLand and CVMLand)
  • Mouse Disease
  • Rat Disease

Single-Cell Studies

UMI-based Single-Cell expression

Non-UMI-based Single-Cell expression

Cell Line treatments

  • LINCS

Virtual Lands

Any Lands with the same genome build and gene model can be combined into a Virtual Land, allowing direct comparisons across Lands.

For example, data from TCGA, GTEx, and CCLE Lands can be integrated to visualize expression in tumor samples (TCGA), normal tissues (GTEx), and cell lines (CCLE).

In the same way, users can combine Internal Lands with any compatible OmicSoft Lands. Data must be processed using the same reference genome and gene model.

Internal Lands

GeneticsLand

Restricted Access Lands

File:GeneticsLandReleaseWhitePaper.pdf

  • GxL.TCGA_B37 - Germline genotypes from TCGA normal samples generated from whole exome sequencing
  • GxL.TCGA_WGS_B37 - Germline genotypes from TCGA normal samples generated from whole genome sequencing using joint-genotyping methods
  • GxL.TCGA_WGS_B38 - Build 38 version, Germline genotypes from TCGA normal samples generated from whole genome sequencing using joint-genotyping methods
  • GxL.TCGA_WGS_Somatic_B37 - Somatic mutations from TCGA samples in PanCancer Analysis of Whole Genomes (PCAWG) consortium obtained from International Cancer Genome Consortium (ICGC)

Open Access Lands

  • GxL.Assocations - Association-based Land (GWAS), curated and standardized using OmicSoft developed pipelines
  • GxL.PheWAS - PheWAS based Land, curated and standardized using OmicSoft developed pipelines
  • GxL.1000G_B37 - Phase 3 genotypes as published by the International Genome Sample Resource (IGSR; www.internationalgenome.org)

Additional Content

  • GTEx Version 6 Single-Tissue eQTLs - eQTLs can be integrated as tables into any GeneticsLand (Gene.EqtlTable or Variant.EqtlTable views). Access to these data require application and approval from dbGaP, and as such, these tables are not available by default. Contact OmicSoft to discuss how to add these views into OmicSoft curated GeneticsLands or to internal data built into a GeneticsLand framework.
  • GRASP Version 2 Table - Genetic association results from the Genome-Wide Repository of Associations Between SNPs and Phenotypes is integrated as a table view (GRASP2 Table) in all GeneticsLands. These data are Open Access.