Introduction to Land Content

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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

DiseaseLand collection

Disease-Focused Studies

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

  • 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

Open Access Lands

  • GxL.Assocations_B37 - Association-based Land (GWAS), curated and standardized using OmicSoft developed pipelines
  • GxL.PheWAS_B37 - 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.