Introduction to Land Content

From Array Suite Wiki

Revision as of 11:16, 16 April 2020 by Michelle (Talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


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.

Some Land content is restricted based on patient privacy, and can be accessed with a co-application for the controlled access data. For more information, see Controlled_Land_Data_Access.

To request additional public datasets to be added to the Land content, please contact omicsoft.support@qiagen.com with a list of Project IDs or disease area(s) of interest. These requests will be submitted to the Land content team and processed for inclusion in a future Lands content release.

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.

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.

Restricted Lands

For more information on this topic, see Controlled_Land_Data_Access. Briefly, if you are interested in filing a data co-application with OmicSoft to access controlled access data with your Land subscription, please e-mail omicsoft.support@qiagen.com to get a data application instruction package.

In the past, these are the datasets we've successfully been approved for, and shared controlled access Lands; OmicSoft will be happy to submit a co-application with you to provide the data via Lands.

ControlledAccessSummary.png


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_Somatic_B37 - All somatic data from TCGA samples from whole genome sequencing. Metadata for these samples was combined from PCAWG, GxL.TCGA_B37, and OncoLand metadata.
  • 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.