Introduction to CGCI Land Content

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Contents

CGCI_B37 and CGCI_B38

The Cancer Genome Characterization Initiative (CGCI) applies advanced sequencing and other genome-based methods to find new genetic abnormalities in tumors, hoping to inform better cancer diagnosis and treatment. OmicSoft's CGCI lands contain RNA-Seq data for Diffuse large B-Cell and follicular lymphomas.

Data Source

CGCI

Land Version Genome Build Gene Model
CGCI_B37 Human.B37.3 OmicsoftGene20130723
CGCI_B38 Human.B38 OmicsoftGenCode_V24

Data Types

  • RNA-Seq, including:
    • Single-end and Paired-end fusion calling
    • RNA-Seq mutation
    • Exon Junction and Exon Usage
    • Expression (Gene- and Transcript- level quantification)

Laboratory Methods

Illumina HiSeq RNA sequencing

Processing Methods

RNA-Seq data: OmicScript Pipeline and Building Land From RNA-Seq Data

Key Meta Data Columns

  • Tumor Type: CGCI Land currently has NHL-DLBCL (Diffuse Large B-Cell Lymphoma) and NHL-FL (follicular lymphoma).
  • Sample Type: The types of sample indicating where the sample is from. It includes information such as whether it is from normal or tumor tissue.
  • Land Tissue: The tissue from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
  • Land Sample Type: A detailed description of the cell type from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary.
  • Tumor or Normal: Indicates whether a sample is from a tumor or normal sample.
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Key Views

Gene Expression: The users can use CGCI Land to research RNA-seq based gene expression, mutation and fusion events in lymphoma samples.

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Example: Gene expression of NFkB1 (FPKM) in NHL-FL and NHL-DLBCL samples.


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