cgci.yaml

Name: Cancer Genome Characterization Initiatives - Burkitt Lymphoma, HIV+ Cervical Cancer
Description: >
  The Cancer Genome Characterization Initiatives (CGCI) program supports cutting-edge genomics
  research of adult and pediatric cancers. CGCI investigators develop and apply advanced sequencing
  methods that examine genomes, exomes, and transcriptomes within various types of tumors. The
  program includes Burkitt Lymphoma Genome Sequencing Project (BLGSP) project and HIV+ Tumor
  Molecular Characterization Project - Cervical Cancer (HTMCP-CC) project.
  
  The dataset contains open Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression
  Quantification, miRNA-Seq Isoform Expression Quantification, and miRNA Expression Quantification
  data.

  This dataset also contains controlled WGS/Targeted Sequencing/RNA-Seq/miRNA-Seq Aligned Reads,
  and RNA-Seq Splice Junction Quantification
Documentation: https://ocg.cancer.gov/programs/cgci
Contact: dcf-support@datacommons.io
ManagedBy: "[Center for Translational Data Science at The University of Chicago](https://ctds.uchicago.edu/)"
UpdateFrequency: |
  Genomic Data Commons (GDC) is source of truth for this dataset; GDC offers monthly data releases,
  although this dataset may not be updated at every release.
Tags:
  - aws-pds
  - cancer
  - genomic
  - life sciences
  - transcriptomics
  - STRIDES
License: "NIH Genomic Data Sharing Policy: https://gdc.cancer.gov/access-data/data-access-policies"
Resources:
  - Description: |                                                                                  
      Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq
      Isoform Expression Quantification, miRNA-Seq miRNA Expression Quantification 
    ARN: arn:aws:s3:::gdc-cgci-blgsp-phs000235-2-open
    Region: us-east-1
    Type: S3 Bucket
  - Description: |                                                                                  
      Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq
      Isoform Expression Quantification, miRNA-Seq miRNA Expression Quantification 
    ARN: arn:aws:s3:::gdc-cgci-phs000235-2-open
    Region: us-east-1
    Type: S3 Bucket
  - Description: |                                                                                  
      WGS/Targeted Sequencing/RNA-Seq/miRNA-Seq Aligned Reads, RNA-Seq Splice Junction
      Quantification 
    ARN: arn:aws:s3:::gdc-cgci-phs000235-2-controlled
    Region: us-east-1
    Type: S3 Bucket
    ControlledAccess: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000235.v14.p2
DataAtWork:
  Tools & Applications:
    - Title: Genomic Data Commons
      URL: https://portal.gdc.cancer.gov/projects/CGCI-BLGSP
      AuthorName: National Cancer Institute
      AuthorURL: https://gdc.cancer.gov/
  Publications:
    - Title: |
        Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and
        sporadic Burkitt lymphoma
      URL: https://doi.org/10.1182/blood-2018-09-871418
      AuthorName: |
         Grande B. M., Gerhard D. S., Jiang A., Griner N. B., Abramson J. S., Alexander T. B., et al.