Skip to content

Metadata Provided

Each data request includes a text file called SAMPLE_INFO.txt that provides a number of file level properties (sample identifiers, clinical attributes, etc). The following is a list of properties provided.

Property Description
file_path The path to the file in your St. Jude Cloud project.
subject_name A unique subject identifier assigned internally at St. Jude.
sample_name A unique sample identifier assigned internally at St. Jude.
sample_type One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft
sequencing_type Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq.
file_type One of BAM, CNV, gVCF, Somatic_VCF
description Optional field that may contain additional file information.
j_diseases Short disease identifier used internally at St. Jude. When determining primary diagnosis, use attr_diagnosis instead!
sj_datasets If present, the datasets in the data browser which this file is associated with.
sj_pmid_accessions If the file was associated with a paper, the related Pubmed accession number.
sj_ega_accessions If the file was associated with a paper, the related EGA accession number.
attr_age_at_diagnosis Age at first diagnosis (normalized as a decimal value).
attr_diagnosis Primary diagnosis.
attr_ethnicity Self-reported ethnicity according to the US Census Bureau classifications.
attr_race Self-reported race according to the US Census Bureau classifications.
attr_sex Self-reported sex.
sj_dataset_accession If present, the permanent accession number assigned in St. Jude Cloud.
sj_embargo_date The embargo date, which specifies the first date which the files can be used in a publication.