Resources for Vaske et al. (2019) "Comparative tumor RNA-Seq analysis..."

Clinical Fields

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This dataset was finalized on September 10, 2019; any updates or changes to the values since that date are not reflected in the dataset.

Field Definition
Treehouse_sample_IDTreehouse-assigned sample identifier. TH indicates a partner sample and THR a repository sample; TCGA and TARGET samples are listed under their original identifiers. The first two digits are the coded site identifier, followed by a unique four-digit donor identifier and then a two-digit sample identifier to distinguish between multiple samples from the same donors.
DiseaseCancer diagnosis of the donor; harmonized by Treehouse.
Source_or_accessionStudy identifier or institution name of the data source.
Site_IDCoded site identifier for the data source; also appears at the beginning of Treehouse sample identifiers.
DOIDOI link for the data source.
Original_donor_IDData source's identifier for the donor. May contain multiple identifiers separated with commas.
Original_sample_IDsData source's identifier for this sample. May contain multiple identifiers separated with commas.
Original_diagnosisCancer diagnosis of the donor as provided by the data source.
Vaske_2019_diseaseCancer diagnosis of the donor as harmonized by Treehouse at the time of data analysis. May differ from the more recent harmonized diagnosis, found in "Disease".
Age_at_diagnosisAge in years of the donor at time of diagnosis.
Pediatric_or_AYAThe pediatric or adolescent / young adult status of the donor at the time of diagnosis; the age cutoff is 29 years and under.
SexSex of the donor.
RaceRace of the donor.
EthnicityEthnicity of the donor.
Diagnosis_groupGroup of related cancers which contains this donor's cancer diagnosis; harmonized by Treehouse. (Field available for Participants only)
Primary_tumor_locationSite of primary tumor as provided by the data source.
HistologyHistology of this sample as provided by the data source.
StageStage of this sample as provided by the data source; staging systems may differ.
GradeGrade of this sample as provided by the data source; grading systems may differ.
SubcategorySubcategory or subtype of this sample as provided by the data source.
Metastatic_statusMetastatic status of the donor as known to Treehouse as of September 10, 2019.
Metastasis_locationLocation of the donor's metastasis if relevant, as known to Treehouse as of September 10, 2019.
Primary_or_relapseTumor type of this sample; e.g. primary, relapse, metastasis, cell line, or patient-derived xenograft.
Tissue_sourceSource of this sample; e.g. biopsy, bone marrow, peripheral blood, or resection.
Tissue_sample_locationAnatomical location of the tissue sample as provided by the data source.
Cancer_predisposition_syndromeCancer predisposition syndrome of the donor as provided by the data source.
Diagnosis_typeType of the donor's diagnosis; e.g. initial, progression, relapse, or a secondary disease after treatment for prior cancer, as known to Treehouse as of September 10, 2019.
Collected_before_treatmentCollection time of this sample relative to treatment with immunotherapy or chemotherapy; e.g. pre- or post-treatment.
Freshfrozen_or_FFPEPreservation status of this sample; e.g. fresh frozen or formalin-fixed paraffin-embedded.
PlatformRNA-Seq sequencing platform used for this sample.
Transcript_enrichment_methodTranscript enrichment method of this sample, e.g. exome capture, poly A capture, or Ribosomal RNA depletion.
Sequence_lengthSequence length of the reads of this sample.
StrandednessStrandedness of this sample's RNA-Seq sequence data; either stranded or non stranded.
RNASeq_versionSoftware version of the analysis pipeline used to translate this sample's sequence data into RNA expression levels.
Input_filenamesFilename(s) of the sequence data files provided as input to the expression level analysis pipeline.
MENDCount of mapped exonic non-duplicate reads in this sample's sequence data.
QCQuality control status of this sample; whether it passes or fails the QC threshold of at least ten million MEND reads.