Resources for Vaske et al. (2019) "Comparative tumor RNA-Seq analysis..."
Clinical Fields
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_ID | Treehouse-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. |
Disease | Cancer diagnosis of the donor; harmonized by Treehouse. |
Source_or_accession | Study identifier or institution name of the data source. |
Site_ID | Coded site identifier for the data source; also appears at the beginning of Treehouse sample identifiers. |
DOI | DOI link for the data source. |
Original_donor_ID | Data source's identifier for the donor. May contain multiple identifiers separated with commas. |
Original_sample_IDs | Data source's identifier for this sample. May contain multiple identifiers separated with commas. |
Original_diagnosis | Cancer diagnosis of the donor as provided by the data source. |
Vaske_2019_disease | Cancer 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_diagnosis | Age in years of the donor at time of diagnosis. |
Pediatric_or_AYA | The pediatric or adolescent / young adult status of the donor at the time of diagnosis; the age cutoff is 29 years and under. |
Sex | Sex of the donor. |
Race | Race of the donor. |
Ethnicity | Ethnicity of the donor. |
Diagnosis_group | Group of related cancers which contains this donor's cancer diagnosis; harmonized by Treehouse. (Field available for Participants only) |
Primary_tumor_location | Site of primary tumor as provided by the data source. |
Histology | Histology of this sample as provided by the data source. |
Stage | Stage of this sample as provided by the data source; staging systems may differ. |
Grade | Grade of this sample as provided by the data source; grading systems may differ. |
Subcategory | Subcategory or subtype of this sample as provided by the data source. |
Metastatic_status | Metastatic status of the donor as known to Treehouse as of September 10, 2019. |
Metastasis_location | Location of the donor's metastasis if relevant, as known to Treehouse as of September 10, 2019. |
Primary_or_relapse | Tumor type of this sample; e.g. primary, relapse, metastasis, cell line, or patient-derived xenograft. |
Tissue_source | Source of this sample; e.g. biopsy, bone marrow, peripheral blood, or resection. |
Tissue_sample_location | Anatomical location of the tissue sample as provided by the data source. |
Cancer_predisposition_syndrome | Cancer predisposition syndrome of the donor as provided by the data source. |
Diagnosis_type | Type 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_treatment | Collection time of this sample relative to treatment with immunotherapy or chemotherapy; e.g. pre- or post-treatment. |
Freshfrozen_or_FFPE | Preservation status of this sample; e.g. fresh frozen or formalin-fixed paraffin-embedded. |
Platform | RNA-Seq sequencing platform used for this sample. |
Transcript_enrichment_method | Transcript enrichment method of this sample, e.g. exome capture, poly A capture, or Ribosomal RNA depletion. |
Sequence_length | Sequence length of the reads of this sample. |
Strandedness | Strandedness of this sample's RNA-Seq sequence data; either stranded or non stranded. |
RNASeq_version | Software version of the analysis pipeline used to translate this sample's sequence data into RNA expression levels. |
Input_filenames | Filename(s) of the sequence data files provided as input to the expression level analysis pipeline. |
MEND | Count of mapped exonic non-duplicate reads in this sample's sequence data. |
QC | Quality control status of this sample; whether it passes or fails the QC threshold of at least ten million MEND reads. |