Dear GLASS Consortium, I am working with the RNA-seq dataset from the GLASS project and obtained the count matrix file transcript_count_matrix_all_samples.tsv. I am experiencing two issues ID Mapping: The column names in the count matrix do not directly align with the IDs in the clinical metadata table. I would appreciate guidance on which key/mapping table (e.g., sample/aliquot dictionary) should be used to link these count matrix headers to the patient (case_barcode) metadata. Paired / Longitudinal Information: I am specifically interested in analyzing paired (initial vs. recurrent) samples. Is there a single comprehensive metadata file or database view that links the count matrix sample IDs directly to paired clinical information?Any guidance or link to the appropriate files on Synapse/GLASS database would be greatly appreciated.

Created by Elif Emanetci EEmanetci
Thank you for your questions. ID Mapping: The GLASS Synapse portal explains the barcode structure. Each RNA-seq sample should have its own aliquot barcode, with R in place of 01D and RNA in place of WGS. For example, the aliquot barcode GLSS-MD-0043-R3-01D-WGS-ASEGFI corresponds to the sample barcode GLSS-MD-0043-R3 and the case barcode GLSS-MD-0043. You can extract the sample and case barcodes from the RNA-seq aliquot barcodes and use them to link the count matrix columns to the clinical data. Paired and longitudinal information: The posted Gold Set and Silver Set tables contain paired initial and recurrent DNA samples; they are not RNA-seq pairing tables. You can use their case barcodes to identify patients with paired DNA samples, then check the RNA-seq count matrix and its sample barcodes to determine which patients also have RNA-seq data at both timepoints. I hope this answers your questions. Please don’t hesitate to reach out if you have any others. Erica

Mapping data columns to clinical metadata and paired sample pairs information page is loading…