Data repository for "Plasma-derived extracellular vesicle analysis and deconvolution enables prediction and tracking of melanoma checkpoint blockade outcome" by Shi et al. in Science Advances.
- The pipeline used to generate processed data uploaded here is described in the methods and material section of the main text. Supplemental Figure 1 has a detailed schematic of the full processing pipeline
- The full paper data is split into a discovery cohort package and a validation cohort package:
- Each package contains a normalized, batch-corrected expression file, which contains the normalized log2 expression values from our EV-Microarray experiments and log CPM values from our EV-RNAseq experiments, a full data metadata spreadsheet with all available clinical information for each sample, and a "simple" metadata file with the contrasts used for limma DEG calling.
- We are currently working with NCBI GEO to upload the full raw dataset. The target date for release is: TBA.
- In the meantime, you can email alvinshi@mit.edu for access to full data repository for both the discovery cohort ev-microarray data (12.5 GB) and/or the ev-RNA-seq data (386 GB). I will provide you with a dropbox link to the raw data files and associated metadata files upon reasonable request.