Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence

TABLE OF CONTENTS GENERAL INFORMATION TITLE AUTHORS AND BEST CONTACT LICENSES USEFUL LINKS DATE OF DATA COLLECTION FILE ORGANIZATION FUNDING ---- Release Notes: This is a pre-publication placeholder for primary data release for the publication listed below. In common with GEO, PRIDE, and other data repositories, this will be populated with final data following peer review. ---- GENERAL INFORMATION Publication Title: Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence Authors: Zoltan Maliga, Daniel Y. Kim, Ai-Tram N. Bui, Jia-Ren Lin, Anna K. Dewan, George G. Murphy, Ajit J. Nirmal, Christine G. Lian, Peter K. Sorger, Nicole R. LeBoeuf Contact Information Nicole LeBoeuf, MD, MPH Vice Chair of Dermatology, Dana-Farber Cancer Institute,; Chief, Division of Oncodermatology, Brigham and Women's Hospital; Clinical Director, Center for Cutaneous Oncology, Dana-Farber/Brigham Cancer Center, Harvard Medical School nleboeuf@partners.org Publications that cite or use the data:** Maliga, M, Kim, DY, Tram, B, Lin, JR, Dewan, AK, Jadeja, S, Murphy, G, Nirmal, AJ, Lian, C, Sorger, PK, LeBoeuf, NR. Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence. https://doi.org/10.1101/2023.04.03.535435 Licenses/restrictions placed on the data: CC BY https://creativecommons.org/licenses/by/4.0/ ---- FILE ORGANIZATION FILE TYPES/SUMMARY: Each folder corresponds to a patient sample (N). The following files are available for each patient and are located on [Synapse/AWS/Etc]. File Type Description Location N.ome.tif Stitched multiplex CyCIF image pyramid in ome.tif format AWS N_IHC.ome.tiff Immunohistochemistry stained image of serial FFPE tissue section in .ome.tiff format AWS N_HE.ome.tiff Hematoxylin and eosin stained image of FFPE tissue section in .ome.tiff format AWS markers.csv List of all markers in ome.tif image Synapse N_Quantification.csv Single-cell feature table, including intensity data for all channels Synapse segmentation/ Folder of segmentation maps for tissue image in .tif format AWS Synapse Library: Edit this to link directly to your public Synapse Library Free account registration is required to download files from Synapse. Images and metadata are available in the bucket at the following AWS location: [ADD BUCKET DETAILS] To browse and download the data use either a graphical file transfer application that supports S3 such as CyberDuck, or the AWS CLI tools. A graphical tool may be more convenient but the CLI tools will likely offer higher download speeds. FILE LIST N.ome.tif LSP Slide ID File Name File Size LSP10925 LSP10925_CyCIF_Image.ome.tif 9.3 GB LSP10929 LSP10929_CyCIF_Image.ome.tif 6.0 GB LSP10931 LSP10931_CyCIF_Image.ome.tif 8.7 GB LSP10933 LSP10933_CyCIF_Image.ome.tif 6.7 GB LSP10951 LSP10951_CyCIF_Image.ome.tif 11 GB LSP10980 LSP10980_CyCIF_Image.ome.tif 9.3 GB 51 GB markers.csv File name File Size Synapse ID markers.csv 0.7 KB N_Quantification.csv LSP Slide ID File Name File Size Synapse ID LSP10925 LSP10925_CyCIF_Quantification.csv 20 MB LSP10929 LSP10929_CyCIF_Quantification.csv 12 MB LSP10931 LSP10931_CyCIF_Quantification.csv 5.9 MB LSP10933 LSP10933_CyCIF_Quantification.csv 7.5 MB LSP10951 LSP10951_CyCIF_Quantification.csv 8.3 MB LSP10980 LSP10980_CyCIF_Quantification.csv 12 MB segmentation/ LSP Slide ID File Name File Size LSP10925 LSP10925_cellRingMask.tif 20 MB LSP10929 LSP10929_cellRingMask.tif 12 MB LSP10931 LSP10931_cellRingMask.tif 5.9 MB LSP10933 LSP10933_cellRingMask.tif 7.5 MB LSP10951 LSP10951_cellRingMask.tif 8.3 MB LSP10980 LSP10980_cellRingMask.tif 12 MB 66 MB N_IHC.ome.tiff LSP Slide ID Description File name File Size LSP16237 CD103 Image LSP16237_IHC_CD103.ome.tiff 2.8 GB LSP16240 PD1 Image LSP16240_IHC_PD1.ome.tiff 3.1 GB LSP16241 MART1 Image LSP16241_IHC_MART1.ome.tiff 2.9 GB LSP16242 FOXP3 Image LSP16242_IHC_FOXP3.ome.tiff 3.5 GB LSP16243 CD3 Image LSP16243_IHC_CD3.ome.tiff 2.9 GB LSP16244 CD4 Image LSP16244_IHC_CD4.ome.tiff 3.2 GB LSP16245 CD8 Image LSP16245_IHC_CD8.ome.tiff 3.2 GB LSP16246 CD20 Image LSP16246_IHC_CD20.ome.tiff 3.2 GB LSP16247 CD19 Image LSP16247_IHC_CD19.ome.tiff 3.7 GB LSP16248 CD163 Image LSP16248_IHC_CD163.ome.tiff 4.0 GB LSP16249 PDL1 Image LSP16249_IHC_PDL1.ome.tiff 3.7 GB LSP16250 CD69 Image LSP16250_IHC_CD69.ome.tiff 3.2 GB 39 GB N_HE.ome.tiff LSP Slide ID Description File name File Size LSP16237 H&E Image LSP16234_HE.ome.tiff 14 GB 14 GB ---- FUNDING R50-CA252138, U2C-CA233262 and Ludwig Cancer Researc