labsyspharm/CRC_atlas_2022

Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancerJia-Ren Lin*, Shu Wang*, Shannon Coy*, Yu-An Chen, Clarence Yapp, Madison Tyler, Maulik K. Nariya, Cody N. Heiser, Ken S. Lau, Sandro Santagata†, and Peter K. Sorger† Associated publication DOI: 10.1016/J.CELL.2022.12.028Learn more: tissue-atlas.org/atlas-datasets/lin-wang-coy-2021/ ----- VIEW IMAGE DATA ONLINE Some data is available as narrated data explorations (with text and audio narration) for anonymous on-line browsing using MINERVA software (Rashid et al., 2022), which allows users to pan and zoom through the images without requiring any software installation. To view the Minerva stories, please visit tissue-atlas.org/atlas-datasets/lin-wang-coy-2021/#data-explorations. ---- ACCESS THE DATA The dataset consists of 47 CRC1 images (2.1 TB) and CRC2-17 images (4.4 TB). All full resolution images, derived image data (e.g., segmentation masks), and cell count tables have been released via the NCI-sponsored repository for Human Tumor Atlas Network (HTAN; humantumoratlas.org/explore). The dataset is also available through Amazon Web Services S3 in the following bucket: s3://lin-2021-crc-atlas/data/ The list of S3 objects in the bucket can be accessed at https://lin-2021-crc-atlas.s3.amazonaws.com/ For instructions on how to access primary image data through AWS, see "Access Laboratory of Systems Pharmacology Datasets on AWS," DOI: 10.5281/zenodo.10223573. LIST OF ALL FILES: The tables below inventory the dataset, which includes: CRC1 images and image metadataCRC2-17 images and image metadataSpatial features tablesSingle-cell sequencing data and GeoMX count tables --- CRC1 Images The following table contains summary biospecimen and file metadata for all 47 sections. Section Internal_Biospecimen_ID Method Thickness (μm) Size (GB) Image Filename Metadata Filename 1 WD-76845-001 H&E 5 12.2 WD-76845-001.ome.tif WD-76845-001-metadata.csv 2 WD-76845-002 t-CyCIF 5 88 WD-76845-002.ome.tif WD-76845-002-metadata.csv 6 WD-76845-006 H&E 5 11 WD-76845-006.ome.tif WD-76845-006-metadata.csv 7 WD-76845-007 t-CyCIF 5 80.2 WD-76845-007.ome.tif WD-76845-007-metadata.csv 13 WD-76845-013 H&E 5 11.9 WD-76845-013.ome.tif WD-76845-013-metadata.csv 14 WD-76845-014 t-CyCIF 5 72.4 WD-76845-014.ome.tif WD-76845-014-metadata.csv 19 WD-76845-019 H&E 5 12.7 WD-76845-019.ome.tif WD-76845-019-metadata.csv 20 WD-76845-020 t-CyCIF 5 83.6 WD-76845-020.ome.tif WD-76845-020-metadata.csv 24 WD-76845-024 H&E 5 11 WD-76845-024.ome.tif WD-76845-024-metadata.csv 25 WD-76845-025 t-CyCIF 5 83.6 WD-76845-025.ome.tif WD-76845-025-metadata.csv 28 WD-76845-028 H&E 5 10.1 WD-76845-028.ome.tif WD-76845-028-metadata.csv 29 WD-76845-029 t-CyCIF 5 74.4 WD-76845-029.ome.tif WD-76845-029-metadata.csv 33 WD-76845-033 H&E 5 11.8 WD-76845-033.ome.tif WD-76845-033-metadata.csv 34 WD-76845-034 t-CyCIF 5 82.2 WD-76845-034.ome.tif WD-76845-034-metadata.csv 38 WD-76845-038 H&E 5 11.3 WD-76845-038.ome.tif WD-76845-038-metadata.csv 39 WD-76845-039 t-CyCIF 5 80.2 WD-76845-039.ome.tif WD-76845-039-metadata.csv 43 WD-76845-043 H&E 5 11 WD-76845-043.ome.tif WD-76845-043-metadata.csv 44 WD-76845-044 t-CyCIF 5 76.6 WD-76845-044.ome.tif WD-76845-044-metadata.csv 48 WD-76845-048 H&E 5 11.2 WD-76845-048.ome.tif WD-76845-048-metadata.csv 49 WD-76845-049 t-CyCIF 5 76.6 WD-76845-049.ome.tif WD-76845-049-metadata.csv 50 WD-76845-050 t-CyCIF 5 80.2 WD-76845-050.ome.tif WD-76845-050-metadata.csv 51 WD-76845-051 t-CyCIF 5 76.6 WD-76845-051.ome.tif WD-76845-051-metadata.csv 52 WD-76845-052 t-CyCIF 5 80.2 WD-76845-052.ome.tif WD-76845-052-metadata.csv 53 WD-76845-053 H&E 5 10.5 WD-76845-053.ome.tif WD-76845-053-metadata.csv 54 WD-76845-054 t-CyCIF 5 74.5 WD-76845-054.ome.tif WD-76845-054-metadata.csv 58 WD-76845-058 H&E 5 10.5 WD-76845-058.ome.tif WD-76845-058-metadata.csv 59 WD-76845-059 t-CyCIF 5 80.2 WD-76845-059.ome.tif WD-76845-059-metadata.csv 63 WD-76845-063 H&E 5 10.5 WD-76845-063.ome.tif WD-76845-063-metadata.csv 64 WD-76845-064 t-CyCIF 5 74.4 WD-76845-064.ome.tif WD-76845-064-metadata.csv 68 WD-76845-068 H&E 5 10.1 WD-76845-068.ome.tif WD-76845-068-metadata.csv 69 WD-76845-069 t-CyCIF 5 69.5 WD-76845-069.ome.tif WD-76845-069-metadata.csv 73 WD-76845-073 H&E 5 9.1 WD-76845-073.ome.tif WD-76845-073-metadata.csv 74 WD-76845-074 t-CyCIF 5 69.5 WD-76845-074.ome.tif WD-76845-074-metadata.csv 77 WD-76845-077 H&E 5 10.5 WD-76845-077.ome.tif WD-76845-077-metadata.csv 78 WD-76845-078 t-CyCIF 5 69.5 WD-76845-078.ome.tif WD-76845-078-metadata.csv 83 WD-76845-083 H&E 5 9.6 WD-76845-083.ome.tif WD-76845-083-metadata.csv 84 WD-76845-084 t-CyCIF 5 69.5 WD-76845-084.ome.tif WD-76845-084-metadata.csv 85 WD-76845-085 H&E 4 10.6 WD-76845-085.ome.tif WD-76845-085-metadata.csv 86 WD-76845-086 t-CyCIF 4 72.4 WD-76845-086.ome.tif WD-76845-086-metadata.csv 90 WD-76845-090 H&E 4 9.9 WD-76845-090.ome.tif WD-76845-090-metadata.csv 91 WD-76845-091 t-CyCIF 4 72.4 WD-76845-091.ome.tif WD-76845-091-metadata.csv 96 WD-76845-096 H&E 4 10.6 WD-76845-096.ome.tif WD-76845-096-metadata.csv 97 WD-76845-097 t-CyCIF 4 74.5 WD-76845-097.ome.tif WD-76845-097-metadata.csv 101 WD-76845-101 H&E 4 10.5 WD-76845-101.ome.tif WD-76845-101-metadata.csv 102 WD-76845-102 t-CyCIF 4 72.4 WD-76845-102.ome.tif WD-76845-102-metadata.csv 105 WD-76845-105 H&E 4 9.6 WD-76845-105.ome.tif WD-76845-105-metadata.csv 106 WD-76845-106 t-CyCIF 4 69.5 WD-76845-106.ome.tif WD-76845-106-metadata.csv ---- CRC2-17 Images Files CRC02 to CRC17 derive from additional patients from the Brigham and Women’s Hospital. H&E Patient Data filename Metadata filename File size (GB) CRC02 data/CRC02-HE.ome.tif - 17.2 CRC03 data/CRC03-HE.ome.tif - 12.9 CRC04 data/CRC04-HE.ome.tif - 15.5 CRC05 data/CRC05-HE.ome.tif - 12.8 CRC06 data/CRC06-HE.ome.tif - 16.2 CRC07 data/CRC07-HE.ome.tif - 10.9 CRC08 data/CRC08-HE.ome.tif - 18.0 CRC09 data/CRC09-HE.ome.tif - 12.6 CRC10 data/CRC10-HE.ome.tif - 19.5 CRC11 data/CRC11-HE.ome.tif - 13.6 CRC12 data/CRC12-HE.ome.tif - 15.0 CRC13 data/CRC13-HE.ome.tif - 7.5 CRC14 data/CRC14-HE.ome.tif - 13.2 CRC15 data/CRC15-HE.ome.tif - 12.6 CRC16 data/CRC16-HE.ome.tif - 15.4 CRC17 data/CRC17-HE.ome.tif - 16.5 Main CyCIF panel Patient Data filename Metadata filename File size (GB) CRC02 data/CRC02.ome.tif metadata/CRC202105 HTAN channel metadata.csv 93.4 CRC03 data/CRC03.ome.tif metadata/CRC202105 HTAN channel metadata.csv 72.6 CRC04 data/CRC04.ome.tif metadata/CRC202105 HTAN channel metadata.csv 70.6 CRC05 data/CRC05.ome.tif metadata/CRC202105 HTAN channel metadata.csv 54.7 CRC06 data/CRC06.ome.tif metadata/CRC202105 HTAN channel metadata.csv 74.5 CRC07 data/CRC07.ome.tif metadata/CRC202105 HTAN channel metadata.csv 61.2 CRC08 data/CRC08.ome.tif metadata/CRC202105 HTAN channel metadata.csv 86.2 CRC09 data/CRC09.ome.tif metadata/CRC202105 HTAN channel metadata.csv 68.1 CRC10 data/CRC10.ome.tif metadata/CRC202105 HTAN channel metadata.csv 62.5 CRC11 data/CRC11.ome.tif metadata/CRC202105 HTAN channel metadata.csv 59.6 CRC12 data/CRC12.ome.tif metadata/CRC202105 HTAN channel metadata.csv 76.7 CRC13 data/CRC13.ome.tif metadata/CRC202105 HTAN channel metadata.csv 49.6 CRC14 data/CRC14.ome.tif metadata/CRC202105 HTAN channel metadata.csv 75.5 CRC15 data/CRC15.ome.tif metadata/CRC202105 HTAN channel metadata.csv 75.1 CRC16 data/CRC16.ome.tif metadata/CRC202105 HTAN channel metadata.csv 81.7 CRC17 data/CRC17.ome.tif metadata/CRC202105 HTAN channel metadata.csv 79.6 Immune-focused CyCIF panel Patient Data filename Metadata filename File size (GB) CRC02 data/73-8/TNPCRC_01.ome.tif metadata/73-8-channel-metadata.csv 111.2 CRC03 data/73-8/TNPCRC_02.ome.tif metadata/73-8-channel-metadata.csv 70.1 CRC04 data/73-8/TNPCRC_03.ome.tif metadata/73-8-channel-metadata.csv 100.3 CRC05 data/73-8/TNPCRC_04.ome.tif metadata/73-8-channel-metadata.csv 81.9 CRC06 data/73-8/TNPCRC_05.ome.tif metadata/73-8-channel-metadata.csv 118.3 CRC07 data/73-8/TNPCRC_06.ome.tif metadata/73-8-channel-metadata.csv 65.8 CRC08 data/73-8/TNPCRC_08.ome.tif metadata/73-8-channel-metadata.csv 75.1 CRC09 data/73-8/TNPCRC_09.ome.tif metadata/73-8-channel-metadata.csv 81.0 CRC10 data/73-8/TNPCRC_10.ome.tif metadata/73-8-channel-metadata.csv 103.0 CRC11 data/73-8/TNPCRC_11.ome.tif metadata/73-8-channel-metadata.csv 84.3 CRC12 data/73-8/TNPCRC_12.ome.tif metadata/73-8-channel-metadata.csv 52.4 CRC13 data/73-8/TNPCRC_13.ome.tif metadata/73-8-channel-metadata.csv 78.5 CRC14 data/73-8/TNPCRC_14.ome.tif metadata/73-8-channel-metadata.csv 86.5 CRC15 data/73-8/TNPCRC_15.ome.tif metadata/73-8-channel-metadata.csv 86.0 CRC16 data/73-8/TNPCRC_16.ome.tif metadata/73-8-channel-metadata.csv 105.8 CRC17 data/73-8/TNPCRC_17.ome.tif metadata/73-8-channel-metadata.csv 137.5 Tumor-focused CyCIF panel Patient Data filename Metadata filename File size (GB) CRC02 data/73-9/TNPCRC_01.ome.tif metadata/73-9-channel-metadata.csv 100.1 CRC03 data/73-9/TNPCRC_02.ome.tif metadata/73-9-channel-metadata.csv 67.4 CRC04 data/73-9/TNPCRC_03.ome.tif metadata/73-9-channel-metadata.csv 104.8 CRC05 data/73-9/TNPCRC_04.ome.tif metadata/73-9-channel-metadata.csv 69.4 CRC06 data/73-9/TNPCRC_05.ome.tif metadata/73-9-channel-metadata.csv 125.5 CRC07 data/73-9/TNPCRC_06.ome.tif metadata/73-9-channel-metadata.csv 98.5 CRC08 data/73-9/TNPCRC_08.ome.tif metadata/73-9-channel-metadata.csv 90.6 CRC09 data/73-9/TNPCRC_09.ome.tif metadata/73-9-channel-metadata.csv 87.8 CRC10 data/73-9/TNPCRC_10.ome.tif metadata/73-9-channel-metadata.csv 111.6 CRC11 data/73-9/TNPCRC_11.ome.tif metadata/73-9-channel-metadata.csv 104.8 CRC12 data/73-9/TNPCRC_12.ome.tif metadata/73-9-channel-metadata.csv 59.3 CRC13 data/73-9/TNPCRC_13.ome.tif metadata/73-9-channel-metadata.csv 97.3 CRC14 data/73-9/TNPCRC_14.ome.tif metadata/73-9-channel-metadata.csv 98.5 CRC15 data/73-9/TNPCRC_15.ome.tif metadata/73-9-channel-metadata.csv 104.0 CRC16 data/73-9/TNPCRC_16.ome.tif metadata/73-9-channel-metadata.csv 120.4 CRC17 data/73-9/TNPCRC_17.ome.tif metadata/73-9-channel-metadata.csv 147.4 ---- Access Spatial feature tables (main CyCIF panel; CRC1-17) CRC01-002 (46 MB) CRC01-007 (45 MB) CRC01-014 (41 MB) CRC01-020 (38 MB) CRC01-025 (39 MB) CRC01-029 (41 MB) CRC01-034 (54 MB) CRC01-039 (45 MB) CRC01-044 (36 MB) CRC01-049 (52 MB) CRC01-050 (49 MB) CRC01-051 (60 MB) CRC01-052 (55 MB) CRC01-054 (49 MB) CRC01-059 (46 MB) CRC01-064 (57 MB) CRC01-069 (48 MB) CRC01-074 (56 MB) CRC01-078 (54 MB) CRC01-084 (56 MB) CRC01-086 (55 MB) CRC01-091 (49 MB) CRC01-097 (55 MB) CRC01-102 (55 MB) CRC01-106 (53 MB) CRC02 (58 MB) CRC03 (50 MB) CRC04 (75 MB) CRC05 (57 MB) CRC06 (39 MB) CRC07 (51 MB) CRC08 (67 MB) CRC09 (22 MB) CRC10 (41 MB) CRC11 (34 MB) CRC12 (69 MB) CRC13 (24 MB) CRC14 (32 MB) CRC15 (56 MB) CRC16 (22 MB) CRC17 (79 MB) ---- Single-cell sequencing data & GeoMX count tables The single-cell sequncing data of this study could be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166319 The GeoMX data (count tables) could be download from here: https://github.com/labsyspharm/CRC_atlas_2022/tree/main/GeoMX_data