labsyspharm/CRC_atlas_2022

Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer
Jia-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.2022.12.028
Learn more: tissue-atlas.org/atlas-datasets/lin-wang-coy-2021/

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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.

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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 metadata
CRC2-17 images and image metadata
Spatial features tables
Single-cell sequencing data and GeoMX count tables

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CRC1 Images

The following table contains summary biospecimen and file metadata for all 47 sections.

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CRC2-17 Images

Files CRC02 to CRC17 derive from additional patients from the Brigham and Women’s Hospital.

H&E

Main CyCIF panel

Immune-focused CyCIF panel

Tumor-focused CyCIF panel

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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)

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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