HTA CRC Atlas 1 primary data

V1.0 ReadMe

April 8, 2021

This data in this folder represent minimally processed (Level 2) image data relevant to HMS HTAN Center CRC Atlas 1. Images are subjected to additional quality control, segmentation and quantification to generate final data. Primary image data files below are OME-TIFF tiled pyramid images, and spatial feature tables are zipped CSV files. The total data size is 3.2 TB.

Data were collected using cyclic immunofluorescence as described in https://dx.doi.org/10.17504/protocols.io.bjiukkew. Each file corresponds to a multiplexed image mosaic for ~1.5 cm x ~1.5 cm FFPE tissue section 5 microns thick. Each image is assembled from a series of ~400 successive megapixel image tiles stitched together and flat-fielded using MCMICRO software to generate whole-slide images each with ~10^9 pixels. Tiles were collected for each CyCIF round (8 in total) and these are combined in the mosaic image to generate a composite with 25 or more channels.

The data were collected on a RareCyte Inc. CyteFinder slide scanning fluorescence microscope using a 20x 0.75 NA objective.

Files CRC01-001 to CRC01-106 derive from specimen CRC1, provided by the Cooperative Human Tissue Network (CHTN) and resected from the cecum of a 69-year old male; pathology revealed a poorly differentiated stage IIIB adenocarcinoma (pT3N1bM0) with microsatellite instability (MSI-H) and a BRAFV600E (c.1799T>A) mutation. The tumor had an extended front invading into the muscularis propria and connective tissue.

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

Additional information on antibodies and specimen are available at https://labsyspharm.github.io/HTA-CRCATLAS-1/.

All files below may be downloaded directly. For bulk downloads you may use wish to use an Amazon Web Services S3 compatible download tool, connecting to the following address:

s3://lin-2021-crc-atlas/data/

OME-TIFF primary image data

Spatial feature tables (CSV)