Document Type
Article
Publication Date
5-20-2024
Original Citation
Domanskyi S,
Srivastava A,
Kaster J,
Li H,
Herlyn M,
Rubinstein J,
Chuang J.
Nextflow pipeline for Visium and H&E data from patient-derived xenograft samples. Cell Rep Methods. 2024;4(5):100759.
Keywords
JGM, Humans, Animals, Mice, Heterografts, Gene Expression Profiling, Eosine Yellowish-(YS), Hematoxylin, Transcriptome, Image Processing, Computer-Assisted, Xenograft Model Antitumor Assays
JAX Source
Cell Rep Methods. 2024;4(5):100759.
ISSN
2667-2375
PMID
38626768
DOI
https://doi.org/10.1016/j.crmeth.2024.100759
Grant
J.H.C. acknowledges support from grants NCI U24-CA224067, R01CA230031, and P30CA034196.
Abstract
We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole-slide image (WSI), optimized for patient-derived xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genome input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.