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| Status |
Public on May 21, 2024 |
| Title |
Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
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 genomes 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.
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| Overall design |
The PDX model WISTAR WM4237-1 is a BRAF V600E mutant metastatic melanoma of a subcutaneously implanted solid tumor on NSG mouse #1337, passage 0. The tumor was grown untreated by any therapy. The four samples are near adjacent tissue sections from the tumor tissue block. The samples were analyzed with 10x Visium Spatial Gene Expression.
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| Contributor(s) |
Sergii D, Anuj S, Jessica K, Haiyin L, Meenhard H, Jill RC, Jeffrey CH |
| Citation(s) |
38626768 |
| Submission date |
Jul 21, 2023 |
| Last update date |
Jun 12, 2024 |
| Contact name |
Jeffrey H Chuang |
| E-mail(s) |
jeff.chuang@jax.org
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| Organization name |
The Jackson Laboratory for Genomic Medicine
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| Street address |
10 Discovery Drive
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| GSM7657717 |
WM4237-1, mouse 1337, untreated, sample S1 |
| GSM7657718 |
WM4237-1, mouse 1337, untreated, sample S2 |
| GSM7657719 |
WM4237-1, mouse 1337, untreated, sample S3 |
| GSM7657720 |
WM4237-1, mouse 1337, untreated, sample S4 |
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| Relations |
| BioProject |
PRJNA997362 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE238004_RAW.tar |
161.5 Mb |
(http)(custom) |
TAR (of CSV, JPG, JSON, MTX, PNG, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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