Datasets

Appendiceal scRNAseq

Cellranger outputs from single-cell RNA sequencing of Appendiceal mucinous neoplasms (AMN), pseudomyxoma peritonei (PMP) and paired normal tissue.

Download the following files at: https://dna-discovery.stanford.edu/publicmaterial/datasets/appendix_scRNAseq/.

  • Raw output: appendiceal_scRNAseq_raw.zip
  • Filtered output: appendiceal_scRNAseq_filtered.zip
  • Readme file: appendiceal_scRNAseq_README.txt

For more details see:  Distinct cell states define the developmental trajectories of mucinous appendiceal neoplasms towards pseudomyxoma metastases.

Ayala C*, Sathe A*, Bai X, Grimes SM, Shen J, et al. Frontiers in Genetics, 2025, doi: 10.3389/fgene.2025.1536982

Gastric Cancer (GC) and Metastatic Colorectal Cancer (mCRC) single-cell multi-omic datasets (scDNA & scRNA)

Single-cell multi-omic datasets (scRNA-seq & scDNA-seq) for the primary gastric (GC) and metastatic colon (mCRC) cancers. Both scDNA-seq and scRNA-seq assays on thousands of single cells derived from the same specimen. Cellranger outputs from scRNA-seq and copy number variation matrix from scDNA-seq.

For more details see: “Single cell multi-omic mapping of subclonal architecture and pathway phenotype in primary gastric and metastatic colon cancers”

Bai, X., Lau, B., Sathe, A., Grimes, S. M., Almeda, A., & Ji, H. P. bioRxiv, (2024).

GITR and TIGIT immunotherapy tumor slice culture scRNA-seq

Cellranger outputs from single-cell RNA sequencing gastric and colorectal cancer (‘T0) and their
tumor slice cultures treated with control, PMA/Ionomycin, GITR agonist or TIGIT antagonist.

For more details see:  GITR and TIGIT immunotherapy provokes divergent multi-cellular
responses in the tumor microenvironment of gastrointestinal cancers

Sathe A, Ayala C, Bai X, Grimes SM, et al. Genome Medicine, 2023

Metastatic Colorectal Cancer (mCRC) scRNA-seq

Cellranger outputs from single-cell RNA sequencing of Metastatic Colorectal Cancer (mCRC), paired normal liver tissue and peripheral blood mononuclear cells.

For more details see:  Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblasts.

Sathe A, Mason M, Grimes SM, Zhou Z, et al. Clinical Cancer Research, 2022

Pangenome Conservation and Divergence

Structural variants have been poorly characterized due to various limitations including sequencing technologies and the reference genome. In particular, many specific sequence features are not represented in the current reference build and making comparisons with other assemblies can be challenging. We propose a rapid and scalable framework to identify highly conserved and divergent regions across a large set of haploid assemblies using a highly conserved subset of unique short sequences.

Download bed format files at https://dna-discovery.stanford.edu/publicmaterial/datasets/pangenome.

  • Pan-conserved sequences and their GRCh38 coordinates: pan-conserved_seq.grch38.zip
  • Pan-conserved sequences and their CHM13 coordinates: pan-conserved_seq.chm13.zip
  • All measured interval lengths between the selected pan-conserved sequences pairs: interval_length_matrix.zip

SARS-CoV-2 Mutation Fingerprints

Datasets and tables for the publication “Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies” by Billy T. Lau, Dmitri S. Pavlichin, Anna C. Hooker, Alison Almeda, Giwon Shin, Jiamin Chen, Malaya K. Sahoo, ChunHong Huang, Benjamin A. Pinsky, HoJoon Lee, and Hanlee P. Ji.

For more project details, see: https://dna-discovery.stanford.edu/research/web-resources/sars-cov-2-mutation-fingerprints/.

Gastric scRNAseq

Cellranger outputs from single-cell RNA sequencing of gastric cancer, metaplasia, paired normal tissue and PBMCs (right-click link and select “Open in New Window”):

For more details see: Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment. Sathe A, Grimes SM, Lau BT, Chen J, Suarez C, Huang RJ, et al. Clin Cancer Res 2020doi 10.1158/1078-0432.CCR-19-3231.

Lymphoma scRNAseq

Cellranger outputs from single-cell RNA sequencing of follicular lymphoma tumor cells and tumor-infiltrating lymphocytes (right-click link and select “Open in New Window”):

For more details see: Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints; Andor N, Simonds EF, Czerwinski DK, Chen J, Grimes SM, Wood-Bouwens C, Zheng GXY, Kubit MA, Greer S, Weiss WA, Levy R, Ji HP: Blood, 2019 Mar 7;133(10):1119-1129.

The single-cell spatial landscape of stage III colorectal cancers

The files of H&E images for the publication of “The single-cell spatial landscape of stage III colorectal cancers”. 

All H&E images can be downloaded here.

Metastatic Colorectal Cancer (mCRC) CODEX

CODEX analysis of Metastatic Colorectal Cancer (mCRC)

· Cell-intensity matrices: mCRC_CODEX_intensities.zip

· Readme file: mCRC_CODEX _README.txt

· Cell labels: mCRC_CODEX_cell_labels.csv

For more details see: Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblasts

Sathe A, Mason M, Grimes SM, Zhou Z, et al. Clinical Cancer Research, 2022