Datasets

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.