Data and Code

Public sequencing datasets and analysis resources.

Selected Vignali Laboratory publications provide public sequencing datasets that can be reanalyzed through GEO, SRA, and BioProject records, alongside shared code resources from the lab GitHub organization.

Sequencing Resources

Published datasets linked to the original papers.

Each entry lists the GEO accession, related publication, assay type, species, and disease or tumor model so users can quickly decide whether the dataset is relevant for reanalysis.

Code

Vignali Lab GitHub

Open GitHub

GSE262740

LAG3 and PD1 synergize on CD8+ T cells to drive T cell exhaustion and hinder autocrine IFN gamma-dependent anti-tumor immunity.

Data type: Single-cell RNA-seq with CITE-seq hashtagging and TCR-seq.
Species: Murine
Disease model: Melanoma mouse models; polyclonal and pMEL CD8+ T cells with PD1 and/or LAG3 deficiency.

scRNA-seqCITE-seqTCR-seqMurineMelanomaCD8 T cells

GSE239750

Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells.

Data type: Single-cell RNA-seq/CITE-seq plus bulk RNA-seq of BATF knockout human activated Tregs.
Species: Human
Disease model: Cancer; intratumoral Tregs in HNSCC, melanoma, NSCLC, SCLC, tonsil tissue, PBMC, and in vitro activated Tregs.

scRNA-seqCITE-seqBulk RNA-seqHumanCancerTregs

GSE225063

Blockade of LAG3 and PD1 leads to co-expression of cytotoxic and exhaustion gene modules in CD8+ T cells to promote antitumor immunity.

Data type: Single-cell RNA-seq, CITE-seq, and TCR-seq.
Species: Human
Disease model: Advanced melanoma; PBMC and tumor biopsies before and after relatlimab, nivolumab, or combination treatment.

scRNA-seqCITE-seqTCR-seqHumanMelanomaImmunotherapy

GSE139324

Immune landscape of viral- and carcinogen-driven head and neck cancer.

Data type: Single-cell RNA-seq.
Species: Human
Disease model: Head and neck squamous cell carcinoma; HPV-positive and HPV-negative tumors, PBMC, healthy donor PBMC, and tonsil tissue.

scRNA-seqHumanHNSCCCancerTumor immunity

GSE193911

Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment.

Data type: Single-cell RNA-seq.
Species: Human
Disease model: ER-positive invasive ductal carcinoma and invasive lobular breast cancer; tumor, tumor-adjacent tissue, and peripheral blood immune landscapes.

scRNA-seqHumanBreast cancerIDCILC

GSE223210

IFN gamma-induction of TH1-like regulatory T cells controls antiviral responses.

Data type: RNA-seq.
Species: Murine
Disease model: Chronic viral infection; IFN gamma-induced TH1-like regulatory T cell responses in mouse antiviral immunity.

RNA-seqMurineViral infectionTregsIFN gamma

GSE127735

Adaptive plasticity of IL-10+ and IL-35+ Treg cells cooperatively promotes tumor T cell exhaustion.

Data type: Bulk RNA-seq.
Species: Murine
Disease model: Cancer; CD8+ T cells and IL-10+/IL-35+ Treg subpopulations in mouse tumor models.

Bulk RNA-seqMurineCancerTregsCD8 T cells

GSE126184

Adaptive plasticity of IL-10+ and IL-35+ Treg cells cooperatively promotes tumor T cell exhaustion.

Data type: Single-cell RNA-seq.
Species: Murine
Disease model: Cancer; Tregs from unchallenged lymph nodes and day 14 B16 tumors in Foxp3Cre-YFP mice.

scRNA-seqMurineCancerTregsB16

GSE199357

Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3.

Data type: Bulk RNA-seq, single-cell RNA-seq, paired TCR-seq, CITE-seq, and single-cell multiome ATAC/RNA-seq.
Species: Murine
Disease model: Autoimmune diabetes; islet and lymph-node CD8+ T cell states in a mouse disease model.

Bulk RNA-seqscRNA-seqTCR-seqCITE-seqMultiomeMurineAutoimmunity

GSE246703

Regulatory T cells in the tumor microenvironment display a unique chromatin accessibility profile.

Data type: ATAC-seq and RNA-seq.
Species: Murine
Disease model: Cancer; regulatory T cells in mouse tumor microenvironment models.

ATAC-seqRNA-seqMurineCancerTregs

GSE158801

Metabolic support of tumour-infiltrating regulatory T cells by lactic acid.

Data type: RNA-seq.
Species: Murine
Disease model: Cancer; tumor-infiltrating and lymph-node regulatory T cell metabolism in mouse tumor models.

RNA-seqMurineCancerTregsMetabolism