Data and Software Resources
The Diaz Lab develops and shares genomic datasets, single-cell and spatial resources, and open-source software for studying tumor evolution, cellular lineage, and therapeutic response. Public and controlled-access resources are organized below by study and scientific use.
Data resources
Longitudinal evolution of SHH medulloblastoma
Longitudinal single-nucleus transcriptomic, chromatin-accessibility, and spatial profiling of sonic hedgehog medulloblastoma, integrating treatment-naive and recurrent tumors to investigate cellular evolution, developmental programs, and therapeutic vulnerabilities.
Data:
GEO: GSE287107 — processed Visium spatial transcriptomics.
GEO: GSE287108 — processed single-nucleus ATAC-seq.
GEO: GSE287109 — processed single-nucleus RNA-seq.
These GEO records are currently private; public release is scheduled for January 9, 2027.
EGA: EGAS50000000816 — raw sequencing data. Controlled access; dataset release pending, with access subject to the applicable Data Access Committee. Study metadata are publicly visible.
(Jain et al., Genome Medicine 2026, accepted)
Diffuse midline glioma response and resistance to imipridones
Single-nucleus transcriptomic and chromatin-accessibility profiling of postmortem diffuse midline glioma specimens from patients treated with imipridones or standard care, supporting analyses of tumor-cell states, the microenvironment, and mitochondrial adaptation associated with treatment resistance.
Data:
EGA: EGAS50000001447 — raw single-nucleus RNA and chromatin-accessibility sequencing reads. Controlled access; dataset release pending, with access subject to the applicable Data Access Committee. Study metadata are publicly visible.
UCSC Cell Browser — public processed single-nucleus RNA expression matrices and cell annotations, with visualization and data-download links.
(Okada et al., Neuro-Oncology 2026)
MAPK-driven glioma progression
Single-nucleus profiling of MAPK-driven glioma progression and associated changes in the tumor immune response.
Data:
GEO: GSE312124 — raw sequencing via SRA and processed single-nucleus expression matrices.
(Hashemi et al., Neuro Oncol 2026)
PNOC005 pediatric oncolytic-virus immunotherapy
Transcriptomic resources from the PNOC005 measles-virus immunotherapy study and complementary preclinical models.
Data:
GEO: GSE294899 — processed mouse single-cell expression matrices.
GEO: GSE294901 — processed bulk expression tables from human and mouse samples.
EGA: EGAS50000000811 — controlled sequencing, including human blood/PBMC samples. Controlled access; application required.
(Yu et al., Clin Cancer Res 2025)
T-cell receptor landscape of childhood brain tumors
Single-cell expression and T-cell receptor analysis objects for studying the immune landscape of childhood brain tumors.
Data:
Zenodo: 14846954 — single-cell and TCR analysis objects; restricted access. Restricted access; application required.
(Raphael et al., Sci Transl Med 2025)
Longitudinal molecular profiling of adult glioma
DNA methylation resources from a longitudinal glioblastoma study, with an IDH-mutant astrocytoma comparison cohort.
Data:
GEO: GSE279073 — raw methylation-array IDAT files and processed tables for glioblastoma.
GEO: GSE260850 — raw methylation-array IDAT files for the astrocytoma comparison cohort.
(Lucas et al., Neuro Oncol 2025)
Glioblastoma-associated hybrid neutrophils
Single-cell profiling of blood and tumor-associated neutrophils in a study of glioblastoma-driven myeloid differentiation.
Data:
GEO: GSE271618 — raw sequencing via SRA and processed single-cell expression matrices.
(Lad et al., Cancer Cell 2024)
Vessel co-option and treatment resistance in glioblastoma
Transcriptomic and proteomic profiles of the vessel-co-opting glioblastoma state associated with chemoradiation resistance.
Data:
GEO: GSE218860 — raw RNA-seq via SRA and processed TPM expression tables.
PRIDE: PXD042606 — proteomic and phosphoproteomic study files.
(Pichol-Thievend et al., Nat Commun 2024)
Alternative-splicing-derived glioma surface antigens
Long-read transcript data supporting the investigation of tumor-specific alternative-splicing-derived cell-surface antigens in glioma.
Data:
GEO: GSE261440 — raw Nanopore reads via SRA and processed transcript counts.
PP2Ac loss and glioblastoma immunogenicity
Expression and exome resources for studies of PP2Ac loss, STING signaling, and glioblastoma immunogenicity.
Data:
GEO: GSE213309 — bulk and single-cell RNA study series.
BioProject/SRA: PRJNA973640 — raw exome sequencing reads from mouse models.
Figshare: 21094390 — cell annotations, analysis outputs, and supporting code.
(Mondal et al., Cancer Res 2023)
Glioblastoma-associated fibroblasts
Bulk transcriptomic profiles of isolated glioblastoma-associated fibroblasts complement the study’s single-cell and spatial analyses.
Data:
GEO: GSE132825 — raw bulk RNA-seq via SRA and normalized expression tables.
(Jain et al., J Clin Invest 2023)
Glioblastoma evolution under therapy
Longitudinal and multimodal resources for studying glioblastoma evolution under therapy, including expression, chromatin, and spatial profiles.
Data:
GEO: GSE174554 — processed expression matrices, chromatin peaks, and spatial transcriptomic/proteomic tables.
EGA: EGAS00001004909 — controlled human single-nucleus sequencing. Controlled access; application required.
(Wang et al., Nat Cancer 2022)
Cell states and spatial organization of diffuse midline glioma
Single-cell, chromatin, genomic, and spatial resources spanning diffuse midline glioma locations and ages.
Data:
GEO: GSE184357 — processed RNA and chromatin-accessibility matrices with cell metadata.
EGA: EGAS00001006431 — controlled tumor exome and targeted sequencing. Controlled access; application required.
Zenodo: 6807534 — HybISS expression maps, cell-type maps, and annotated spatial data.
Pan-cancer tumor immune archetypes
Tumor and immune expression resources supporting a pan-cancer census of dominant immune archetypes.
Data:
GEO: GSE184398 — raw sequencing via SRA and processed bulk and single-cell expression matrices.
ATRX, glial identity, and the glioma immune environment
Chromatin and expression resources from studies of ATRX-dependent glial identity and tumor immune composition.
Data:
GEO: GSE155430 — processed accessibility, expression, and CTCF profiling files.
EGA: EGAS00001004523 — controlled human single-cell chromatin-accessibility sequencing. Controlled access; application required.
(Babikir et al., Genome Biol 2021)
Alternative splicing in glioblastoma under therapy
Longitudinal glioblastoma expression and sequencing resources for studying the evolution of alternative splicing during treatment.
Data:
GEO: GSE155434 — processed human RNA expression tables.
EGA: EGAS00001004524 — controlled RNA and exome sequencing. Controlled access; application required.
(Wang et al., Genome Biol 2021)
miRNA-independent functions of pri-miRNA loci
Expression, chromatin, and imaging resources for studies of long noncoding primary-miRNA loci.
Data:
GEO: GSE137048 — raw sequencing via SRA and processed RNA/chromatin files.
Mendeley Data: 10.17632/c443rtpbyk.1 — immunocytochemistry images.
(He et al., Proc Natl Acad Sci U S A 2021)
Outer radial glia-like glioblastoma stem cells
Single-cell sequencing and analysis tables for investigating outer radial glia-like cancer stem cells in glioblastoma.
Data:
BioProject/SRA: PRJNA579593 — raw single-cell RNA sequencing reads.
Mendeley Data: 10.17632/ky8vs4xhp8.1 — cell annotations, clinical metadata, differential expression, and exome-result tables.
(Bhaduri et al., Cell Stem Cell 2020)
Proliferating glioblastoma cellular states
Single-cell expression and chromatin-accessibility resources for mapping proliferative states in glioblastoma.
Data:
EGA: EGAS00001003845 — controlled single-cell RNA and single-nucleus chromatin sequencing. Controlled access; application required.
(Wang et al., Cancer Discov 2019)
Temperature sensing in the mouse preoptic area
Single-neuron expression data from studies of temperature-dependent prostaglandin signaling and thermoregulation.
Data:
GEO: GSE126657 — raw sequencing via SRA and processed single-cell expression tables.
Pediatric glioma peptide-vaccine response
Peripheral-blood transcriptomic resources for studies of immune response patterns during pediatric glioma peptide vaccination.
Data:
BioStudies/ArrayExpress: E-MTAB-6270 — PBMC RNA-seq study records and linked sequencing data.
(Müller et al., JCI Insight 2018)
Glioma macrophage states and subclonal analysis
Single-cell sequencing resources for investigating glioma-associated macrophages and tumor subclones. The CONICS demonstration data share this study deposit.
Data:
EGA: EGAS00001002185 — controlled human single-cell RNA sequencing. Controlled access; application required.
(Müller et al., Genome Biol 2017; Müller et al., Bioinformatics 2018)
Translation and embryonic stem-cell chromatin
Chromatin-accessibility and histone-acetylation profiles linking translational output to embryonic stem-cell chromatin state.
Data:
GEO: GSE98358 — raw sequencing via SRA and processed signal tracks and peak files.
(Bulut-Karslioglu et al., Cell Stem Cell 2018)
PDGF- and EGF-driven glioma phylogenies
Sequencing resources connecting glioma cell-expression states with mutational phylogenies.
Data:
EGA: EGAS00001001900 — controlled single-cell RNA and exome sequencing. Controlled access; application required.
(Müller et al., Mol Syst Biol 2016)
Long noncoding RNAs in developing human neocortex
Expression resources for mapping long noncoding RNAs in the developing neocortex.
Data:
GEO: GSE71315 — raw bulk RNA sequencing and processed transcript annotations and expression tables.
(Liu et al., Genome Biol 2016)
Glioblastoma epimutations and gene-body promoters
Foundational collaborative resources for studying epimutations, gene-body promoters, expression, and copy number in glioblastoma.
Data:
EGA: EGAS00001000685 — controlled methylation and H3K4me3 sequencing. Controlled access; application required.
GEO: GSE49412 — raw expression-array CEL files and processed expression tables.
GEO: GSE49808 — raw and processed copy-number array files.
(Nagarajan et al., Genome Res 2014)
Polycomb recruitment in embryonic stem cells
Foundational collaborative chromatin-profiling resources for studies of Polycomb recruitment and embryonic stem-cell self-renewal.
Data:
GEO: GSE28325 — raw ChIP-seq alignments/reads and processed peak files.
(Hunkapiller et al., PLoS Genet 2012)
Software resources
SPICE
Single-cell Plasticity Inference and Clonal Evolution: workflows for somatic-variant filtering, clone reconstruction, and cellular plasticity analysis. Software / GitHub.
CONICS
Integrates single-cell RNA profiles with DNA sequencing to infer tumor subclones. Software / GitHub. (Müller et al., Bioinformatics 2018)
ELSA
Ensemble learning for classifying single-cell profiles and projecting them across reference atlases. Software / GitHub. (Wang et al., Bioinformatics 2020)
SCell
An integrated workflow for single-cell RNA-seq analysis. Software / GitHub. (Diaz et al., Bioinformatics 2016)
HiTSelect
Analysis and hit selection for high-complexity pooled genetic screens. Software / GitHub. (Diaz et al., Nucleic Acids Res 2015)
CHANCE
Quality control and validation of ChIP-seq experiments. Software / GitHub. (Diaz et al., Genome Biol 2012)