figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Data Sheet 1_Exploiting RAG1-deficient chickens to construct a single-cell transcriptional atlas of chicken heterophils during inflammation.xlsxIntroduction<p>Avian heterophils naturally lack myeloperoxidase (MPO), making chicken a unique evolutionary model for investigating MPO-independent innate immune strategies. However, the molecular programs governing heterophil maturation and activation remain largely unexplored.</p>Methods<p>Using single-cell RNA sequencing in a RAG1-deficient chicken model, we mapped heterophil maturation during
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Supplementary file 1_Case Report: Melanocyte-associated mTORC1-related molecular features in an atypical large congenital melanocytic naevus.docx<p>Congenital melanocytic naevi (CMN) are usually associated with activating alterations in NRAS or BRAF, but some extensive lesions lack detectable canonical hotspot variants. We report a 9-year-old boy with a large craniofacial CMN involving the face, scalp, upper eyelid and bulbar conjunctiva, with deep extension, mechanical ptosis and secondary amblyopia. Histology showed benign dermal melanoc
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Table 2_Longitudinal single-cell analysis identifies a chemotherapy-suppressed proliferative program associated with adverse prognosis in neuroblastoma.xlsxBackground<p>High-risk neuroblastoma frequently relapses after intensive therapy, but the treatment-associated malignant-neuroblast programs that inform baseline tumor risk remain incompletely defined. We used longitudinal single-cell/single-nucleus RNA-seq data to identify post-treatment transcriptional changes in malignant neuroblasts and evaluated their prognostic relevance in diagnostic bulk R
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Table 1_Exploiting RAG1-deficient chickens to construct a single-cell transcriptional atlas of chicken heterophils during inflammation.docxIntroduction<p>Avian heterophils naturally lack myeloperoxidase (MPO), making chicken a unique evolutionary model for investigating MPO-independent innate immune strategies. However, the molecular programs governing heterophil maturation and activation remain largely unexplored.</p>Methods<p>Using single-cell RNA sequencing in a RAG1-deficient chicken model, we mapped heterophil maturation during
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Data Sheet 3_Exploiting RAG1-deficient chickens to construct a single-cell transcriptional atlas of chicken heterophils during inflammation.xlsxIntroduction<p>Avian heterophils naturally lack myeloperoxidase (MPO), making chicken a unique evolutionary model for investigating MPO-independent innate immune strategies. However, the molecular programs governing heterophil maturation and activation remain largely unexplored.</p>Methods<p>Using single-cell RNA sequencing in a RAG1-deficient chicken model, we mapped heterophil maturation during
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Table 1_Longitudinal single-cell analysis identifies a chemotherapy-suppressed proliferative program associated with adverse prognosis in neuroblastoma.xlsxBackground<p>High-risk neuroblastoma frequently relapses after intensive therapy, but the treatment-associated malignant-neuroblast programs that inform baseline tumor risk remain incompletely defined. We used longitudinal single-cell/single-nucleus RNA-seq data to identify post-treatment transcriptional changes in malignant neuroblasts and evaluated their prognostic relevance in diagnostic bulk R
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Single-cell RNA-seq data from Sakimoto et al, 2024<p dir="ltr">Seurat object (Filtered, processed scRNA-seq data) from Sakimoto et al, BJC Reports, 2024 (https://doi.org/10.1038/s44276-024-00112-3).</p>
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Data Sheet 4_Exploiting RAG1-deficient chickens to construct a single-cell transcriptional atlas of chicken heterophils during inflammation.xlsxIntroduction<p>Avian heterophils naturally lack myeloperoxidase (MPO), making chicken a unique evolutionary model for investigating MPO-independent innate immune strategies. However, the molecular programs governing heterophil maturation and activation remain largely unexplored.</p>Methods<p>Using single-cell RNA sequencing in a RAG1-deficient chicken model, we mapped heterophil maturation during
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Data Sheet 2_Exploiting RAG1-deficient chickens to construct a single-cell transcriptional atlas of chicken heterophils during inflammation.xlsxIntroduction<p>Avian heterophils naturally lack myeloperoxidase (MPO), making chicken a unique evolutionary model for investigating MPO-independent innate immune strategies. However, the molecular programs governing heterophil maturation and activation remain largely unexplored.</p>Methods<p>Using single-cell RNA sequencing in a RAG1-deficient chicken model, we mapped heterophil maturation during
figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Table 3_Longitudinal single-cell analysis identifies a chemotherapy-suppressed proliferative program associated with adverse prognosis in neuroblastoma.xlsxBackground<p>High-risk neuroblastoma frequently relapses after intensive therapy, but the treatment-associated malignant-neuroblast programs that inform baseline tumor risk remain incompletely defined. We used longitudinal single-cell/single-nucleus RNA-seq data to identify post-treatment transcriptional changes in malignant neuroblasts and evaluated their prognostic relevance in diagnostic bulk R
ZivaHub + Deakin Research Online + DMU Figshare + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Table 1_Single-cell profiling of peripheral immune remodeling in BK polyomavirus–associated nephropathy after kidney transplantation.xlsx<p>BK polyomavirus–associated nephropathy (BKPyVAN) remains a major cause of allograft dysfunction after kidney transplantation. To define peripheral immune signatures associated with distinct clinical states of BKPyV infection, we performed single-cell RNA sequencing of peripheral blood mononuclear cells from kidney transplant recipients across three clinical states: stable graft function (n = 1)
ZivaHub + Deakin Research Online + DMU Figshare + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Table 4_Single-cell profiling of peripheral immune remodeling in BK polyomavirus–associated nephropathy after kidney transplantation.xlsx<p>BK polyomavirus–associated nephropathy (BKPyVAN) remains a major cause of allograft dysfunction after kidney transplantation. To define peripheral immune signatures associated with distinct clinical states of BKPyV infection, we performed single-cell RNA sequencing of peripheral blood mononuclear cells from kidney transplant recipients across three clinical states: stable graft function (n = 1)
HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · RNA sequencing
All_genes_pseudobulk_Healthy_4wk_6wk<p dir="ltr">Pseudobulk genome-wide transcription from whole adult mouse lung. Three groups: healthy (no treatment), 4wkHDM (after 4 weeks of intranasal house dust mite exposure), and 6wkHDM (after 6 weeks of intranasal house dust mite exposure).</p>
ZivaHub + Deakin Research Online + DMU Figshare2026 · Single-cell RNA sequencing
Image 4_MTHFD1L-associated branched-chain amino acid degradation transcriptional signature represents a conserved metabolic program in Epstein-Barr virus-associated malignancies.jpg<p>Epstein-Barr virus (EBV)-associated malignancies encompass multiple tumor types with distinct tissue origins, yet the extent to which they share conserved metabolic programs remains poorly understood. Here, we performed an integrated cross-cancer transcriptomic analysis of nasopharyngeal carcinoma, EBV-associated gastric cancer, and EBV-associated plasmablastic lymphoma to identify conserved me
ZivaHub + Deakin Research Online + DMU Figshare + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · RNA sequencing
Supplementary data for transcriptomic analysis of suicide in bipolar disorder<p dir="ltr">This repository contains supplementary datasets associated with the manuscript, including differential gene expression (DEG) results, Gene Ontology biological process (GO BP) enrichment analyses, gene lists for WGCNA modules, and functional annotations of co-expression modules.</p>
ZivaHub + Deakin Research Online + DMU Figshare + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · RNA sequencing
Data and code for metabolic decompensation under co-occurring thermal-hypoxic stress in Pacific oysters<p dir="ltr">Processed data and analysis workflows supporting the study “Metabolic decompensation under co-occurring thermal-hypoxic stress: ESRRA alternative splicing drives non-additive oyster responses to coastal compound climate stress.” The package includes environmental temperature, salinity, and dissolved-oxygen data for oyster-associated shallow habitats (1995–2025), RNA-seq and ATAC-seq m
ZivaHub + Deakin Research Online + DMU Figshare2026 · RNA sequencing
Bioinformatics-driven insights into the role of cathepsins in tumour biology<div>Cysteine cathepsins are proteolytic enzymes implicated in cancer progression through their involvement in tumour growth, extracellular matrix (ECM) remodelling, and modulation of the tumour microenvironment (TME). This thesis examines the molecular roles of two cysteine cathepsins, cathepsin S (CTSS) and cathepsin V (CTSV), with a focus on their relevance to breast cancer biology and disease
ZivaHub + Deakin Research Online + DMU Figshare + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · RNA sequencing
Cell death-inducing effectors in the latent necrotrophic pathogen Cercospora zeina of maize<p dir="ltr">The datasets underpin a PhD study titled "Transcriptomics and structural phylogenetics reveals cell death-inducing effectors in the latent necrotrophic pathogen Cercospora zeina of maize." This fungal pathogen enters the stomata, developing asymptomatically, without producing haustoria-like structures for up to 28 days before symptoms develop. RNA sequencing was used to characterise t
ZivaHub + Deakin Research Online + DMU Figshare + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Single-cell RNA sequencing
Table 1_Patient-aware single-cell analysis of fibrovascular remodeling in a predominantly colorectal cancer immunotherapy cohort.xlsxBackground<p>Cancer-associated fibroblasts (CAFs) and vascular mural cells may shape extracellular matrix organization in colorectal cancer. However, single-cell comparisons are susceptible to unequal cell recovery, ambient RNA, doublets, treatment-stage mixing, and repeated sampling within patients. We investigated fibrovascular remodeling using patients as the inferential unit and distinguished
ZivaHub + Deakin Research Online + DMU Figshare2026 · Single-cell RNA sequencing
Image 5_MTHFD1L-associated branched-chain amino acid degradation transcriptional signature represents a conserved metabolic program in Epstein-Barr virus-associated malignancies.jpg<p>Epstein-Barr virus (EBV)-associated malignancies encompass multiple tumor types with distinct tissue origins, yet the extent to which they share conserved metabolic programs remains poorly understood. Here, we performed an integrated cross-cancer transcriptomic analysis of nasopharyngeal carcinoma, EBV-associated gastric cancer, and EBV-associated plasmablastic lymphoma to identify conserved me
ZivaHub + Deakin Research Online + DMU Figshare2026 · RNA sequencing
Impact of immune status and clinical outcomes in oropharyngeal cancerBackground: Oropharyngeal squamous cell carcinoma (OPSCC) is a biologically and clinically heterogeneous disease, known for having distinct molecular and prognostic features primarily driven by smoking, alcohol and human papillomavirus (HPV) infection. The immune system has emerged as a critical factor influencing cancer prognosis and survival. However, reliable, scalable, and interpretable approa
ZivaHub + Deakin Research Online + DMU Figshare2026 · RNA sequencing
Simplifying transcriptomic profiling and molecular subtyping of colorectal cancerWe hypothesised that the use of a high-throughput RNA-sequencing (RNA-seq) technology paired with an easy-to-use data analysis application could open the field of transcriptomic subtyping to a broader user base. TempO-Seq is particularly amenable to clinically relevant samples such as FFPE and remains an extremely high throughput sequencing technology. This thesis investigates the utility of the T
ZivaHub + Deakin Research Online + DMU Figshare2026 · Single-cell RNA sequencing
Image 2_MTHFD1L-associated branched-chain amino acid degradation transcriptional signature represents a conserved metabolic program in Epstein-Barr virus-associated malignancies.jpg<p>Epstein-Barr virus (EBV)-associated malignancies encompass multiple tumor types with distinct tissue origins, yet the extent to which they share conserved metabolic programs remains poorly understood. Here, we performed an integrated cross-cancer transcriptomic analysis of nasopharyngeal carcinoma, EBV-associated gastric cancer, and EBV-associated plasmablastic lymphoma to identify conserved me
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · RNA sequencing · unknown
Implementation of global miRNA biomarker discovery in human plasmaPrecision medicine is improving health outcomes by tailoring patient care to specific individuals. The improved patient stratification needed to support further implementation of precision medicine will require developments in molecular diagnostics and identification of novel biomarkers. Small non-coding RNAs, specifically miRNAs, have been shown to exist extracellularly and are stable in biofluid
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · RNA sequencing · unknown
Androgen receptor mediated gene regulatory networks in prostate cancerProstate cancer (PCa) is the most common cancer diagnosed in men. The androgen receptor (AR) is a well-studied master regulator of PCa. Patients with metastatic PCa develop resistance to AR-targeted therapies, which can arise in part from tumour microenvironment signaling. AR activity is often maintained in treatment-resistant metastatic PCa alongside other important changes including epithelial-t