Project description:Fresh frozen samples from human white matter MS lesions. Using Stereo-seq we compared mixed active/inactive lesions with lipid-laden foamy microglia with lesions containing ramified microglia. Study includes post-mortem subcortical white matter (WM) tissue of n = 7 donors with MS (5 females, 2 males). Scripts used for analysis are available stored on github under doi: 10.5281/zenodo.19710470
Project description:Current tools for functionally profiling T cell receptors with respect to cytotoxic potency and cross-reactivity are hampered by difficulties in establishing model systems to test these proteins in the contexts of different HLA alleles and against broad arrays of potential antigens. We have implemented a granzyme-activatable sensor of T cell cytotoxicity in a universal prototyping platform which enables facile recombinant expression of any combination of TCR-, peptide-, and class I MHC-coding sequences and direct assessment of resultant responses. This system consists of an engineered cell platform based on the immortalized natural killer cell line, YT-Indy, and the MHC-null antigen-presenting cell line, K562. These cells were engineered to furnish the YT-Indy/K562 pair with appropriate protein domains required for recombinant TCR expression and function in a non-T cell chassis, integrate a fluorescence-based target-centric early detection reporter of cytotoxic function, and deploy a set of protective genetic interventions designed to preserve antigen-presenting cells for subsequent capture and downstream characterization. As part of the development of the system, we conducted an RNA-seq study to characterize transcript expression in the base YT-Indy cell line, the genome engineered YT-rCTL version in the presence or absence of cognate antigen-presenting cells, and primary tissue derived TCR-T comparator cells in the presence or absence of cognate antigen-presenting cells. These data represent a supplement to the bioRxiv pre-print (DOI 10.1101/2023.11.20.567960) and the final published version in npj Precision Oncology (2024). An identical dataset corresponding to this entry has also been previously deposited in the Zenodo repository (DOI 10.5281/zenodo.8428843).
Project description:ScRNAseq data from human donors with or without T1D. Please see the associated GitHub repository for recapitulation of the analysis: https://github.com/Lab-of-Adaptive-Immunity/dia and the associated Zenodo link: 10.5281/zenodo.17280189
Project description:Visium Spatial dataset of 20-months and 3-months old transgenic mice. The model demonstrates α-syn oligomer spread and accumulation at synapses within specific forebrain and midbrain regions, including the SNpc, enabling the observation of α-syn oligomer propagation by including a human α-syn protein complementation system expressing α-syn fused to non-fluorescent Venus YFP halves (V1S and SV2), which can reconstitute to fluorescent Venus YFP (V1S/SV2) when α-syn oligomerization takes place. This dataset includes 3 animals per condition with 3-4 slices per animal. Processed count matrices, metadata and objects with filtered, clustered, and annotated data can be found on Zenodo: 1. 10.5281/zenodo.15274014 2. 10.5281/zenodo.14988055
Project description:Using 23-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000. Processed count matrices, metadata and objects with filtered, clustered, and annotated data can be found on Zenodo: 10.5281/zenodo.14988055
Project description:We used Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale, for profiling spatial transcriptome associated with biopsy-associated colon injury. Raw 1st-Seq FASTQ with intact tile and coordinate information could be retrieved from https://doi.org/10.5281/zenodo.13118097
Project description:This dataset contains LC-MS/MS data for the identification of Phasianidae species (Gallus gallus and Phasianus colchicus) from the Gungok-ri site in South Korea. The repository includes raw files from nine specimens (two modern reference samples and seven archaeological samples). Corresponding MALDI-FT-ICR-MS data can be found on Zenodo (DOI: 10.5281/zenodo.17933349)
Project description:To facilitate new studies in the Amaryllidoideae subfamily, we present AmarylOmicBase, a unified transcriptomic database that integrates assemblies, annotations, and expression profiles from 39 studies, covering 27 species and 4 hybrid cultivars across 13 genera of Amaryllidoideae. The AmarylOmicBase (v2, https://doi.org/10.5281/zenodo.20349158) consists of de novo assemblies generated from published raw data using Trinity or IsoSeq workflows and provides standardized functional annotation and quantitative expression datasets. Preprint - https://doi.org/10.1101/2025.11.24.690262
Project description:To facilitate new studies in the Amaryllidoideae subfamily, we present AmarylOmicBase, a unified transcriptomic database that integrates assemblies, annotations, and expression profiles from 39 studies, covering 27 species and 4 hybrid cultivars across 13 genera of Amaryllidoideae. The AmarylOmicBase (v2, https://doi.org/10.5281/zenodo.20349158) consists of de novo assemblies generated from published raw data using Trinity or IsoSeq workflows and provides standardized functional annotation and quantitative expression datasets. Preprint - https://doi.org/10.1101/2025.11.24.690262