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97 results for “expression matrix”
Gene expression count matrix for 4 T cell subtypes from ROSMAP participants
<p><span>Peripheral blood mononuclear cells (PBMCs) from participants in the Rush Religious Orders Study/Memory and Aging Project (ROSMAP) were isolated by Ficoll gradient centrifugation, then sorted by high-speed flow cytometry into the following T cell subtypes:<span> </span>CD4+CD45RO-, CD4+CD45RO+, CD8+CD45RO-, and CD8+CD45RO+.<span> </span>Total RNA was extracted using buffer TCL (Qiagen), then RNA-seq libraries were prepared according to the Single Cell RNA Barcoding and Sequencing method originally developed for single-cell RNA-seq</span><span>, adapted for extracted total RNA.<span> </span>RNA libraries were collected on a single 384-well plate and sequenced on the Illumina HiSeq </span><span>using the High-throughput 3<span>’</span> Digital Gene Expression (DGE) library</span><span>.<span> The "RNA count matrix" file is the raw counts from the 384-well plate, while the "ROSMAP_Tcell_DGE_PlateMap" file contains metadata for the wells on the plate, by well position.</span></span></p>
Generating an expression matrix for droplet single-cell RNA-seq (dscRNA-seq) data
<p>This tutorial is adapted from the 'Generating an expression matrix' training session at the EBI (https://www.ebi.ac.uk/training/events/2019/single-cell-rna-seq-analysis-questions-clusters).</p>
Stereo-seq E12.5_E1S3 bin 200 expression matrix (dgC Matrix), spatial locations (.csv), and h5ad file (scanpy flavor)
<p>Expression matrix in rds file format and spatial locations of E12.5_E1S3 downloaded from the Mouse Organogenesis Spatiotemporal Transcriptomic Atlas. Files were processed using an adapted version of the STOMICS Analysis Workflow (SAW) pipeline. </p>
Example gene expression matrix used in SimpleTidy_GeneCoEx repo
<p>Gene expression matrix generated by kallisto. Data from Shinozaki et al., 2018. (DOI: 10.1038/s41467-017-02782-9)</p>
Spatial-temporal expression analysis of lineage-restricted shell matrix proteins in the slipper snail Crepidula atrasolea reveals shell field regionalization and distinct cell populations
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Data from: Expression of matrix Metalloproteinases-2 and aquaporin-1 in corneoscleral junction after angle-closure in rabbits
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Data from: Extracellular matrix-associated gene expression in adult sensory neurons cultured on laminin substrates
Background: In our previous investigations of the role of the extracellular matrix (ECM) in promoting neurite growth we have observed that a permissive laminin (LN) substrate stimulates differential growth responses in subpopulations of mature dorsal root ganglion (DRG) neurons. DRG neurons expressing Trk and p75 receptors grow neurites on a LN substrate in the absence of neurotrophins, while isolectin B4-binding neurons (IB4+) do not display significant growth under the same conditions. We set out to determine whether there was an expression signature of the LN-induced neurite growth phenotype. Using a lectin binding protocol IB4+ neurons were isolated from dissociated DRG neurons, creating two groups - IB4+ and IB4-. A small-scale microarray approach was employed to screen the expression of a panel of ECM-associated genes following dissociation (t=0) and after 24 hr culture on LN (t=24LN). This was followed by qRT-PCR and immunocytochemistry of selected genes. Results: The microarray screen showed that 36 of the 144 genes on the arrays were consistently expressed by the neurons. The array analyses showed that six genes had lower expression in the IB4+ neurons compared to the IB4- cells at t=0 (CTSH, Icam1, Itgβ1, Lamb1, Plat, Spp1), and one gene was expressed at higher levels in the IB4+ cells (Plaur). qRT-PCR was carried out as an independent assessment of the array results. There were discrepancies between the two methods, with qRT-PCR confirming the differences in Lamb1, Plat and Plaur, and showing decreased expression of AdamTs1, FN, and Icam in the IB4+ cells at t=0. After 24 hr culture on LN, there were no significant differences detected by qRT-PCR between the IB4+ and IB4- cells. However, both groups showed upregulation of Itgβ1 and Plaur after 24 hr on LN, the IB4+ group also had increased Plat, and the IB4- cells showed decreased Lamb1, Icam1 and AdamTs1. Further, the array screen also detected a number of genes (not subjected to qRT-PCR) expressed similarly by both populations in relatively high levels but not detectably influenced by time in culture (Bsg, Cst3, Ctsb, Ctsd, Ctsl, Mmp14, Mmp19, Sparc. We carried out immunohistochemistry to confirm expression of proteins encoded by a number of these genes. Conclusions:Our results show that 1B4+ and IB4- neurons differ in the expression of several genes that are associated with responsiveness to the ECM prior to culturing (AdamTs1, FN, Icam1, Lamb1, Plat, Plaur). The data suggest that the genes expressed at higher levels in the IB4- neurons could contribute to the initial growth response of these cells in a permissive environment and could also represent a common injury response that subsequently promotes axon regeneration. The differential expression of several extracellular matrix molecules (FN, Lamb1, Icam) may suggest that the IB4- neurons are capable of maintaining /secreting their local extracellular environment which could aid in the regenerative process. Overall, these data provide new information on potential targets that could be manipulated to enhance axonal regeneration in the mature nervous system.
Matrix Metalloproteinases Expression in the Neointimal Hyperplasia Induced by Drug Eluting Stent (DES) Implantation
ClinicalTrials.gov study NCT03375528. IPD Sharing: YES. Countries: 0. Publications: 2.
Data from: Extracellular matrix-associated gene expression in adult sensory neurons cultured on laminin substrates
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The expression profiles of extracellular matrix-related genes in the presence or absence of IL-17A or -17F as measured with the PCR array in systemic sclerosis (SSc) dermal fibroblasts
GEO Series GSE33581. Homo sapiens. 3 samples. Type: Expression profiling by RT-PCR.
Three Distinct Cell Types Express Extracellular Matrix Proteins In Different Niches During Skeletal Muscle Fibrosis
GEO Series GSE89633. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Systems biology of gene expression of bladder papilloma cells modulated by a malignant-derived extracellular matrix
GEO Series GSE9291. Homo sapiens. 11 samples. Type: Expression profiling by array.
Single cell differences in matrix gene expression do not predict matrix deposition
GEO Series GSE76881. Bos taurus. 18 samples. Type: Expression profiling by high throughput sequencing.
A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages
GEO Series GSE213189. Mus musculus. 36 samples. Type: Expression profiling by high throughput sequencing.
The bone transcription factor Osterix controls extracellular matrix and node of Ranvier related gene expression in oligodendrocytes [RNA-seq]
GEO Series GSE221192. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
The tissue-engineered human cornea as a model to study expression of matrix metalloproteinases during corneal wound healing
GEO Series GSE75336. Homo sapiens. 27 samples. Type: Expression profiling by array.
LYVE-1-expressing macrophages modulate the extracellular matrix in the mammary gland and contribute to mammary tumor growth
GEO Series GSE241469. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Effect of Combinatorial Extracellular Matrix and Substrate Stiffness Gene Expression and Chromatin Accessibility of Activated Hepatic Stellate Cells
GEO Series GSE210967. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Differential expression of genes cultured on extracellular matrix from control or irradiated astrocytes
GEO Series GSE145060. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
miRNA expression profile of mouse Lewis lung carcinoma LLC1 cell line cultivated in 2-dimensional or 3-dimensional cell culture enriched with laminin rich extracellular matrix proteins
GEO Series GSE75862. Mus musculus. 6 samples. Type: Non-coding RNA profiling by array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.