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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SnRNA-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

ABSTRACT: These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snRNA-seq data is uploaded here.

INSTRUMENT(S): 10x Chromium, NextSeq 550

ORGANISM(S): Homo sapiens

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PROVIDER: E-MTAB-13651 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-13652

REPOSITORIES: biostudies-arrayexpress

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snATAC-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snATAC-seq data is uploaded here.

2025-04-22 | E-MTAB-13652 | biostudies-arrayexpress

Posterior brain organoids multi-omics atlas

Project description:Here, we generated multiome (coupled scRNA-seq and scATAC-seq) data over a time course of mid- and hindbrain organoid development to map cell composition and explore the regulatory mechanisms underlying cell type maturation. The dataset incorporates 5 time points from day 7 to day 120 from 3 human induced pluripotent stem cell (iPSC) lines using 2 previously established protocols. The protocols differentially generate ventral and dorsal cell types, and together cover regions such as floor-plate, dorsal and ventral midbrain, cerebellum, and additional parts of hindbrain. Comparing the data to a reference atlas of the developing human brain and to an integrated neural organoid cell atlas, we find that the gene regulatory architecture in organoid cells is predictive of primary counterparts and also that multiple regions are under-represented in existing organoid models.

2026-03-17 | E-MTAB-15659 | biostudies-arrayexpress

Single-nucleus RNA-seq of human tendon and myotendinous junction after acute exercise

Project description:Mechanical loading promotes structural and functional improvements in muscle and tendon, protecting against injury at their interface – the myotendinous junction (MTJ) and within the tendon matrix. However, the early cellular and molecular mechanisms underlying these adaptations in humans remain poorly understood. To address this, we used single-nucleus RNA sequencing and in situ hybridization to map the acute response of the human muscle-tendon unit to a single bout of eccentric resistance exercise, with a focus on extracellular matrix (ECM) regulation. We identified four transcriptionally distinct fibroblast subtypes with high expression of ECM components COL1A1 and DCN. Three of these subtypes were exercise-responsive: two localized to tendon fascicles or the MTJ, and a third enriched in the interfascicular matrix. Notably, this interfascicular population, marked by PDGFRA, showed the strongest transcriptional response to exercise, including upregulation of PRG4 and VCAN, ECM genes linked to tissue lubrication and resilience. In parallel, we discovered dynamic ECM remodeling in muscle-derived myonuclei, particularly for a distinct subset of type II myonuclei at the MTJ that expanded in number and strongly upregulated COL22A1, a collagen critical for MTJ integrity. Together, these findings reveal a spatially coordinated program of ECM remodeling involving both fibroblasts and myonuclei, highlighting the compartmentalized and cell type-specific nature of early tissue adaptation to mechanical load in the human muscle-tendon unit.

2025-10-10 | E-MTAB-15400 | biostudies-arrayexpress

GRO-seq in HeLa cells

Project description:Mapping the nascent RNA transcriptome of HeLa cells with GRO-seq Standard GRO-seq assay from two replicates in HeLa cells

2014-10-04 | E-GEOD-62046 | biostudies-arrayexpress

Single-nucleus data for Uncovering the Molecular Logic of Cortical Wiring between Neuronal subtypes Across Development Through Ligand–Receptor Inference

Project description:The cerebral cortex comprises diverse excitatory and inhibitory neuron subtypes, each with distinct laminar positions and connectivity patterns. Yet, the molecular logic underlying their precise wiring remains poorly understood. To identify ligand–receptor (LR) interactions involved in cortical circuit assembly, we tracked gene expression dynamics across major neuronal populations at 17 developmental stages using single-cell transcriptomics. This generated a comprehensive atlas of LR-mediated communication between excitatory and inhibitory neuron subtypes, capturing known and novel interactions. Notably, we identify neogenin-1 as the principal receptor for Cbln4 during the perinatal period, mediating synapse formation between somatostatin-expressing interneurons and glutamatergic neurons. We also identify cadherin superfamily members as candidate regulators of perisomatic inhibition onto deep and superficial excitatory neurons by parvalbumin-expressing basket cells, with opposing effects on synapse formation. These findings suggest a context-dependent role for cadherins in synaptic specificity and underscore the power of single-cell transcriptomics for decoding molecular mechanisms of cortical wiring.

2025-12-14 | E-MTAB-16355 | biostudies-arrayexpress

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-04 | E-GEOD-62047 | biostudies-arrayexpress

scRNAseq datasets of human brain organoids generated for the manuscript "Morphodynamics of human early brain organoids

Project description:Here we have provided scRNAseq datasets of unguided human brain organoids. The organoids were sequenced as a 1) Timecourse, 2) With different extracellular matrix treatments, 3) chemical treatment and 4) from organoids ere generated with a gene knockout cell line. Brain organoids enable the mechanistic study of human brain development, and provide opportunities to explore self-organization in unconstrained developmental systems. We have established long-term, live light sheet microscopy on unguided brain organoids generated from fluorescently labeled human induced pluripotent stem cells, which enables tracking of tissue morphology, cell behaviors, and subcellular features over weeks of organoid development. Based on imaging and single-cell transcriptome modalities, we find that lumenal expansion and cell morphotype composition within the developing neuroepithelium are associated with modulation of gene expression programs involving extracellular matrix (ECM) pathway regulators and mechanosensing. We show that an extrinsically provided matrix enhances lumen expansion as well as telencephalon formation, and unguided organoids grown in the absence of an extrinsic matrix have altered morphologies with increased neural crest and caudalized tissue identity. Matrix induced regional guidance and lumen morphogenesis are linked to the WNT and Hippo (YAP1) signaling pathways, including spatially restricted induction of the Wnt Ligand Secretion Mediator (WLS) that marks the earliest emergence of non-telencephalic brain regions. Altogether, our work provides a new inroad into studying human brain morphodynamics, and supports a view that matrix-linked mechanosensing dynamics play a central role during brain regionalization.

2025-04-30 | E-MTAB-15057 | biostudies-arrayexpress

snRNA-seq for Macaque LIP

Project description:snRNA-sequencing data for macaque LIP area. We isolated single nuclei from the LIP region. annotating the dataset with the canonical classification and integration with other datasets.

2026-05-31 | E-MTAB-13364 | biostudies-arrayexpress

Multiomic (Joint snRNA/snATAC) sequencing data of intestinal crypts and epithelial only organoids derived from human fetal duodenum

Project description:Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added. Fresh crypts were not placed in culture but rather immediately frozen for multiomic processing.

2022-07-16 | E-MTAB-11908 | biostudies-arrayexpress

Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation

Project description:We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved. From an initial 143 cells we identified 107 high quality samples with deep genic coverage, including 13 brown adipocytes, 19 cardiomyocytes, 19 cortical pyramidal neurons and 18 hippocampal pyramidal neurons from embryonic mouse, 8 cortical pyramidal neurons and 8 hippocampal pyramidal neurons from embryonic rat, and 22 serotonergic neurons from adult mouse. While mouse data is collected from three strains of mice at different ages, each cell type dataset is internally consistent. There are no technical replicates of single-cell samples. We additionally prepared 30 control samples, amplifications of bulk total cardiomyocyte RNA diluted to single cell quantities.

2015-05-21 | E-GEOD-56638 | biostudies-arrayexpress

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