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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

SUBMITTER:

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

SECONDARY ACCESSION(S): E-MTAB-13652E-MTAB-13655

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

Fate and State Transitions during Human Blood Vessel Organoid Development: Time Course

Project description:Human blood vessel organoids (hBVOs) derived from human pluripotent stem cells have emerged as a novel system to understand human vascular development, model disorders, and develop regenerative therapies. However, it was unclear which molecular states constitute hBVOs and how cells differentiate and self-organize within hBVOs in vitro and after transplantation. Here we reconstruct hBVO development over a time course using single-cell transcriptomics. Data includes day 3, 4, 5, 6, 7, 14 and 21 of hBVO differentiation, as well as 2 months post-transplantation of 14-day hBVOs into immunocompromised mice. We observe progenitor states that bifurcate into endothelial and mural fates, and find that hBVOs do not acquire definitive arterio-venous endothelial identities in vitro. Chromatin accessibility profiling at days 3, 4 and 7 identifies gene regulatory network (GRN) features associated with endothelial and mural fate decisions. Transcriptome-coupled lineage recording reveals multipotent progenitor states within BVOs. These data provide the first comprehensive cell state atlas of BVO development.

2025-03-21 | E-MTAB-14807 | biostudies-arrayexpress

Single-cell RNA+ATAC sequencing of human CRL-1459 colonic fibroblasts

Project description:The 10x multiome (RNA+ATAC) kit was applied to CRL-1459 cells in culture at passage 10 and 15

2024-07-13 | E-MTAB-14220 | 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

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

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

Single-cell multiome analysis of human tonsil B cells

Project description:B cells from tonsils of human donors were extracted for combined RNAseq+ATACseq from the same cell. One sample was prepared separately ("old") and is of lower quality, but still included. It primarily holds ATACseq information.

2023-04-13 | E-MTAB-12632 | biostudies-arrayexpress

Spatially resolved multiomics of human cardiac niches - Multiome GEX

Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.

2023-06-13 | E-MTAB-12916 | biostudies-arrayexpress

Spatially resolved multiomics of human cardiac niches - Multiome ATAC

2023-06-13 | E-MTAB-12919 | 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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