Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Johan Henriksson

PROVIDER: E-MTAB-14220 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Multiome RNA+ATAC on human PBMCs (snATAC-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11226 | biostudies-arrayexpress

Multiome RNA+ATAC on human PBMCs (snRNA-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11225 | biostudies-arrayexpress

Single-cell multiome analysis of human in vitro activated CD4 T cells

Project description:This study looks at the ATAC+RNA profiles of human CD4 T cells under bioreactor-like conditions as ACT. Cells were stimulated toward Th1,Th2,Treg and Th17 under anti-CD3/28 activation, and profiled on day 5.

2024-01-31 | E-MTAB-13711 | biostudies-arrayexpress

Single-nuclei Multiome (RNA+ATAC) analysis of embryonic AGM+VU from Runx1 +23 enhancer-reporter transgenic mouse

Project description:During embryonic development, haematopoietic stem and progenitor cells originate from haemogenic endothelium (HE) via an endothelial-to-haematopoietic transition (EHT), which is dependent on the transcription factor Runx1. Here, we measure gene expression and DNA accessibility in single nuclei isolated from the Aorta-gonad-mesonephros (AGM) and vitelline and umbilical arteries (VU) of pooled E9 (33 embryos, 20-25 sp) and E10 (24 embryos, 32-36 sp) 23GFP Tg embryos.

2026-07-31 | E-MTAB-15412 | biostudies-arrayexpress

GBM-Space: Joint Transcriptome and Chromatin Accessibility Profiling of Glioblastoma (10x Genomics - Multiome)

Project description:Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This submission contains the Cell Ranger ARC processed outputs from single nuclei joint transcriptome- and chromatin accessibility-sequencing (10x Genomics). We also provide an integrated single nuclei transcriptomics dataset, comprised of malignant and tumour microenvironment cell type annotations.

2026-06-12 | E-MTAB-17183 | biostudies-arrayexpress

Single nuclei RNA-seq and snATAC-seq multiome performed in WT and Dhx36 conditional KO hearts at postnatal day 7 (PD7)

Project description:In these experiments, we aimed to investigate the role of cardiomyocyte-specific deletion of the G-quadruplex resolvase Dhx36 in heart development and cardiomyocyte differentiation. To achieve this, we conducted multi-omics analysis using single-nuclei RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on hearts from postnatal day 7 (PD7) wild-type (WT) and Dhx36 conditional knockout (cKO) mice. Our findings reveal that Dhx36 plays a critical role in the development of the cardiac conduction system (CCS) and in the differentiation of both CCS and working cardiomyocytes

2024-09-15 | E-MTAB-14442 | biostudies-arrayexpress

Single nuclei RNA-seq and snATAC-seq multiome performed in WT and Dhx36 conditional KO hearts at postnatal day 7 (PD7)

2024-09-15 | E-MTAB-14441 | biostudies-arrayexpress

A Human Fetal Cochlear Cell Atlas Reveals a Regulatory Blueprint for Spatial Patterning - sn-Multiome

Project description:Single-nucleus multiomic data was generated from human fetal cochleae across 11, 14, and 16 post-conceptual weeks (PCW) using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression platform. Snap-frozen tissues were minced and lysed in ice-cold Nuclei Lysis Buffer, followed by filtration through a 40 μm strainer and centrifugation. Nuclear integrity was confirmed via trypan blue staining prior to mild permeabilization using 0.1× Lysis Buffer. After quenching and washing, nuclei were resuspended in Diluted Nuclei Buffer and concentration was adjusted to 4,000–8,000 nuclei/μL. Libraries were prepared following the standard 10X Multiome protocol for simultaneous gene expression and chromatin accessibility profiling. Sequencing was performed on the Illumina platform, producing paired-end reads. Raw data were processed through the Cell Ranger ARC pipeline (v2.0.0) with alignment to the GRCh38 human genome. The final output comprises paired gene expression matrices and chromatin accessibility peaks, both linked to the same individual nuclei through shared barcodes.

2026-02-04 | E-MTAB-16331 | biostudies-arrayexpress

Single-nucleus ATAC sequencing of human fetal lung from 4 anatomic regions

Project description:We performed micro-dissections of developing human lungs during the late pseudoglandular stage and performed single nuclear ATAC-sequencing (n = 2; biological replicates from 103-122 PCD) on trachea, bronchi, non-cartilaginous airways, and distal lung.

2026-07-18 | E-MTAB-17243 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data