Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatially resolved multiomics of human cardiac niches - Multiome ATAC

ABSTRACT: 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.

INSTRUMENT(S): Single nuclei were captured using the 10x Genomics Chromium Controller., Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Kazumasa Kanemaru

PROVIDER: E-MTAB-12919 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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 - Visium

2023-06-01 | E-MTAB-12975 | biostudies-arrayexpress

A Multi-omic Atlas of Human Embryonic Skeletal Development -Multiome GEX+ATAC

Project description:Two distinct and anatomically restricted modes of ossification, which are endochondral ossification and intramembranous ossification, govern osteogenesis and joint formation throughout the human skeleton and, to our knowledge, the cellular bases by which they form and mature remain incompletely described in human development at single-cell resolution. To address this, we apply single-nuclei paired RNA and ATAC sequencing to decipher the molecular gene regulatory programmes that mediate maturation of the distinct bone and joint-forming niches in the cranium and appendicular skeleton across space and time from 5-11 PCW.

2024-10-09 | E-MTAB-14385 | biostudies-arrayexpress

Transcriptional profile of sustained ligand-activated preconditioning in pre- and post-ischemic myocardium

Project description:Analysis of left venticular myocardium following morphine-induced sustained ligand activated preconditioning (SLP). Results provide insight into the molecular pathways affected by morphine-induced SLP in the pre- and post-ischemic heart. Total RNA obtained from isolated ventricular myocardium subjected to 5 days of morphine induced sustained ligand activated preconditioning (SLP) compared to placebo control ventricular myocardium, tissue collected pre- and post-ischemia (n=6/group).

2012-10-01 | E-GEOD-39407 | 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

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

Urine recirculation prolongs normothermic kidney perfusion for via more optimal metabolic homeostasis – a proteomics study

Project description:We describe a proteomics analysis to determine the molecular differences between normothermically perfused (normothermic machine perfusion, NMP) human kidneys with urine recirculation (URC) and urine replacement (UR). Proteins were extracted from 16 kidney biopsies with URC (n=8 donors after brain death (DBD), n=8 donors after circulatory death (DCD)) and three with UR (n=2 DBD, n=1 DCD), followed by quantitative analysis by mass spectrometry. Damage-associated molecular patterns (DAMPs) were decreased in kidney tissue after six hours NMP with URC, suggesting reduced inflammation. Vasoconstriction was also attenuated in kidneys with URC as angiotensinogen levels were reduced. Strikingly, kidneys became metabolically active during NMP, which could be enhanced and prolonged by URC. For instance, mitochondrial succinate dehydrogenase enzyme levels as well as carbonic anhydrase were enhanced with URC, contributing to pH stabilisation. Levels of cytosolic and the mitochondrial phosphoenolpyruvate carboxykinase were elevated after 24 hours of NMP, more prevalent in DCD than DBD tissue. Key enzymes involved in glucose metabolism were also increased after twelve and 24 hours of NMP with URC, including mitochondrial malate dehydrogenase and glutamic-oxaloacetic transaminase, predominantly in DCD tissue. We conclude that NMP with URC permits prolonged preservation and revitalises metabolism to possibly minimize better cope with ischemia reperfusion injury in discarded kidneys.

2020-10-20 | PXD021507 | Pride

snRNA-seq of platypus (Ornithorhynchus anatinus) adult testis

Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 6,751 nuclei in platypus adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.

2021-11-08 | E-MTAB-11070 | biostudies-arrayexpress

snRNA-seq of chicken (Gallus gallus) adult testis

Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 8,413 nuclei in chicken adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.

2021-11-08 | E-MTAB-11073 | biostudies-arrayexpress

Single-cell RNA-Seq of bovine macrophage cell lines from two cow strains infected with Theileria

Project description:To understand the immune response of cows to the apicomplexan parasite Theileria annulata, we used ex vivo isolate cells derived from two infected calve : Holstein 12886 (Bos taurus), which is known to be susceptible to the disease, and Sahiwal 82H (Bos indicus), which is known to be resistant. The infected bovine macrophages of the two species with Theileria were collected and performed multiome 10X Chromium genomics scRNA-Seq.

2024-10-09 | E-MTAB-14450 | 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