Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A single-cell transcriptome atlas of the human pancreas [CEL-seq2]

ABSTRACT: To understand organ function it is important to have an inventory of the cell types present in the tissue and of the corresponding markers that identify them. This is a particularly challenging task for human tissues like the pancreas, since reliable markers are limited. Transcriptome-wide studies are typically done on pooled islets of Langerhans, which obscures contributions from rare cell types and/or potential subpopulations. To overcome this challenge, we developed an automated single-cell sequencing platform to sequence the transcriptome of thousands of single pancreatic cells from deceased organ donors, allowing in silico purification of all main pancreatic cell types. We identify cell type-specific transcription factors, a subpopulation of REG3A-positive acinar cells, and cell surface markers that allow sorting of live alpha and beta cells with high purity. This resource will be useful for developing a deeper understanding of pancreatic biology and pathophysiology of diabetes mellitus.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85241 | GEO | 2016/10/04

SECONDARY ACCESSION(S): PRJNA337935

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A single-cell transcriptome atlas of the human pancreas

2016-06-24 | GSE81076 | GEO

A single-cell transcriptome atlas of the human pancreas

Project description:To understand organ (dys)function it is important to have a complete inventory of its cell types and the corresponding markers that unambiguously identify these cell types. This is a challenging task, in particular in human tissues, because unique cell-type markers are typically unavailable, necessitating the analysis of complex cell type mixtures. Transcriptome-wide studies on pancreatic tissue are typically done on pooled islet material. To overcome this challenge we sequenced the transcriptome of thousands of single pancreatic cells from deceased organ donors with and without type 2 diabetes (T2D) allowing in silico purification of the different cell types. We identified the major pancreatic cell types resulting in the identification of many new cell-type specific and T2D-specific markers. Additionally we observed several subpopulations within the canonical pancreatic cell types, which we validated in situ. This resource will be useful for developing a deeper understanding of pancreatic biology and diabetes mellitus. Human cadaveric pancreata were used to extract islets of Langerhans, which were kept in culture until single-cell dispersion and FACS sorting. Single-cell transcriptomics was performed on live cells from this mixture using CEL-seq or on cells stained for CD63, CD13, TGFBR3 or CD24 and CD44. The RaceID algorithm was used to identify clusters of cells corresponding to the major pancreatic cell types and to mine for novel cell type-specific genes as well as subpopulations within the known pancreatic cell types.

2016-06-24 | E-GEOD-81076 | biostudies-arrayexpress

An atlas of pancreatic function for ruminating goats mapped by single cell transcriptomics

Project description:The objectives of this study were to elucidate the development of pancreatic function from the non-ruminating to ruminating stage, including characterizing the inventory of cell types and their corresponding marker genes in the pancreas, using single-cell transcriptomic techniques.Pancreas of adult twin female goats at ruminating stage were collected after harvesting and the pancreas of neonatal twin female goats at non-ruminating stage were used as control.

2024-11-25 | GSE207644 | GEO

Single cell RNA-seq defines novel heterogeneity within the pancreatic ductal tree

Project description:Lineage tracing using genetically engineered mouse models has become an essential tool for investigating cell-fate decisions of progenitor cells and biology of mature cell types, with respect to physiology and disease progression. To study disease development, an inventory of an organ’s cell types and understanding of physiologic function is paramount. Here, we performed single-cell RNA sequencing to examine heterogeneity of murine pancreatic duct cells, pancreatobiliary cells, and intrapancreatic bile duct cells. We isolated duct cells within the murine pancreas using the DBA lectin sorting strategy that labels all pancreatic duct cell types. Our data contest the paradigm suggested by previous single cell studies that murine pancreatic duct cells are homogenous. We describe an epithelial mesenchymal transitory axis among our two subpopulations of pancreatic duct cells and identify SPP1 as a regulator of this phenotype and human duct cell de-differentiation. Our results further define functional heterogeneity of pancreatic duct subpopulations by elucidating a role for Geminin in accumulation of DNA damage in the setting of chronic pancreatitis. Our findings implicate diverse functional roles for subpopulations of pancreatic duct cells in disease progression and establish a comprehensive road map of murine pancreatic duct cell, pancreatobiliary cell, and intrapancreatic bile duct cell homeostasis.

2021-02-28 | GSE159343 | GEO

Cell-type identity of the avian utricle

Project description:The avian utricle, a vestibular organ of the inner ear, displays turnover of sensory hair cells throughout life. This is in sharp contrast to the mammalian utricle, which shows limited regenerative capacity. Here, we use single-cell RNA-sequencing to identify distinct marker genes for the different sensory hair cell subtypes of the chicken utricle, which we validated in situ . We provide markers for spatially distinct supporting cell populations, and identified two transitional cell populations of dedifferentiating supporting cells and developing hair cells. Trajectory reconstruction resulted in an inventory of gene expression dynamics of natural hair cell generation in the avian utricle.

2022-09-07 | GSE212831 | GEO

Pathways for intervention to optimize donor organ quality uncovered: a genome wide gene expression study

Project description:Background: Strategies to improve long term renal allograft survival have been directed to recipient dependent mechanisms of renal allograft injury. In contrast, no such efforts have been made to optimize organ quality in the donor. In order to get insight into the deleterious gene pathways expressed at different time points during deceased kidney transplantation, transcriptomics was performed on kidney biopsies from a large cohort of deceased kidney transplants. Methods: A total of 554 kidney biopsies were taken from living and deceased donor kidneys at donation, after cold ischemia and after reperfusion. Transcriptomics by means of whole genome micro-array analyses followed by functional pathway analyses was performed. Results: Oxidative stress and complement- and coagulation pathways were uncovered as potential pathways for intervention in deceased donors. No genes were found to be differentially expressed between donation and cold ischemia. After reperfusion, pathways related to oxidative stress, NOD-like signalling, MAPK, cytokine-cytokine receptor, complement- and-coagulation and chemokines were enriched in kidneys from deceased organ donors. Pathways related to prolonged and worsening deprivation of oxygen were associated with delayed graft function of DCD grafts. Conclusions: The present study reveals oxidative stress and enrichment of complement and coagulation pathways in deceased donor kidneys. Future intervention therapies to optimize donor organ quality and prolong allograft survival should target oxidative stress and innate immune activation in the donor.

2015-04-02 | GSE43974 | GEO

Detailed transcriptome atlas of the pancreatic beta cell

2008-12-31 | GSE13381 | GEO

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Project description:The goal of this project is to perform a systematic comparison of immune cell lineages across human tissues. To this end, we collected up to 16 tissues from twelve adult deceased organ donors, isolated immune cells and profiled them using single-cell RNA sequencing and VDJ sequencing generating a dataset of around 360,000 cells.

2022-04-13 | E-MTAB-11536 | biostudies-arrayexpress

Detailed transcriptome atlas of the pancreatic beta cell

Project description:The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing ?-cell gene expression, the beta-Cell Gene Atlas (BCGA). INS-1 cells, primary rat beta-cells (>87% beta-cells) and non-beta-cells (<3% beta cells, mostly alpha) were isolated by FACS mediated purification of two different rat islet preparations.

2008-12-31 | E-GEOD-13381 | biostudies-arrayexpress

Diabetes Remission Using Glucose-Responsive Insulin-Producing Human α-Cells

Project description:Natural and stable cell identity switches, where terminally-differentiated cells convert into different cell-types when stressed, represent a widespread regenerative strategy in animals, yet they are poorly documented in mammals. In mice, some glucagon-producing pancreatic α-cells become insulin expressers upon ablation of insulin-secreting β-cells, promoting diabetes recovery. Whether human islets also display this plasticity for reconstituting β-like cells, especially in diabetic conditions, remains unknown. Here we show that two different islet non-β-cell types, α- and γ–cells, obtained from deceased non-diabetic or diabetic human donors can be lineage-traced and induced to produce insulin and secrete it in response to glucose. When transplanted into diabetic mice, converted human α-cells reverse diabetes and remain producing insulin even after 6 months. Insulin-producing α-cells maintain α-cell markers, as seen by deep transcriptomic and proteomic characterization, and display hypo-immunogenic features when exposed to T-cells derived from diabetic patients. These observations provide conceptual evidence and a molecular framework for a mechanistic understanding of in situ cell plasticity in islet cells, as well as in other organs, as a therapy for degenerative diseases by fostering the highly-regulated intrinsic cell regeneration.

2018-12-13 | GSE117454 | GEO

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