Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-seq of CD4+ Treg and Tmem cells from different tissues in mouse and human

ABSTRACT: Non-lymphoid tissues (NLTs) harbour a pool of adaptive immune cells distinct from their counterparts in lymphoid tissues, and their development and phenotype remains largely unexplored. We used scRNA-seq to survey CD4+ T regulatory (Treg) and memory T (Tmem) cells in spleen, lymph nodes, skin and colon in an unbiased way, in mouse and human. This cross-tissues, cross-species comparison allows us to obtain marker genes for immune populations in specific locations with likely relevance for human studies. Additionally, a continuous phenotype of Treg migration can be modelled from the mouse data, unravelling the transcriptional stages through which these cells transition between tissues.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Tomas Gomes

PROVIDER: E-MTAB-6072 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-seq of CD4+ Treg and Tmem cells from different tissues in mouse (Chromium 10x data)

Project description:Non-lymphoid tissues (NLTs) harbour a pool of adaptive immune cells distinct from their counterparts in lymphoid tissues, and their development and phenotype remains largely unexplored. We used scRNA-seq to survey CD4+ T regulatory (Treg) and memory T (Tmem) cells in spleen, lymph nodes, skin and colon in an unbiased way, in mouse. This cross-tissues comparison allows us to obtain marker genes for immune populations in specific locations, as well as examine each population's heterogeneity. Additionally, a continuous phenotype of Treg migration can be modelled from the mouse data, unravelling the transcriptional stages through which these cells transition between tissues.

2019-05-20 | E-MTAB-7311 | biostudies-arrayexpress

Transcription profiling of human lymphatic endothelial cells, mouse dermal cells and human skin cells reveals an inflammation-induced mechanism for leukocyte transmigration of lymphatic vessel endothelium.

Project description:The exit of antigen-presenting cells (APC) and lymphocytes from inflamed skin to afferent lymph is vital for the initiation and maintenance of dermal immune responses. How such exit is achieved and how cells transmigrate the distinct endothelium of lymphatic vessels is however unknown. Here we show that inflammatory cytokines trigger activation of dermal lymphatic endothelial cells (LEC) leading to expression of the key leukocyte adhesion receptors ICAM-1, VCAM-1 and E-selectin, as well as a discrete panel of chemokines and other potential regulators of leukocyte transmigration. Furthermore, we show that both ICAM-1 and VCAM-1 are induced in the dermal lymphatic vessels of mice exposed to skin contact hypersensitivity where they mediate lymph node trafficking of DC via afferent lymphatics. Lastly, we show that TNF_-stimulates both DC adhesion and transmigration of dermal LEC monolayers in vitro and that the process is efficiently inhibited by ICAM-1 and VCAM-1 adhesion-blocking mAbs. These results reveal a CAM-mediated mechanism for recruiting leukocytes to the lymph nodes in inflammation and highlight the process of lymphatic transmigration as a potential new target for anti-inflammatory therapy. Experiment Overall Design: Global gene expression profile of normal dermal lymphatic endothelial cells cultured in media alone (no TNF) compared to that of normal dermal lymphatic endothelial cells stimulated with TNFalpha, 1 ng/ml for 48h.Triplicate biological samples were analyzed from human lymphatic endothelial cells (3 x controls; 3 x TNF treated) and a single sample analyzed from mouse lymphatic endothelial cells (1 x controls; 1 x TNF treated).

2008-11-07 | E-GEOD-6257 | biostudies-arrayexpress

An epithelial integrin regulates the amplitude of protective lung interferon responses

Project description:Integrins facilitate intercellular movement and communication. Unlike the promiscuous activities of many integrins, Î²6 integrin is restricted to epithelia and partners exclusively with integrin Î±V to modulate acute lung injury (ALI). Given that ALI is a complication of respiratory infection, we used mice lacking Î²6 integrin (Î²6 KO) to probe the role of the epithelial layer in controlling the lung microenvironment during infection. We found Î²6 KO mice were protected from disease caused by influenza and Sendai virus infections. They were also protected from disease caused by Streptococcus pneumoniae infection alone and after prior influenza virus infection, the co-infection representing an often-lethal condition in humans. Resistance in the absence of epithelial Î²6 integrin was caused by intrinsic priming of the lung microenvironment by type I interferons through a mechanism involving transforming growth factor-Î² regulation. Expression of Î²6 on epithelia suppresses the production of interferons, providing an advantage to the pathogen. Acute inhibition of Î²6 function may therefore provide a means to improve outcomes in lung microbial infections. We used microarrays to explore the gene expression profiles differentially expressed in resident alveolar macrophage cells from wild-type and Î²6 integrin knockout mice. Cells were purified by sorting from lung digests. The comparison made was CD11c+, autofluorescent+ cells from wild-type controls to the dominant CD11c+, CD11b+, autofluorescent+ cells in the knockout. Note that conventional CD11c+ alveolar macrophages do not exist in the knockout mice.

2016-07-18 | E-GEOD-68802 | biostudies-arrayexpress

Single-cell RNA sequencing reveals a dynamic stromal niche within the evolving tumour microenvironment

Project description:We employed single-cell RNA sequencing to understand stromal changes in murine melanomas and draining lymph nodes at single cell resolution at different points of tumour development.

2019-01-04 | E-MTAB-7427 | biostudies-arrayexpress

Transformation of Naked Mole-Rat Cells

Project description:The naked mole-rat (NMR), Heterocephalus glaber, is a mouse-sized subterranean rodent native to East Africa. Research on NMRs is intensifying in an effort to gain leverage from their unusual physiology, long-life span and cancer resistance for the development of new theraputics. Few studies have attempted to explain the reasons behind the NMR’s cancer resistance, but most prominently Tian et al. reported that NMR cells produce high-molecular weight hyaluronan as a potential cause for the NMR’s cancer resistance. Tian et al. have shown that NMR cells are resistant to transformation by SV40 Large T Antigen (SV40LT) and oncogenic HRAS (HRASG12V), a combination of oncogenes sufficient to transform mouse and rat fibroblasts. We have developed a number of lentiviral vectors to deliver both these oncogenes and generated 106 different cell lines from five different tissues and eleven different NMRs, and report here that contrary to Tian et al.’s observation, NMR cells are susceptible to oncogenic transformation by SV40LT and HRASG12V. Our data thus point to a non-cell autonomous mechanism underlying the remarkable cancer resistance of NMRs. Identifying these non-cell autonomous mechanisms could have significant implications on our understanding of human cancer development.

2020-06-12 | E-MTAB-8932 | biostudies-arrayexpress

Single cell RNA-seq of human breast skin cells

Project description:Cells were generated for a single cell atlas of adult human skin to dissect the cellular and molecular organisation underpinning human skin immune barrier function. Surplus skin from breast reconstruction surgery was collected (n=3), then the top 200 μm layer was taken. Epidermis was separated from the dermis, and both layers were separately digested. Single cells were FACS sorted into eight categories, then loaded onto a 10x Genomics Chromium Controller, and sequenced on an Illumina HiSeq 4000.

2021-02-10 | E-MTAB-8142 | biostudies-arrayexpress

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - 10x data

Project description:To explore the interactions between the range of maternal and fetal placental cell types present, we profiled the transcriptomes of more than 50,000 single cells from matched first trimester samples of maternal blood and decidua, as well as fetal cells from the placenta itself. RNA-seq was done using the standard 10x chromium v2 chemistry.

2018-10-02 | E-MTAB-6701 | biostudies-arrayexpress

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - whole genome sequencing

Project description:To explore the interactions between the range of maternal and fetal placental cell types present, we profiled the transcriptomes of more than 50,000 single cells from matched first trimester samples of maternal blood and decidua, as well as fetal cells from the placenta itself. Demuxlet was used to discern between cells of fetal and maternal origin, from SNPs inferred from genotyping.

2018-10-17 | E-MTAB-7304 | biostudies-arrayexpress

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - Smartseq 2 data

Project description:To explore the interactions between the range of maternal and fetal placental cell types present, we profiled the transcriptomes of more than 50,000 single cells from matched first trimester samples of maternal blood and decidua, as well as fetal cells from the placenta itself. This part contains RNA-seq of Decidua cells using Smartseq 2

2019-08-21 | E-MTAB-6678 | biostudies-arrayexpress

scRNAseq/snucRNAseq of human implantation sites, placenta and decidua.

Project description:These samples are part of a study to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. Here we profiled three human implantation sites (between 6 and 9 post-conceptional weeks, PCW) with snucRNAseq; five decidual and three placental samples from 8-13 PCW by scRNA-seq/snRNA-seq.

2023-02-09 | E-MTAB-12421 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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