Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq of Mus musculus subcutaneous Lin- cells derived from the subcutaneous adipose stromal vascular fraction

ABSTRACT: We used the resolving power of single-cell transcriptional profiling to molecularly characterize the mouse adipose stem and progenitor cell-enriched, subcutaneous adipose stromal vascular fraction. We molecularly assessed CD45- CD31- SVF cells using the 10x Genomics Chromium (10x) platform.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Petra Catalina Schwalie

PROVIDER: E-MTAB-6677 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A stromal cell population that inhibits adipogenesis in mammalian fat depots.

Schwalie Petra C PC Dong Hua H Zachara Magda M Russeil Julie J Alpern Daniel D Akchiche Nassila N Caprara Christian C Sun Wenfei W Schlaudraff Kai-Uwe KU Soldati Gianni G Wolfrum Christian C Deplancke Bart B

Nature 20180620 7712

Adipocyte development and differentiation have an important role in the aetiology of obesity and its co-morbidities1,2. Although multiple studies have investigated the adipogenic stem and precursor cells that give rise to mature adipocytes3-14, our understanding of their in vivo origin and properties is incomplete2,15,16. This is partially due to the highly heterogeneous and unstructured nature of adipose tissue depots17, which has proven difficult to ...[more]

PMID: 29925944

Similar Datasets

scRNA-seq of stromal, tumor and immune cells from EMT6 tumors treated with aTGFb/aPD-L1

Project description:We performed 10x single cell RNA-seq on sorted populations: T cell (7AAD- Calcein blue+ CD45+ THY1.1- TCRb+), fibroblasts (7AAD- Calcein Blue+ CD45- THY1.1- CD31- PDPN+), myeloid cells (7AAD- Calcein Blue+ CD45+ THY1.1- CD11b+) and tumor cells (7AAD- Calcein Blue+ CD45- THY1.1+) from cells in an orthotopic EMT6 tumor model 7 days after treatment initiation in four experimental groups: 1) Control 2) aPD-L1 3) aTGFb 4) aPD-L1 and aTGFb.

2023-06-30 | E-MTAB-13072 | biostudies-arrayexpress

scRNA-seq of stromal vascular cells from 48 week (aged) mouse subcutaneous adipose tissue compared to control 10 week (young) mouse SVF

Project description:Adipose tissue mass and adiposity change throughout the lifespan. During aging, while visceral adipose tissue (VAT) tends to increase, peripheral subcutaneous adipose tissue (SAT) decreases significantly. Unlike VAT, which is linked to metabolic diseases, SAT has beneficial effects. However, the molecular details behind aging-associated loss of SAT remain unclear. Here we compare scRNA-seq of total SVF of SAT from young and aging mice to identify a novel Aging-dependent Regulatory Cell (ARC) that emerges in SAT of aged mice. Inguinal white adipose tissue (iWAT) was used as a representative SAT; iWAT pads of 2 mice from each age group were subjected to collagenase digestion and treated with a hypotonic buffer to remove red blood cells before subjection to scRNA-seq by 10X Genomics Chromium Single Cell Kit. The findings showed that ARCs express adipogenic markers but lack adipogenic capacity and inhibit differentiation of neighboring adipose precursors.

2021-03-25 | E-MTAB-10221 | biostudies-arrayexpress

Single-cell RNA-sequencing of cells from spinal cord central canal region of young adult and aged mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. This neural stem cell potential is known to decline with age in the mouse. Here, we microdissected and dissociated into single cells the central canal region from the spinal cord of 4 young adult (3-to-4-month old) and 4 aged (18-to-19-month old) C57BL/6J mice to profile the transcriptomes of cells in and around the central canal using 10x Genomics technology.

2022-12-13 | E-MTAB-11561 | biostudies-arrayexpress

Single cell CITE-seq and VDJ sequencing of epidermal and blood T cells

Project description:The aim of the experiment was to investigate the clonal relationship between CD8+ T cell subsets of donor matched blood with epidermal CD8+ T cells. Abdominal skin (n=8) was separated into dermis and epidermis, followed by epidermal skin and PBMC isolation. Single CD8+ T cells (n=6) and CD3+ T cells (n=2) were FACS sorted, processed with the 5’ 10x Genomics workflow and sequenced at NGI Sweden.

2023-06-12 | E-MTAB-12839 | biostudies-arrayexpress

scRNA-seq of Multi-lineage differentiating Stress Enduring (Muse) cell and non-Muse cells isolated from bone marrow-derived mesenchymal stem cells

Project description:MSCs comprise several percent of pluripotent-like cells named Multilineage-differentiating stress enduring (Muse) cells that express pluripotent markers at moderate levels, are collectable as cells positive for the pluripotent surface marker SSEA-3, are able to differentiate into triploblastic lineage cells, and self-renew at the single cell level (Kuroda et al, PNAS, 2010; Wakao et al, PNAS, 2011). Importantly, MSCs also comprise cells other than SSEA-3(+)-Muse cells, namely multipotent SSEA-3(-)-non-Muse MSCs that correspond to ~98% of the total MSC population. These SSEA-3(-)-non-Muse MSCs exhibit the same properties as conventional MSCs, although the non-Muse MSCs are multipotent, they are not pluripotent. In the present study, to clarify the key molecules that characterize pluripotent-like vs multipotent somatic stem cells, we separated human MSCs into SSEA-3(+)-Muse cells and SSEA-3(-)-non Muse MSCs, and analyzed both populations by scRNA-seq. SSEA-3(+) Muse cells and SSEA-3(-) non-Muse MSCs were sorted from human BM-MSCs. Sequencing libraries were prepared using Chromium single cell 3' Kit v3 (10x Genomics, Pleasanton, CA, USA) and sequenced on HiSeq2500 (Illumina, San Diego, CA, USA). Transcripts were mapped with CellRanger pipeline v3 (10x Genomics). Library construction, sequencing, and initial analysis were performed by GENEWIZ (South Plainfield, NJ, USA).

2022-10-26 | E-MTAB-10854 | biostudies-arrayexpress

Single-cell RNA sequencing of human liver cells

Project description:To examine the heterogeneity and dynamic crosstalk of human liver cells, ~18,000 freshly isolated human liver cells from 6 donors were profiled using the 10x Genomics Chromium platform.

2021-09-29 | E-MTAB-10553 | biostudies-arrayexpress

scRNA-seq of CD45+ cells taken from the ear epidermis from K14E7 transgenic and wildtype C57/BL6 mice

Project description:Langerhans cells (LC) in skin help initiate the immune response to locally presented antigens. We performed high-resolution single-cell RNA-sequencing (scRNAseq) analysis for antigen presenting cells including LC in normal mouse skin, and in mouse skin expressing the human papillomavirus (HPV) 16 E7 oncogene. Ear skin was collected from normal and trangenic mice. Dissociated CD45+ cells were processed for scRNA-seq using the 10X Genomics Chromium 3' gene expression kit (v2).

2021-10-15 | E-MTAB-8199 | biostudies-arrayexpress

CITE-seq of human blood CD8+ T cells

Project description:The purpose of the experiment was to investigate the differentiation state gradient among antigen-experienced CD8+ T cells in healthy human blood. This was a sub-goal within a larger experiment, which aimed to investigate the clonal relationship between CD8+ T cells in blood and skin of matched donors. The blood T cells were sorted as CD8+ T cells (n=4) or CD3+ T cells (n=2), processed according to the 5´prime 10x genomic workflow, and sequenced at NGI Sweden.

2023-06-30 | E-MTAB-13034 | biostudies-arrayexpress

Single cell sequencing of the proliferative endometrium

Project description:Endometrial biopsies were collected on menstrual cycle day 7 from healthy fertile women age 24-42. Biopsies were processed to a single cell suspension and submitted for single cell sequencing on the 10x platform.

2021-09-18 | E-MTAB-10947 | biostudies-arrayexpress

scRNA seq analysis of CD45+ tumor infiltrating cells (TICs) of B16F10 tumor-bearing Trem1+/+ and Trem1-/- mice.

Project description:To gain a global understanding of the impact of TREM1 silencing, we analyzed the CD45+ tumor infiltrating cells (TICs) of B16F10 tumor-bearing Trem1+/+ and Trem1-/- mice. Utilizing the 10x Genomics Chromium Platform, we analyzed approximately 5390 cells per sample with a coverage rate of 15493 genes per cell.

2023-09-27 | E-MTAB-13237 | 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