Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq of dendritic cells from mouse lymph nodes

ABSTRACT: Dendritic cells were sorted from Lymph nodes and subject to single-cell sequencing. Gating strategy: CD45+ Lin- (CD3, CD19), F4/80-, CD64-, MHC+, CD11c+.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Soren Muller

PROVIDER: E-MTAB-10196 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gremlin 1+ fibroblastic niche maintains dendritic cell homeostasis in lymphoid tissues

Project description:In an effort to define transcriptional heterogeneity in the stromal cell compartment of lymph nodes scRNA-seq analysis of CD45- cells from skin-draining LNs (SLN) was performed. Flow sorted CD45 depleted single cell suspension from SLN of ten mice were profiled by 10x 3’ single-cell RNA-sequencing in two runs, each containing cells from five mice.

2021-04-10 | E-MTAB-10197 | biostudies-arrayexpress

ScRNA-seq of stromal cells in WT and LRRC15 DTR mice

Project description:KPR tumors were subcutaneously implanted in Lrrc15DTRGFPwt/wt (DTR–) or Lrrc15DTRGFPwt/ki (DTR+) mice and DT treatment was initiated in both DTR– and DTR+ mice when tumors reached a mean volume of 100-200mm3. scRNAseq of CD24-CD45- stromal cells from a total of 40 tumor-bearing animals across both DTR– and DTR+ genotypes was carried out at four different time points including 10 days post tumor implantation and immediately prior to initiation of DT treatment (IOT) (referred to as day 0) and on days 7, 14, and 21 post IOT.

2022-08-17 | E-MTAB-12036 | biostudies-arrayexpress

ScRNA-seq of stromal and immune cells in WT and TGFBR2 KO mice

Project description:Single-cell RNA-seq in mice with subcutaneous tumors was used to determine if TGFβR2 signaling in DPT+ universal fibroblasts drives LRRC15+ myofibroblast differentiation using DptIresCreERT2Tgfbr2fl/fl and WT control mice.

2022-08-16 | E-MTAB-12028 | biostudies-arrayexpress

Single-cell RNA-seq of human LN stromal and dendritic cells

Project description:To identify heterogeneity of stromal cells in human lymph nodes, we performed single-cell RNA-seq of stromal cells (CD45-, CD31- PDPN+) from 3 donors. Additionally, dendritic cells (DCs, CD45+, CD11C+) were isolated from the LNs of the same donors to predict potential interactions between these two types of cells. As potentially human identifiable data, he raw sequencing data files for this experiment will be deposited in the controlled-access EGA archive.

2021-04-10 | E-MTAB-10206 | biostudies-arrayexpress

MPS vaccination alters long-term gene expression of antigen-presenting cells in lymph nodes

Project description:Given the importance of sustained antigen presentation in maintenance of lymph node (LN) immune responses, we hypothesized that vaccine antigen availability and antigen-presenting cell (APC) populations may affect LN expansion. Compared to LNs of mice given the full MPS vaccine, LNs of mice given an MPS vaccine without antigen became prominently less enlarged and contracted sooner.To identify potential mediators of this differential, antigen-dependent response, we next focused the analysis of our scRNA-seq dataset on LN APC populations.

2024-04-05 | E-MTAB-13698 | biostudies-arrayexpress

Stromal evolution of cancer-associated fibroblasts in PDAC GEMMs

Project description:With the advent of cancer immunotherapy, intense investigation has been focused on tumor-infiltrating immune cells. With only a fraction of patients responding to these new therapies, a better understanding of all elements of the tumor microenvironment (TME) that may influence therapeutic outcome is needed. Stromal elements of the TME, chiefly fibroblasts, have emerged as potential contributors to tumor progression and most recently resistance to immunotherapy, but their precise composition and clinical relevance remain incompletely understood. Here we use single-cell transcriptomics to chart the fibroblastic landscape during pancreatic ductal adenocarcinoma (PDAC) progression in animal models, identifying two healthy tissue fibroblast subsets that co-evolve along individual trajectories into four subsets of carcinoma-associated fibroblasts (CAFs).

2019-10-31 | E-MTAB-8483 | biostudies-arrayexpress

Single cell RNA-seq profiling of T cells isolated from MC38 mouse tumors

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

2019-05-12 | E-MTAB-7919 | biostudies-arrayexpress

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

Single cell RNA-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling.

2021-02-16 | E-MTAB-9274 | biostudies-arrayexpress

Single-cell RNA-seq of mouse cardiac interstitial cells 3 & 7 days after sham or myocardial infarction injury

Project description:The aims of the experiment were to profile the cell types in the adult mouse cardiac interstitium (non-myocyte cells) and how they respond to myocardial infarction injury. Adult, male, Pdgfra +/GFP mice were subject to either a myocardial infarction or sham injury, with cells isolated from cardiac ventricles 3 or 7 days following surgery. We obtained scRNA-seq profiles of two cell fractions: total interstitial (non-myocyte) cell population (TIP) and FACS-sorted GFP+/Cd31- cells (GFP).

2019-03-28 | E-MTAB-7376 | 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