Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Sequencing of CD169+ lymph node macrophages isolated from naïve or tumor-bearing mice

ABSTRACT: CD169+ macrophages residing in naïve or tumor-draining inguinal lymph nodes revealed their protective role in tumor metastasis

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Carlotta Tacconi

PROVIDER: E-MTAB-8482 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression analysis of mouse lymphatic endothelial cells (LECs) from the subcapsular sinus (SS, afferent) and lymphatic sinus (LS, efferent)

Project description:Afferent lymphatic vessels bring antigens and diverse populations of leukocytes to draining lymph nodes, but efferent lymphatics allow only lymphocytes to leave the nodes. Despite fundamental importance of afferent vs. efferent lymphatics in immune response and cancer spread, molecular characteristics of these different arms of the lymphatic vasculature are largely unknown. In this work we report marked transcriptional differences between afferent and efferent lymphatic endothelial cells. Mouse inguinal, axillary, and brachial lymphnodes were collected and cryomolds prepared for laser-capture microdissection. Frozen sections were stained with various cell marker antibodies and micro-dissection performed to collect lymphatic endothelial cells. Total RNA was extracted from the cells and used in microarray analysis. Alternatively, popliteal, caudal, lumbar, inguinal, mesenteric, renal, axillary, brachial, deep and superficial cervical LN were enzymatically digested, the cells stained, and FACs sorted before RNA isolation.

2016-08-24 | E-GEOD-68371 | biostudies-arrayexpress

RNA-seq analysis of ID8 ovarian cancer cells after harvest from malignant ascites

Project description:Sequencing of mRNA from ID8 tumor cells and ID8 tumor cells harvested from ascites of mice 11 weeks after intra peritoneal inoculation show acquisition of cancer stem cell-like features in ascitic tumor cells.

2020-01-06 | E-MTAB-8140 | biostudies-arrayexpress

single cell RNA sequencing of migratory dendritic cells after intranasal adjuvant/tolerogen administration

Project description:We compared migratory DCs in draining mediastinal lymph node after intranasal administration of different vaccine adjuvants based on CTA1 subunit of cholera toxin. The goal was to determine different characteristics of dendritic cells subsets after pro-inflammatory vs tolerogenic adjuvant. We had 3 groups: CTA1-DD (pro- inflammatory), CTA1(R7K)-DD (tolerogenic) and PBS to define DC which migrate to LN. All vaccine constructs included 3Ea peptide to allow for sorting of DC which took up the vaccine.

2023-05-15 | E-MTAB-12942 | biostudies-arrayexpress

Alternatively activated mononuclear phagocytes from the skin site of infection and the impact of IL-4RÎ± signaling on CD4+T cell survival in draining lymph nodes after repeated exposure to Schistosoma mansoni cercariae

Project description:In areas endemic for schistosomiasis, repeated exposure to infective cercariae is a frequent occurrence, and repeated exposure of murine skin to Schistosoma mansoni resulted in CD4+ T cells becoming hypo-responsive. Here potential contributory mechanisms were investigated. In the skin infection site, three mononuclear phagocyte populations were identified (tissue macrophages, dendritic cells, and macrophages) which exhibited up-regulation of genes associated with alternative activation, in particular the gene encoding RELMÎ±. However, in repeatedly infected mice deficient in RELMÎ±, there was no change in the abundance of mononuclear phagocytes in the skin, and CD4+ cells in the skin draining lymph nodes remained hypo-responsive. In mice deficient for IL-4RÎ±, required for alternative activation, levels of dermal regulatory IL-10 were reduced and there was an increase in the abundance of antigen presenting MHC-IIhigh cells, which was accompanied by increased numbers of CD4+ T cells. Although the absence of IL-4RÎ± did not translate into increased CD4+ cell responsiveness, they exhibited lower expression of Fas/FasL, resulting in decreased apoptosis/cell death and increased cell viability. This study highlights a mechanism through which IL-4RÎ± may regulate the immune system through the induction of IL-10 and regulation of Fas/FasL mediated cell death. Mice were infected 1x or 4x with S. mansoni cercariae via the pinnae. Pinnae were harvested 4 days after the final infection and the DEC obtained after an overnight culture in vitro. Cells were then stained with F4/80 APC and MHC-II PE and four different populations sorted (using the MoFlo or the Astrios) based on their expression profiles. Several mice (12-18) from each group were pooled to generate each replicate.

2016-07-26 | E-GEOD-81938 | biostudies-arrayexpress

RNA-seq analysis of macrophages from normal and tumor-infiltrated omentum

Project description:Sequencing of mRNA from tissue-resident and tumor-associated macrophages in murine omentum display distinct transcriptional profile between macrophage subset of different origin

2020-01-06 | E-MTAB-8141 | 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 TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

2022-08-16 | E-MTAB-9734 | biostudies-arrayexpress

The protective effect of inflammatory monocytes during systemic C. albicans infection is dependent on collaboration between C-type lectin-like receptors

Project description:Invasive candidiasis, mainly caused by Candida albicans, is a serious healthcare problem with high mortality rates, particularly in immunocompromised patients. Innate immune cells express pathogen recognition receptors (PRRs) including C-type lectin-like receptors (CLRs) that bind C. albicans to initiate an immune response. Multiple CLRs including Dectin-1, Dectin-2 and Mincle have been proposed individually to contribute to the immune response to C. albicans. However how these receptors collaborate to clear a fungal infection is unknown. Herein, we used novel multi-CLR knockout (KO) mice to decipher the individual, collaborative and collective roles of Dectin-1, Dectin-2 and Mincle during systemic C. albicans infection. These studies revealed an unappreciated and profound role for CLR co-operation in anti-fungal immunity. The protective effect of multiple CLRs was markedly greater than any single receptor, and was mediated through inflammatory monocytes via recognition and phagocytosis of C. albicans, and production of C. albicans-induced cytokines and chemokines. These CLRs were dispensable for mediating similar responses from neutrophils, likely due to lower expression of these CLRs on neutrophils compared to inflammatory monocytes. Concurrent deletion of Dectin-1 and Dectin-2, or all three CLRs, resulted in dramatically increased susceptibility to systemic C. albicans infection compared to mice lacking a single CLR. Multi-CLR KO mice were unable to control fungal growth due to an inadequate early inflammatory monocyte-mediated response. In response to excessive fungal growth, the multi-CLR KO mice mounted a hyper-inflammatory response, likely leading to multiple organ failure. Thus, these data reveal a critical role for CLR co-operation in the effective control of C. albicans and maintenance of organ function during infection.

2019-06-20 | E-MTAB-8030 | biostudies-arrayexpress

Follicular helper T cell signature in Type 1 Diabetes

Project description:This study set out to examine CD4 T cell differentiation in a mouse model of diabetes based on transgenic expression of ovalbumin under the control of the rat insulin promoter and co-expression of the DO11.10 transgene (DO11 x rip-mOVA mice). The transcriptome of T cells isolated from the pancreatic lymph nodes (lymph nodes draining the site of self antigen expression) was compared with that of T cells isolated from inguinal lymph nodes (non-draining lymph nodes). T cells were sorted based on expression of CD4, DO11.10 TCR (KJ-126), CD25 and CD69. Primary cells from 6 week old DO11 x rip-mOVA mice were isolated ex-vivo from the pancreatic lymph nodes or inguinal lymph nodes. Cells were sorted by flow cytometry using antibodies to CD4, DO11.10 TCR (KJ-126+), CD25 and CD69. 3-6 replicates were collected per experimental group with each replicate deriving from 14 mice. RNA was isolated using the RNeasy micro kit (Qiagen).

2014-10-07 | E-GEOD-62104 | biostudies-arrayexpress

Inflammatory type 2 conventional dendritic cells contribute to murine and human cholangitis

Project description:Cholangitis mouse models were characterised by selective intrahepatic expansion of type 2 conventional dendritic cells, whereas plasmacytoid and type 1 conventional dendritic cells were not expanded. Expansion of type 2 conventional dendritic cells in human PSC lesions was confirmed by histology. Depletion studies revealed a pro-inflammatory role of type 2 conventional dendritic cells. Single-cell transcriptomics confirmed inflammatory maturation of the intrahepatic type 2 conventional dendritic cells and identified dendritic cell-derived inflammatory mediators.

2022-07-08 | E-MTAB-11821 | 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