Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of butyrate micelle or control treated murine Ly6Chi CD11b+ myeloid cells

ABSTRACT: We aimed to study the impact of bacteria-derived metabolites in solid organ transplantation. The short-chain fatty acid butyrate was administered using a new drug-delivery method developed by Wang et al. (https://doi.org/10.1038/s41551-022-00972-5). This system is based on a micelle platform that carries and protects butyrate (ButM) from degradation in the upper gastrointestinal tract, to lower distal portions of the gut. Mice (adult B6 females) were treated for 21 days with ButM (100mg/mL) or 1x PBS. Splenic Ly6Chi CD11b+ monocytes were sorted for bulk RNAseq using the Takara SMART-Seq mRNA LP and Unique Dual Index kits. Libraries were sequenced using the Illumina NovaSeq 6000 platform.

INSTRUMENT(S): BD FACSAria III, Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Alexandra Cassano

PROVIDER: E-MTAB-13931 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Heterogeneity in allospecific T cell function in transplant tolerant hosts determines susceptibility to rejection following infection

Project description:CD4+CD45.1+ TCR75/Rag-/- T cells (TCR75) were adoptively transferred into CD45.2+ B6 hosts either untransplanted and immunized with B/c donor splenocytes i.p. (UnTx+DST) to induce memory, or prior to transplantation of a B/c heart (HTx) in the presence of anti-CD154 (day 0, day 7, day 14) and DST (day 0) to induce tolerance (Tol). A group of tolerant mice were infected with Lm on d30 post-transplantation (Tol+Lm). CD45.1+ TCR75 cells were harvested from the spleen and lymph nodes on d35-37 post-transplantation in all groups, enumerated and subjected to bulk RNAseq.

2023-09-29 | E-MTAB-13333 | biostudies-arrayexpress

RNA-seq of monocytes from a variety of mouse tissues

Project description:We investigated the transcriptomes of monocytes in a variety of mouse tissue. Monocytes were were identified as CD45+ Lin(CD3ε, TCR-β, CD19, B220, NK1.1, Ter119, Siglec F, Ly6G)- CD11b+ Ly6Chi CD64- MHCII- and their RNA was sequenced on the Illumina HiSeq2500PE

2021-02-05 | E-MTAB-10039 | biostudies-arrayexpress

Global genome expression analysis of lamina propria derived WT and Nlrp6-/- Ly6C-hi inflammatory monocytes

Project description:Nlrp6-/- lamina propria Ly6C-hi monocytes in response to AOM/DSS have deficient TNFÎ± production, but increased production of other pro-inflammatory cytokines as compared to WT NLRP6 is a member of the Nod-like receptor family, whose members are involved in the recognition of microbes and/or tissue injury. NLRP6 was previously demonstrated to regulate the production of IL-18 and is important for protecting mice against chemically-induced intestinal injury and colitis-associated colon cancer. However, the cellular mechanisms by which NLRP6 reduces susceptibility to colonic inflammation remain unclear. Here, we determined that NLRP6 expression is specifically upregulated in Ly6Chi inflammatory monocytes that infiltrate into the colon during dextran sulfate sodium (DSS)-induced inflammation. Adoptive transfer of WT Ly6Chi inflammatory monocytes into Nlrp6-/- mice was sufficient to protect them from mortality, significantly reducing intestinal permeability and damage. NLRP6-deficient inflammatory monocytes were specifically defective in TNFÎ± production, which was important for reducing DSS-induced mortality and dependent on autocrine IL-18 signaling by inflammatory monocytes. Our data reveal a previously unappreciated role for NLRP6 in inflammatory monocytes, which are recruited during intestinal injury to promote barrier function and limit bacteria-driven inflammation. This study also highlights the importance of early cytokine responses, particularly NLRP6-dependent and IL-18-dependent TNFÎ± production in preventing chronic dysregulated inflammation. Ly6Chi monocytes were sorted from lamina propria of WT or Nlrp6-/- mice at day 10 of AOM/2%DSS. RNA was extracted and hybridized to the mouse 2.1 ST array.

2016-03-27 | E-GEOD-79631 | biostudies-arrayexpress

scRNA-seq of human trophoblast stem cells as a model of trophoblast-cytotrophoblast (TB-CTB)

Project description:Placenta derived Okae et al. human trophoblast stem cells cultured in Okae et al. conditions (ttps://doi.org/10.1016/j.stem.2017.11.004). In addition, we sequenced SHEF6 primed human pluripotent stem cells as a control. Individual cells were manually isolated with a mouth pipette and subjected to single-cell full-lengths transcriptome profiling using a modified version of Smart-Seq2.

2022-06-03 | E-MTAB-10890 | biostudies-arrayexpress

Effects of microbial disruption on intestinal macrophages.

Project description:Intestinal macrophages were isolated from the intestine of mice that had been administered antibiotics for 7 days, prior to 7 days or re-exposure to the microbiota (recolonisation). In some experiments, the short-chain fatty acid butyrate was administered alongside antibiotics prior to recolonisation.

2019-07-22 | E-MTAB-7132 | biostudies-arrayexpress

Single-nucleus RNA-seq2 of liver tissue of 3 months old mice to investigate crosstalk between ploidy and zonation

Project description:Single-nucleus RNA-seq-2 method that allows deep characterization of nuclei isolated from frozen archived tissues. We have used this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy. This method has the potential to explore archived samples, in order to study the development and progression of disease in complex tissues. To illustrate the potential of this method, we have deeply characterized the cellular heterogeneity driven by spatial distribution and different levels of ploidy in the young adult mouse liver.

2021-05-06 | E-MTAB-9333 | biostudies-arrayexpress

RNA-seq of euploid versus aneuploid human embryo trophectoderm biopsies

Project description:Embryos classified as euploid or aneuploid by PGT-A were re-biopsied and processed for RNA-Seq using a commercial kit (Takara Bio, USA, SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing) following the user manual. The resulting cDNAs were converted to libraries using a Nextera XT kit (Illumina, USA), with a modified protocol according to SMART-Seq v4 user manual. These libraries were pooled and sequenced using a NextSeq 550 instrument (Illumina, USA) with a MidOutput cartridge at 2x75 cycles. The sequencing reads in Fastq files were down-sampled to 6M total reads, aligned to the human genome assembly (hg38), and the number of transcripts per million (TPM) was determined using the CLC Genomics Workbench 12 (Qiagen, USA).

2022-09-07 | E-MTAB-12084 | biostudies-arrayexpress

RRBS (DNA methylation) analysis of CD4+ CD8+ and CD4-CD8- fractions of PBMC cells collected from 7 case children, who were positive for type 1 diabetes specific autoantibodies, and their matched controls, sampled at 3, 6, 12, 18, 24, and 36 months of age

Project description:10.1007/s00125-022-05657-x

2022-02-14 | E-MTAB-11088 | biostudies-arrayexpress

Infiltrating monocyte-derived macrophages and resident kupffer cells display different ontogeny and functions in acute liver injury

Project description:Molecular profiling of infiltrating monocyte-derived macrophages versus resident kupffer cells following acute liver injury The liver has a remarkable capacity to regenerate after injury; yet, the role of macrophages (MF) in this process remains controversial mainly due to difficulties in distinguishing between different MF-subsets. Here, we utilized a murine model of acute liver injury caused by overdose of acetaminophen (APAP) and defined three distinct MF subsets that populate the liver following injury. Accordingly, resident Kupffer cells (KC) were significantly reduced upon APAP-challenge and started recovering by self-renewal at resolution phase without contribution of circulating Ly6Chi monocytes. The latter were recruited in a CCR2 and M-CSF mediated pathway at the necro-inflammatory phase and differentiated into ephemeral Ly6Clo MF subset at resolution phase. Moreover, their inducible ablation resulted in impaired recovery. Microarray based molecular profiling uncovered high similarity between steady state KC and those recovered at the resolution phase. In contrast, KC and monocyte-derived MF displayed distinct pro-restorative genetic signature at the resolution phase. Finally, we show that infiltrating monocytes acquire a pro-restorative polarization manifested by unique expression of pro-angiogenesis mediators and genes involved with inhibition of neutrophil activity and recruitment and promotion of their clearance. Collectively, our results present a novel phenotypic, ontogenic and molecular definition of liver-MF compartment following acute injury. 11 Samples (arrays) were performed. We generated pairwise comparison between all the different macrophages stages, using Partek Genomics Suite. Genes with p?5%[FDR] and a fold-change difference of ?2 or <-2 were selected.

2014-08-01 | E-GEOD-55606 | biostudies-arrayexpress

Genome-wide analysis of tissue-specific gene expression by Ly6Chi inflammatory monocytes during Toxoplasma gondii infection

Project description:Analysis of Ly6Chi monocytes from small intestine lamina propria (SILP) and blood of day 8 Toxoplasma gondii infected mice at gene expression level. The hypothesis tested in the present study was that Ly6Chi monocytes from SILP have altered expression of regulatory factors to blood monocytes. Results provide important information on the regulatory to effector balance of genes expressed by Ly6Chi monocytes during an acute inflammatory response. Ly6Chi inflammatory monocytes were sorted by FACS from the blood or small intestine lamina propria (SILP) of Toxoplasma gondii infected C57BL/6 mice. Cells were isolated at day 8 after infection and total RNA obtained from sorted populations. Three biological replicates were acquired for both blood and SILP from pooled animals.

2013-05-25 | E-GEOD-46685 | 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