Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-modal single cell analysis reveals gut microbiota reshapes brain immune landscape in aged mouse model

ABSTRACT: Multi-modal single cell analysis reveals gut microbiota reshapes brain immune landscape in aged mouse model

PROVIDER: PRJNA623317 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11486406.fastq.gz	Fastqsanger.gz
	SRR11486407.fastq.gz	Fastqsanger.gz
	SRR11486408.fastq.gz	Fastqsanger.gz
	SRR11486409.fastq.gz	Fastqsanger.gz
	SRR11486410.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Multi-modal single cell analysis reveals gut microbiota reshapes brain immune landscape in aged mouse model.

Project description:Multi-modal single cell analysis reveals gut microbiota reshapes brain immune landscape in aged mouse model.

| PRJNA673815 | ENA

Multi-modal single cell analysis reveals gut microbiota reshapes brain immune landscape in aged mouse model

Project description:We used CITE-seq (10x Gemoics-based) to profile and compare the transcriptomes and cell surface expression of a set of immune markers of naïve brain myeloid cells from young-adult (12 weeks old) wild type C57Bl/6 mice, aged (72 weeks old) wild type C57Bl/6 mice and young-adult and aged C57Bl/6 mice with antibiotics induced gut microbiota depletion. In one sequencing round, we sequenced a total of 12 different mouse brains (3 young control, 3 aged control, 3 young depleted gut microbiota (ABX) and 3 aged depleted gut microbiota (ABX)). We created an antibody pool consisting of 31 different antibodies (CCR2/CD192, C117/c-kit, CD11b, CD11c, CD172a/SIRPα, CD25, CD3, CD38, CD4, CD44, CD45, CD45R/B220, CD86, CD8a, CD90.1, Cx3cr1, F4/80, I-A/I-E, Ly6C, Ly6G, NK1.1, PD-1, PD-L1, CD169/Siglec-1, Siglec-H, TMEM119, XCR1, CD24, CD103, CD64, CD83) and stained each brain individually with this antibody pool. Then, we stained each brain with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium. Young Control and Young ABX brains were tagged with HTOs 1-6 (HTO 1-3 for young control and HTO 4-6 for young ABX). Aged control and Aged ABX brains were tagged with HTOs 1-6 (HTO 1-3 for aged control and HTO 4-6 for aged ABX). Young and aged were loaded in separate wells on the 10X Chromium. The samples were tagged with unique nextera index primers to allow for preparation of one sequencing library consisting of all 12 samples and were separated in silico by it's unique hashing antibody and nextera index barcode combinations.

2020-11-05 | GSE148127 | GEO

Multi-modal single cell analysis reveals gut microbiota reshapes brain immune landscape in aged mouse model.

Project description:We used 16S V3/V4 region amplification to evaluate the composition of bacteria species in mouse fecal pellets. Fecel pellets were collected from young-adult (12 weeks old) wild type C57Bl/6 mice and aged (72 weeks old) wild type C57Bl/6 mice after 21 days of vehicle or antibiotics treatment (to induce gut microbiota depletion). In one sequencing round, we sequenced a total of 12 different fecal samples (3 young control, 3 aged control, 3 young depleted gut microbiota (ABX) and 3 aged depleted gut microbiota (ABX)). Amplicons were indexed using the Nextera XT Index Kit and pooled into a library for Illumina sequencing.

2020-11-03 | GSE160628 | GEO

Multi-modal analysis of human Plasma-cells

Project description:Multi-modal analysis of human Plasma-cells

| PRJNA785264 | ENA

In situ valence-transited arsenic nanosheets for multi-modal therapy of colorectal cancer

Project description:Late-stage and advanced colorectal cancer (CRC) often prove to be resistant to current treatment regimens, due to the evolving tumor microenvironment. Chemotherapy-dominated multi-modal therapeutic strategies based on the specific CRC microenvironment open a new horizon for eradicating colorectal tumors. Here, in situ valence-transited arsenic nanosheets are developed as a multi-modal therapeutic platform by responding to the H2S-enriched CRC microenvironment. Carrier-free pegylated nanosheets of pentavalent arsenic (AsV), aminooxyacetic acid (AOAA), and copper ion (Cu2+) are innovatively self-assembled via coordination with high loading content and good stability. AsV in pegylated arsenic nanosheets (CAA-PEG NSs) is rapidly released and reduced to trivalent arsenic (AsIII) to exert its chemotherapy in the local tumor. Furthermore, the immunosuppressive microenvironment is thoroughly remodeled via H2S depletion of AsV to AsIII conversion and impairment of H2S production by AOAA. Additionally, the in situ produced ultrasmall CuS nanoparticles exhibit photothermal activity against CRC under the guidance of photoacoustic imaging. This multi-modal therapeutic strategy, dominated by chemotherapy, completely inhibits CRC progression and prevents its relapse.

2025-05-07 | PXD059728 | Pride

Multi-modal analysis of human Plasma-cells

Project description:Plasma cells are key components of humoral immunity by secreting antibodies and providing protection against pathogens. These cells can be of IgM, IgA, or IgG subclass and migrate to class-specific niches. Localization and rareness of plasma cells make it challenge to define subclass-specific molecular hallmarks. Here, we describe how in-vitro differentiation of peripheral B-cells results in antibody-secreting plasma cells. Using a single-cell multi-modal sequencing approach (RAID) we find subclass-specific hallmark transcriptional profiles, surface protein expression and signaling pathway activation.

2023-01-02 | GSE189953 | GEO

Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

Project description:We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

2022-02-14 | E-MTAB-10714 | biostudies-arrayexpress

Multi-modal control of dendritic cell functions by nociceptors

Project description:Multi-modal control of dendritic cell functions by nociceptors

| PRJNA899112 | ENA

Multi-modal characterization and simulation of human epileptic circuitry

Project description:Multi-modal characterization and simulation of human epileptic circuitry

| PRJNA895917 | ENA

A single-cell multi-modal ATAC + gene expression sequencing in tendinopathy

Project description:As people become more motivated to exercise regularly and stay healthy, tendinopathy is a common problem in both active athletes and inactive individuals, which imposes a considerable social and economic burden. Here we provide a single-cell multi-modal ATAC + gene expression sequencing in tendinopathy. We have identified pathways and genes regulated in tendinopathy samples that will help contribute to further investigation into the development and molecular hallmarks of tendinopathy.

2023-05-31 | GSE213803 | GEO

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