Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-Cell Profiling of the Inflammatory Microenvironment in the Aged Rats Hippocampus and the Contributions of Cerebrovascular Endothelial Cells

ABSTRACT: To map the cell type-specific transcriptome landscape of the inflammatory microenvironment induced by systemic injection of lipopolysaccharide (LPS), we analyzed the hippocampus of aged rats on day 3 following a single injection to identify key molecules within specific cell subsets by single-cell RNA sequencing (scRNA-seq).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Rattus norvegicus

SUBMITTER: Liu Fangyan

PROVIDER: E-MTAB-15343 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome Profiling of Tumor-Infiltrating Lymphocyte-Mediated Cytotoxicity against Patient-Derived Lung Cancer Organoids

Project description:Non-small cell lung cancer (NSCLC) is a leading cause of cancer mortality, and therapies utilizing tumor-infiltrating lymphocytes (TILs) show significant promise. However, the molecular signatures that define a productive TIL-mediated response against tumors remain poorly characterized. Here, we establish a patient-derived organoid and autologous TIL co-culture platform to dissect this interaction at high resolution. We show that expanded TILs mediate potent and specific cytotoxicity against NSCLC organoids. This functional response is associated with a crucial shift in T-cell states, from proliferative towards effector memory phenotypes, and involves the activation of key signaling networks including the Tumor Necrosis Factor (TNF) and Interleukin-17 (IL-17) pathways. Furthermore, analysis of the T-cell receptor (TCR) repertoire confirms that the expansion process selectively enriches tumor-associated clonotypes, resulting in a more focused repertoire. This work delineates the transcriptional and clonal signatures of an effective anti-tumor immune response, providing a robust framework to guide the development of next-generation personalized TIL therapies.

2025-10-31 | E-MTAB-15782 | biostudies-arrayexpress

Transcriptome Profiling of Tumor-Infiltrating Lymphocyte-Mediated Cytotoxicity against Patient-Derived Lung Cancer Organoids

2025-10-26 | E-MTAB-15784 | biostudies-arrayexpress

Single-cell profiling (scRNA-seq with paired V(D)J) of the splenic response to VLP immunization in MZB KO versus wild-type mice

Project description:The precise role of Marginal Zone B (MZB) cells in shaping the adaptive immune response to virus-like particle (VLP) immunization remains incompletely defined. Here, we combined VLP immunization of wild-type and MZB-deficient mice with single-cell RNA sequencing (scRNA-seq) and paired TCR/BCR profiling of splenocytes. This integrated approach directly links the cellular transcriptome with its unique immune receptor at a single-cell resolution, allowing us to deconvolute the splenic immune landscape and precisely identify the molecular and clonal alterations resulting from the absence of MZB cells.Our analysis provides the first comprehensive insight into the gene expression programs and receptor repertoires that define the disrupted humoral immunity in MZB KO mice following vaccination. This strategy establishes a framework for definitively linking specific immune cell subsets to functional antibody responses and can be broadly applied to dissect the mechanisms of action of other vaccine platforms.

2026-01-01 | E-MTAB-16268 | biostudies-arrayexpress

Deciphering cellular and molecular signatures of malignant progression in Neurofibromatosis type 1 using single-cell transcriptomic analysis

Project description:Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas with currently no effective treatment. While half of MPNSTs arise sporadically, the others are due to the malignant progression of neurofibromas (NFs) in patients with neurofibromatosis type 1 (NF1). NFs are benign nerve sheath tumors due to bi-allelic loss of NF1, encoding a negative regulator of Ras pathway, in the Schwann cell (SC) lineage. We have conceived an Nf1-KO mouse model in which NFs spontaneously transform into MPNSTs To decipher the step-by-step evolution of the cellular composition and biological activities of tumor cells and their microenvironment during the transformation process, we performed single-cell transcriptomic profiling of pNFs, dyNFs and MPNSTs, all issued from Prss56Cre, Nf1fl/fl cohort, using 10x Chromium platform. We discovered that malignant transformation is initiated by a molecular transition of tumor SCs from glial to mesenchymal identity (GMT).

2025-08-26 | E-MTAB-14222 | biostudies-arrayexpress

Single-cell RNA-seq of PBMCs from HCC patients pre- and post-curative therapy

Project description:This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) collected from six hepatocellular carcinoma (HCC) patients, before and after curative therapy. Samples were profiled using the 10x Genomics Chromium platform. The dataset includes gene expression matrices and associated metadata for 12 samples (6 pre-therapy, 6 post-therapy). These data support the analysis of peripheral immune cell dynamics in response to tumor removal

2026-01-13 | E-MTAB-16408 | biostudies-arrayexpress

Single-cell sequencing of cerebral organoids with familial Alzheimer’s disease (AD) mutation in PSEN1 and non-demented control

Project description:We set up a 3D model based on iPSCs derived from patients with familial forms of Alzheimer’s disease (AD) and healthy non-demented control. We created cerebral organoids (COs), verified their ability to mimic AD in vitro, and used it to explore early events and the progression of AD pathogenesis. Our data reveal that despite similar expression of cell-type-specific genes during CO maturation in vitro, AD-iPSCs derived COs show limited tissue patterning and altered cellular development. These findings complement unique single-cell sequencing data of AD-iPSCs derived COs confirming this observation and uncovering that a sub-set of neurons in AD-iPSCs likely differentiates prematurely while at the same time retaining the expression of progenitor marker PAX6.

2022-07-01 | E-MTAB-11438 | 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

Single-Cell Transcriptomics Sheds Light on the Identity and Metabolism of Developing Arabidopsis Leaf Cells

Project description:Being the main photosynthetic instrument of vascular plants, leaves are crucial and complex plant organs. To establish the single-cell transcriptomic landscape of these different leaf tissues, we performed high-throughput transcriptome sequencing of individual cells isolated from young leaves of Arabidopsis seedlings grown in two different environmental conditions. The detection of ~19,000 different transcripts in over 1,800 high-quality leaf cells revealed 14 cell populations composing the young, differentiating leaf.

2021-10-15 | E-MTAB-11006 | biostudies-arrayexpress

Multiome RNA+ATAC on human PBMCs (snATAC-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11226 | biostudies-arrayexpress

Single cell RNA sequencing (scRNA-seq) of human embryoid body (day 4 of culture)

Project description:Human Primordial Germ Cell (PGC)-like cells (PGCLC) were specified in vitro from naive-like hiPS cell lines. To evaluate the first steps of PGCLC differentiation, we performed scRNA-seq (droplet-based technology, 10x) on cell suspension from embryoid body (EB) obtained after EB aggregation followed by 4 days of culture (EBd4) with cocktail of cytokines (BMP4, LIF, SCF, EGF and ROCK inhibitor) supplemented with 0.1 mM 2-mercaptoethanol and 15% KSR. In this study, two pools of embryoid bodies (EBD4_A, EBD4_B) were cultured independently for for further encapsulation and sequencing.

2022-11-29 | E-MTAB-12089 | 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