Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Tereza Vanova

PROVIDER: E-MTAB-11438 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq of mouse pancreatic islets from non-transgenic and pericyte MyD88-mutated mice

Project description:To elucidate the role of pericytic cytokines in islet inflammation, we interfered with the expression of MyD88, a key modulator of the IL1R1/TLR pathway, in pericytes using transgenic mice (Nkx3.2-Cre;MyD88 flox/flox) . To determine the impact on islet immune cells, we isolated CD45+ cells from the islets of both non-transgenic and Myd88-deficient mice via MACS, pooling samples from 4-5 littermate male mice. Additionally, unsorted islet cells from the same pool were included to meet the cell number requirements for sample preparation using X10 genomics.

2023-12-31 | E-MTAB-13640 | biostudies-arrayexpress

RNA-seq from human peripheral blood isolated and CRISPR/Cas9-mediated BCL11B depleted alpha-beta CD8+ T cells and corresponding not transfected (nt) and mock (mock gRNA transfected) controls.

Project description:B-cell lymphoma/leukemia (BCL) 11B represents a major regulator of vital processes in post-thymic lymphocytes as well as of lymphocyte differentiation by blocking NK cell and promoting T cell development and is thus considered a \\"guardian of T cell fate\\". Interestingly, on the one hand, NK cell maturation correlates with increased expression of BCL11B, on the other hand, native or induced T cell populations characterized by multiple NK cell features showed reduced BCL11B expression. Both NK cells or T cells display unique and desired features for cellular therapies. NK cells are able to efficiently lyse cancerous or virally infected cells but can only be poorly expanded in vitro. In contrast, T cell cytotoxic activity is limited by T cell receptor (TCR) but in vitro expansion is easily achievable. We show that from buffy coats of healthy donors isolated and CRISPR/Cas9-mediated BCL11B knock-out CD8+ T cells stimulated with IL-15 acquired remarkable innate characteristics and combine spontaneous and antibody-dependent NK cell cytotoxicity with T cell capability for rapid in vitro expansion. The observed features of the induced innate CD8+ (iiT8) cells make them an interesting and promising tool for cellular therapy.

2022-12-07 | E-MTAB-12064 | biostudies-arrayexpress

Cholesterol lowering depletes smooth muscle cell-derived fibromyocytes and chondromyocytes from atherosclerotic lesions

Project description:Study of the effect of low-density lipoprotein (LDL)-lowering therapies on the heterogeneous population of proliferating smooth muscle cells (SMCs) derived from atherosclerotic plaques in an atherosclerotic mouse model by inducing hypercholesterolemia followed by high or low fat diet.

2023-12-08 | E-MTAB-12019 | biostudies-arrayexpress

Single cell sequencing analysis of senescence in Mus musculus prostate cancer models

Project description:Acute Pten loss initiates prostate tumorigenesis characterized by cellular senescence response. Here we examine the cellular senescence response in epithelial individual cells, by single-cell RNA sequencing (scRNAseq) in Ptenpc-/- and Ptenpc-/-; Timp1-/- GEMMs. ScRNAseq analysis determines a cluster of senescent cells expressing the senescence-related genes. A significant positive correlation is observed between the senescence score and Bcl2 expression. This provides the rational for targeting senescent cells using Bcl2 inhibitor.

2020-10-09 | E-MTAB-9578 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (scRNA-Seq)

Project description:Cornelia de Lange syndrome (CdLS) is a rare genetic disease associated with cohesinopathy. A novel iPSC line was generated from the CdLS patient carrying a heterozygous missense point-mutation of the NIPBL gene. iPSC lines prepared from the healthy parents and the mutation-corrected isogenic cell lines are used as the respective controls. Upon differentiation into hepatocytes, the patient-derived iPSC demonstrate the capacity to express hepatocyte-specific marker transcripts and the respective proteins, however, the efficiency of differentiation is significantly inferior to those of the respective controls, demonstrated by single-cell RNA sequencing and immune-fluorescent analyses. Global change of transcriptome in the patient-derived iPSC relative to the control cells is associated with altered chromatin accessibility, assessed by RNAseq combined with ATACseq analysis. Differentially down-regulated genes in the patient-derived iPSC, in particular, are those coding for proteins related to neural differentiation and transcription factors, while up-regulated genes contain some of antisense RNA coding genes, pseudo genes and long non-coding RNAs. Some of the differentially regulated genes are consistent with the altered chromatin accessibility and this observation is consistent during hepatocyte differentiation. Thus, the mutation in the NIPBL gene of the CdLS patient could be responsible for defects of differentiation primarily due to alteration of chromatin accessibility.

2023-06-15 | E-MTAB-12636 | biostudies-arrayexpress

Single-cell RNA-sequencing of cells from spinal cord central canal region of young adult and aged mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. This neural stem cell potential is known to decline with age in the mouse. Here, we microdissected and dissociated into single cells the central canal region from the spinal cord of 4 young adult (3-to-4-month old) and 4 aged (18-to-19-month old) C57BL/6J mice to profile the transcriptomes of cells in and around the central canal using 10x Genomics technology.

2022-12-13 | E-MTAB-11561 | biostudies-arrayexpress

Single-cell RNA-seq (10x Chromium V3) of zebrafish csf1ra and csf1rb mutant whole kidney marrows

Project description:Macrophage colony-stimulating factor receptor (M-CSFR/CSF1R) signaling is crucial for the differentiation, proliferation, and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases, including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore, it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human-related diseases. Here, we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single-cell RNA sequencing. Our analysis of adult whole kidney marrow (WKM) hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non-overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease, mostly in cancerogenesis.

2021-04-24 | E-MTAB-10360 | biostudies-arrayexpress

Single cell RNA-sequencing of epithelial cells, endothelial cells and macrophages from mouse submandibular salivary glands

Project description:The salivary glands often become damaged in individuals receiving radiotherapy for head and neck cancer, resulting in chronic dry mouth. This leads to detrimental effects on their health and quality of life, for which there is no regenerative therapy. Macrophages are the predominant immune cell in the salivary glands and are attractive therapeutic targets due to their unrivalled capacity to drive tissue repair. Yet, the nature and role of macrophages in salivary gland homeostasis, and how they may contribute to tissue repair following injury is not well understood. Here, using scRNAseq we profile the transcriptomes of adult mouse salivary gland macrophages at steady state (D0) and at days 3 and 28 after targeted irradiation injury to define the transcriptional profiles of macrophages during homeostasis, acute injury and regeneration. We sorted epithelial cells (CD326+), endothelial cells (CD31+) and macrophages (CD45+CD11b+F4/80+) and sequenced their transcriptomes using 10x Genomics Single Cell 3' (v3.1). For each sample equal numbers of cells from 2 mice were pooled.

2023-10-01 | E-MTAB-13374 | biostudies-arrayexpress

Identification of cell-intrinsic effects of clonal hematopoiesis in heart failure

Project description:Clonal hematopoiesis of indeterminate potential (CHIP) is caused by somatic mutations in hematopoietic stem cells and is associated with worse prognosis in heart failure patients. Patients harboring CHIP mutations show enhanced inflammation. However, whether these signatures are derived from the relatively low number of cells harboring mutations or are indicators of a systemic pro-inflammatory activation that is associated with CHIP is unclear. In this study, we assessed the cell-intrinsic effects of CHIP mutant-carrying cells in patients with heart failure. Using an improved protocol to detect mutant cells on a single cell level (MutDetect-Seq), we show that DNMT3A mutant monocytes exhibit altered gene expression profiles associated with inflammation and phagolysosome function. Gene expression was also significantly altered in DNMT3A mutant CD4+ T cells and NK cells, but not CD8 T cells. DNMT3A silenced CD4+ T cells and NK cells showed increased effector functions. Moreover, increased paracrine signaling pathways are predicted and validated between mutated and wild monocytes and T cells, which amplify inflammatory circuits. Taken together, these data provide novel insights into how CHIP might promote worse prognosis in heart failure patients.

2023-06-15 | E-MTAB-13016 | biostudies-arrayexpress

Single-cell RNA-seq of fetal liver and bile duct organoids to investigate human fetal liver development

Project description:scRNAseq of primary fetal liver (6 post conceptional weeks), fetal biliary organoids, hepatoblast organoids, hepatoblast organoids after withdrawl of Wnt and transfer to hepatozyme medium, hepatoblast organoids after TGFb treatment.

2022-05-04 | E-MTAB-7189 | 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