Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNAseq of Neuronal-derived haploid and diplod human embryonic stem cells

ABSTRACT: Single cell RNAseq of Neural-derived haploid and diplod human embryonic stem cells, validating successful differentiation of haploid hESCs into neurons

INSTRUMENT(S): NextSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Shay Kinreich

PROVIDER: E-MTAB-13620 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq data for Distinct Stem Cell Identities Converge into Shared Erythroid Stress in ERCC6L2 Disease and Shwachman-Diamond Syndrome

Project description:This study includes single-cell RNA sequencing of human samples across ERCC6L2 disease (ED), Shwachman-Diamond syndrome (SDS), acute myeloid leukemia (AML), and healthy controls. ED, SDS, and AML samples were processed for single-cell capture, followed by library preparation and sequencing. Sequencing reads were processed through standard pipelines, including quality control, alignment, and quantification, to generate expression matrices. The dataset contains processed single-cell gene expression data, and curated metadata describing sample identity, cell populations, and disease classification. Related raw sequencing files will be available at FEGA.

2026-06-03 | E-MTAB-16984 | biostudies-arrayexpress

Single cell transcriptomic analysis of bone marrow hematopoietic stem and progenitors cells isolated from 10-week-old wild-type control, Rps19R67∆/R67∆, Rps19R67∆/R67∆ Trp53−/− and Trp53−/− mutant mice.

Project description:This single cell transcriptome sequencing experiment is part of the study \\"Preclinical animal model of Diamond-Blackfan anemia with single amino acid mutation of ribosomal protein Rps19\\". A mouse model with this mutation develops features characteristic of human Diamond-Blackfan anemia, a rare bone marrow failure syndrome, including hematologic dysfunctions, early onset growth delay, intrinsic anemia, severe craniofacial, skeletal, urogenital, cardiovascular, and cerebral abnormalities leading to premature lethality during the adolescence of the mouse. This DBA mouse model exhibits cell intrinsic activation of the Trp53 signaling pathway in hematopoietic stem cells (HSCs) leading to reduced erythroid lineage development that may be rescued after inactivation of the tumor suppressor Trp53. The study uncovers that the development of the DBA phenotype significantly involves non-canonical components of the p53 signaling pathway in the etiopathogenesis of DBA with the Rps19R67∆ mutation leading to the disrupted hematopoietic hierarchy starting at the stage of short-term repopulating stem cells and the central role of induced Trp53 expression and upregulation of its non-canonical targets in the mediation of neural crest lineage deficiency-mediated development of craniofacial malformations in this model.

2023-05-01 | E-MTAB-12446 | biostudies-arrayexpress

Lymphoma-induced regression of high endothelial venules impairs homeostatic lymphocyte trafficking

Project description:Lymphoma growth is facilitated by the well-balanced infrastructure of the microenvironment in lymph nodes (LN). LNs undergo rapid expansion during lymphoma progression, often accompanied by excessive blood vessel growth. Here we report that aggressive lymphoma cause severe high endothelial venule (HEV) regression which impairs lymphocyte recirculation. In this study, we used transferred (i.v.) Eµ-Myc tumor cells as a mouse model of aggressive lymphoma. Blood endothelial cells from tumor bearing and control LNs were isolated by FACS and processed for single-cell RNA sequencing. The results revealed a detrimental mechanisms causing HEV-dedifferentiation during lymphoma growth with potential implications on tumor-targeting immune surveillance and strategies of immune therapy in LNs

2021-10-14 | E-MTAB-10389 | biostudies-arrayexpress

Single-cell RNA sequencing of erythroid and megakaryocytic acute myeloid leukemia patient cells

Project description:Single-cell RNA sequencing was performed on bone marrow mononuclear of a patient with acute myeloid leukemia with erythroid differentiation of the blasts and on peripheral blood mononuclear cells of a patient with acute myeloid leukemia with megakaryocytic differentiation of the blasts. Raw data for this dataset can be found at the EGA under accession EGAS00001006819.

2022-12-05 | E-MTAB-12607 | biostudies-arrayexpress

Single-cell RNA-seq of aortic CD3+ T cells

Project description:We dissected the changes in the infiltrating T cell population in the aorta of cDC1-impaired mice compared with control mice in atheroprone Ldlr-/- mice by scRNAseq. To this aim, lethally irradiated Ldlr-/- CD45.1 mice were grafted with cDC1-impaired Xcr1Cre-DTA or control Xcr1Cre bone marrow (BM) and fed high cholesterol diet (HCD) for 8 weeks. At the endpoint, 10 mice per group were pooled and aortic CD45+ CD3+ CD11c- I-A/I-E– F4/80- Ly6C- Ly6G- NK1.1- were sorted and sequenced. A number of 6259 CD3+ T cells were sequenced in Xcr1Cre control chimeric mice, while 4072 cells were sequenced in cDC1-impaired Xcr1Cre-DTA chimeric mice. Nine different clusters were identified based on the following gene expression profile.

2025-06-18 | E-MTAB-14540 | biostudies-arrayexpress

Testis single-cell RNA-sequencing in the cynomolgus macaque reveals conserved transcriptional profiles during mammalian spermatogenesis

Project description:Spermatogenesis in mammals is a complex and highly orchestrated process, which involves the differentiation of diploid (2n-DNA content) spermatogonia into haploid (n) sperm. This process begins with spermatogonia, a niche of stem cells, which drive this process. Spermatogonial stem cells (SSCs) undergo mitotic self-renewal to maintain this niche, while sub-populations of spermatogonia progressively undergo differentiation and later gain competence to initiate meiosis and form sperm. SSCs undergo extensive chromatin remodelling and major morphological changes, while maintaining genome integrity and parental imprints. To study this in greater detail we performed single-cell RNA sequencing of spermatogenic cells derived from the testis of the non-human primate Macaca fascicularis.

2020-08-13 | E-MTAB-8979 | biostudies-arrayexpress

Anti-CD27 immunotherapy induces intratumoral immunostimulation in B-cell lymphoma: the multi centre RiVa trial (scRNA-Seq Data for RiVa)

Project description:The clinical utility of T-cell agonistic antibodies in cancer therapy, much less their ability to stimulate intratumoral T-cells in patients, has eluded us. T-cell agonistic antibodies such as anti-CD27 can induce clinically meaningful anti-tumor activity. The combination of anti-CD27 agonist varlilumab and tumor-depleting anti-CD20 rituximab was investigated in patients with relapsed/refractory B-cell non-Hodgkin lymphoma (B-NHL) (RiVa trial;NCT03307746). Our experiments detail scRNA-seq data from 6 B-cell NHL patients, including both pre and on-treatment biopsies taken from lymph nodes.

2025-08-09 | E-MTAB-14585 | biostudies-arrayexpress

Single-cell profiling of the leukemic and non-leukemic immune cell compartments in CD8+ T-cell Large Granular Lymphocytic Leukemia

Project description:We performed a detailed and precise characterisation of the clonally expanded leukemic cells in CD8+ T-cell Large Granular Lymphocytic Leukemia (T-LGLL). By combining scRNA+TCRαβ-seq with bulk RNA sequencing data we showed evidence of a strong antigen-driven immune response that shapes the entire immune cell repertoire in T-LGLL. Our study highlights how the whole immune cell repertoire including the hyperexpanded CD8+ T-LGLL cells, the non-leukemic CD8+ cells, CD4+ cells, and monocytes contribute to the CD8+ T-LGLL disease phenotype. The raw data for this study have been deposited to the controlled-access archive EGA under EGAS00001005297.

2021-11-26 | E-MTAB-11170 | biostudies-arrayexpress

Single-cell RNA sequencing and single-cell CRISPR screens of interacting natural killer and blood cancer cells

Project description:To profile the cell states of interacting natural killer (NK) cells and blood cancer cells, we cultured 26 different cell lines representing diverse hematologic neoplasms either alone or with NK cells derived from three healthy human donors. After 24 h co-culture, we labeled the cells from each monoculture or co-culture condition with oligonucleotide-conjugated antibodies against ubiquitously expressed surface proteins (with different oligonucleotide for each mono- or co-culture), enabling multiplexing in the scRNA-seq using the cell hashing method. We additionally performed pooled CRISPR screens with a single-cell transcriptome readout using the CROP-seq platform in blood cancer cells cultured either alone or in the presence of NK cells to study the effects of perturbing genes that influenced sensitivity to NK cell killing in genome-scale CRISPR screens.

2023-07-24 | E-MTAB-13204 | biostudies-arrayexpress

Single cell RNA sequencing of murine gamma delta T cells from wild type and beta2 integrin-deficient (CD18 KO) lungs

Project description:The beta2 integrin subunit (CD18) is thought to regulate gamma delta T cells in vivo. The objective of this study was to determine the gene expression changes mediated by loss of CD18 in lung gamma delta T cells. Single cell RNA sequencing was performed on gamma delta T cells (CD3+ gamma delta TCR+) isolated from the lungs of wild type C57BL/6 mice (N=2) and CD18 knockout (Itgb2-/-) mice (N=1).

2020-08-14 | E-MTAB-8732 | 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