Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic profile of iPSC differentiation process by scRNA-seq

ABSTRACT: Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scRNA-seq.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Dejan Lazarevic

PROVIDER: E-MTAB-10220 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Epigenetic profile of iPSC differentiation process by scGET-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scGET-seq.

2021-08-17 | E-MTAB-10218 | biostudies-arrayexpress

Epigenetic profile of iPSC differentiation process by scGET-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scGET-seq.

2021-08-17 | E-MTAB-9649 | biostudies-arrayexpress

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

Single cell RNA-seq analysis of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points

Project description:This experiment is aimed at studying the effect of two different chemotherapies (FOLFOX and FOLFIRI) on colorectal cancer cell lines (HCT116 and HT29) at different time points. Two early time points (8h and 16h) are used to evaluate the acute response, while a late time point (two weeks, LT) is used to evaluate the long-term effect. After two week exposure, cells are grown without treatments for additional two weeks, to evaluate the transcriptomic of cells which survived the chemotherapy. A pool of the same cells has been independently profiled by scGET-seq.

2023-09-01 | E-MTAB-12949 | biostudies-arrayexpress

Single cell RNA-seq analysis of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points

Project description:This experiment is aimed at studying the effect of two different chemotherapies (FOLFOX and FOLFIRI) on gene expression of HCT116 colorectal cancer cell line at different time points. Two early time points (8h and 16h) are used to evaluate the acute response, while a late time point (two weeks, LT) is used to evaluate the long-term effect. After two week exposure, cells are grown without treatments for additional two weeks, to evaluate the transcriptomic of cells which survived the chemotherapy. For all time points, untreated cells (CTRL) are also collected.

2023-09-01 | E-MTAB-12950 | biostudies-arrayexpress

Single-cell RNAseq of Tal1 knockout chimeric mouse embryos at embryonic day 8.5 of mouse development

Project description:Chimeric embryos were generated to investigate the effect of Tal1 knockout in mouse embryos by single-cell RNA-sequencing. Tal1 is an essential transcription factor for the formation of the embryonic blood. Embryo chimerism permits the analysis of the effects of Tal1 knockout without the confounding effects of the absence of embryonic blood, which results in global developmental failures. Embryos were generated by blastocyst injection of tdTomato-labelled, Tal1-/- mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2018-12-05 | E-MTAB-7325 | biostudies-arrayexpress

Single-cell RNAseq of control chimeric mouse embryos at embryonic days 7.5 and 8.5 of mouse development

Project description:Chimeric mouse embryos were generated as a control experiment to understand the contribution of host vs. injected cells to the developing embryo. Embryos were generated by blastocyst injection of tdTomato-labelled mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2018-12-05 | E-MTAB-7324 | biostudies-arrayexpress

Single-cell RNAseq of additional control chimeric mouse embryos at embryonic day 8.5 of mouse development

Project description:This dataset contains additional data performed as in the experiment stored at accession E-MTAB-7324. Chimeric mouse embryos were generated as a control experiment to understand the contribution of host vs. injected cells to the developing embryo. Embryos were generated by blastocyst injection of tdTomato-labelled mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2020-08-31 | E-MTAB-8812 | biostudies-arrayexpress

Single cell RNA-seq profiles of patient derived organoids

Project description:Three patient-derived organoids from liver metastasis of CRC samples were profiled by scRNA-seq.

2024-02-29 | E-MTAB-13123 | biostudies-arrayexpress

Cellular plasticity and diversity during heart valve epithelial-to-mesenchymal transitions revealed using single-cell RNA-seq

Project description:We have generated scRNA-seq data from embryonic day (E)10.5 and E12.5 atrioventricular canals (primitive heart valves) to assess cellular diversity during the distinct epithelial-to-mesenchymal transitions (EMTs) from endocardium and epicardium that guide the formation of valve mesenchyme. Alongside, wildtype atrioventricular canals, we generated scRNA-seq data from Sox9 conditional knockouts (Sox9fl/fl;Tie2-cre) to explore the role of SOX9 in EMT. Atrioventricular canals were microdissected from cardiac chambers and outflow tract, enriching for heart valve progenitor lineages.

2023-06-30 | E-MTAB-11795 | 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