Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell sequencing of 43,168 cells during the differentiation from human induced pluripotent stem cells to cardiomyocytes

ABSTRACT: Differentiation into diverse cell lineages requires orchestration of gene regulatory networks guiding cell fate choices. Genetic factors acting through changes in transcriptional levels can contribute to cardiovascular disease risk by impacting early stages of development and have cell type-specific effects. We set out to characterize lineage trajectory progression of subpopulations and identify potential disease-related genes by examining their expression changes in single cells during early stages of cardiac lineage specification. Using 43,168 single-cell transcriptomes, we developed novel classification and trajectory analysis methods to dissect cellular composition and gene networks across five discrete time points underlying lineage derivation of mesoderm, definitive endoderm, vascular endothelium, cardiac precursors, and definitive cell types that comprise cardiomyocytes and a previously unrecognized cardiac outflow tract population.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Quan Nguyen

PROVIDER: E-MTAB-6268 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single Cell gene expression profile of MDA-MB-231 TGL cells

Project description:Baseline MDA-MB-231 TGL cells were processed by scRNA-Seq.

2024-07-22 | E-MTAB-13896 | biostudies-arrayexpress

scRNA-seq of CD45+ cells taken from the ear epidermis from K14E7 transgenic and wildtype C57/BL6 mice

Project description:Langerhans cells (LC) in skin help initiate the immune response to locally presented antigens. We performed high-resolution single-cell RNA-sequencing (scRNAseq) analysis for antigen presenting cells including LC in normal mouse skin, and in mouse skin expressing the human papillomavirus (HPV) 16 E7 oncogene. Ear skin was collected from normal and trangenic mice. Dissociated CD45+ cells were processed for scRNA-seq using the 10X Genomics Chromium 3' gene expression kit (v2).

2021-10-15 | E-MTAB-8199 | biostudies-arrayexpress

Transcriptomic profile of human induced pluripotent stem cells at single cell resolution.

Project description:We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlexTM and TeSRTM-E8TM media. Single-cell transcriptome sequencing was performed for 20,962 cells from two cell lines grown in the two media. Analysis of transcriptomic profile revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Single cell analysis of the four samples revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that 60-96% of the cells in the ground/naive subpopulations and 98-99% of the cells in the primed subpopulations are similar between all four samples. The single cell RNA sequencing analysis of iPSC lines grown in both media is the first report of the molecular pathways modulated in StemFlex medium and how they compare to those modulated in TeSR-E8 medium.

2019-05-08 | E-MTAB-6524 | biostudies-arrayexpress

Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia

Project description:In this study, we investigated somatic mutations of CD4+ and CD8+ T cells in patients with immune-mediated aplastic anemia (AA). To understand the role of mutations, we performed single-cell level analysis of 6 longitudinal samples of 2 AA patients carrying STAT3 or KRAS and other mutations in CD8+ T cells. The analysis was performed using V(D)J and 5' gene expression platform (10X Genomics). STAT3 mutated clone was clearly distinguishable from other CD8+ T cells and showed a cytotoxic phenotype, attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells can alter T cell phenotype warranting further investigation of their role in the pathogenesis of immune-mediated AA.

2021-03-24 | E-MTAB-9969 | biostudies-arrayexpress

MPS vaccination alters long-term gene expression of antigen-presenting cells in lymph nodes

Project description:Given the importance of sustained antigen presentation in maintenance of lymph node (LN) immune responses, we hypothesized that vaccine antigen availability and antigen-presenting cell (APC) populations may affect LN expansion. Compared to LNs of mice given the full MPS vaccine, LNs of mice given an MPS vaccine without antigen became prominently less enlarged and contracted sooner.To identify potential mediators of this differential, antigen-dependent response, we next focused the analysis of our scRNA-seq dataset on LN APC populations.

2024-04-05 | E-MTAB-13698 | biostudies-arrayexpress

Single cell TCR-seq of T cells isolated from MC38 mouse tumors

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

2019-05-11 | E-MTAB-7918 | biostudies-arrayexpress

scRNAseq of gastric tumors and adjacent mucosa from Twist2Cre;Lkb1fl/+;Rosa26RTdtomato/+ mice

Project description:5000 target cells per sample where sequenced from 2 gastric tumor samples and 1 sample of adjacent gastric mucosa Twist2Cre;Lkb1fl/+;RosaRTdtomato+/- mice. Drop-seq 10X Genomics (10X v3 library kit) was used for single cell barcoding and library preparation. Samples were sequenced with Novaseq6000.

2024-07-24 | E-MTAB-13624 | biostudies-arrayexpress

Single-cell RNA sequencing of mouse germ cells

Project description:Spermatogenesis is a recurring differentiation process that results in the production of male gametes within the testes. During this process, spermatogonial stem cells differentiate to form spermatocytes, which undergo two rounds of meiotic division to form haploid spermatids. Throughout spermiogenesis, round spermatids elongate to form mature sperm. To profile maturing germ cells during the first wave of spermatogenesis, we generated droplet-based single cell RNAseq from juvenile animals at post-natal day P5-P35 as well as adult animals. Cells were isolated from whole testes. Furthermore, to assay the robustness of the meiotic cell division process, we profiled germ cells of the trans-chromosomal mouse model (Tc1) that carries a copy of the human chromosome 21.

2019-01-25 | E-MTAB-6946 | biostudies-arrayexpress

Rhesus macaque cecal CD45+ leukocytes

Project description:10X transcriptomics + B cell V(D)J sequencing of CD45+ leukocytes

2024-04-30 | E-MTAB-13902 | biostudies-arrayexpress

Charting the age-altered thymic epithelial cell differentiation by lineage tracing from a beta 5-t expressing TEC progenitor

Project description:TEC progenitors that express beta 5-t contribute to both the cortical and medullary TEC compartments. Our initial experiments across ageing thymi identified a population of potential progenitor TECs which expanded with age, and appears to be a progenitor population for mTEC. These lineage tracing experiments are designed to chart the altered differentiation and senescence of mTEC progenitors with age.

2020-09-14 | E-MTAB-8737 | 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