Browse
Submit Data
Databases
API
Help
Login

Dataset Information

84 Views

1410 Connections

0 Citations

0 Reanalyses

22 Downloads

Omics score: 26

Single cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells

ABSTRACT: We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 2 chemistry) system on ~6,000 mouse endothelial cells derived from aorta.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Samuel W Lukowski Kiarash Khosrotehrani

PROVIDER: E-MTAB-7149 | ArrayExpress | 2019-05-27

SECONDARY ACCESSION(S): ERP110412

REPOSITORIES: ArrayExpress, ENA

ACCESS DATA

Json Xml

Similar Datasets

Massively parallel single-cell RNA-sequencing of K14E7 transgenic and wildtype C57BL/6 mice

Project description:We report scRNA-seq data captured from 9,410 cells obtained from the skin of K14E7 transgenic and wildtype C57/BL6 mice. The K14E7 mouse model harbors the HPV16 E7 oncogene driven from a Keratin 14 promoter for keratinocyte-specific expression. We used scRNA-seq to detect and measure E7 transcription with unprecedented accuracy and resolution. With these data, we uncovered transcriptional differences between the individual cells; demonstrated that increased HPV16 E7 copy number is associated with increased expression of E7-induced genes; and showed that E7 expression is predominantly associated with basal keratinocytes.

2018-07-09 | E-MTAB-6429 | 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 | ArrayExpress

An integrated approach to profile lung tumor endothelial cell heterogeneity across species and models and to identify angiogenic candidates

Project description:Heterogeneity of lung tumor endothelial cell (TEC) phenotypes across patients, species (human/mouse) and models (in vivo/vitro) remains poorly inventoried at the single-cell-level. We single-cell RNA-sequenced 56,771 ECs from human/mouse (peri)-tumoral lung and cultured human lung TECs, detected 17 known and discovered 16 novel phenotypes, including TECs presumably regulating immune surveillance. We resolved the canonical tip TECs into a known migratory tip and a novel basement-membrane remodeling breach phenotype. Tip-TEC signatures correlated with patient-survival, and tip/breach TECs were most sensitive to VEGF-blockade. By similarity analysis, only tip-TECs were congruent across species/models and shared conserved markers. Integrated analysis of the scRNA-seq data with orthogonal multi-omics and meta-analysis data across different human tumors, validated by functional analysis, identified collagen-modification as angiogenic candidate pathway.

2019-12-30 | E-MTAB-6308 | ArrayExpress

Single Cell RNAseq from IL6R deficient patient and healthy parent

Project description:To determine the phenotypic differences in blood cells that are regulated by the IL-6R

2019-06-20 | E-MTAB-8034 | ArrayExpress

Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing

Project description:To compare the performance of Illumina and BGI sequencing technologies for high-throughput single cell sequencing, four Chromium single cell libraries of the following human cell types: Induced Pluripotent Stem Cells (hIPSC), cultured Trabecular MeshWork Cells (TMWC) and Peripheral Blood Mononuclear Cells (PBMCs), were sequenced on Illumina sequencers (NextSeq 500, NovaSeq 6000) and a BGI sequencer (MGISEQ-2000). The technologies were benchmarked based on sequencing quality, characterisation of cell populations within samples and for specific single cell analyses such as variant calling and detection of guide RNAs from pooled CRISPR screens.

2020-05-19 | E-MTAB-9024 | ArrayExpress

Single cell RNA-seq of WTC-CRISPRi human induced pluripotent stem cells

Project description:We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 1 chemistry) system on ~19,000 undifferentiated human IPSCs to explore the cellular heterogeneity of a seemingly homogeneous cell population.

2018-08-17 | E-MTAB-6687 | ArrayExpress

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

Project description: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.

2018-10-05 | E-MTAB-6268 | ArrayExpress

Human pluripotent stem cell-derived ROR1e lens epithelial cell single cell RNA-sequencing

Project description:Detailed transcriptomic analyses of differentiated cell populations derived from human pluripotent stem cells is routinely used to assess the identity and utility of the differentiated cells. In particular, single cell RNA-sequencing (scRNA-seq) can provide insights into both the cellular and transcriptional heterogeneity of differentiated cell populations. Here we provide scRNA-seq data obtained from ROR1-expressing lens epithelial cells (ROR1e LECs) obtained via directed differentiation of CA1 human embryonic stem cells. Through the use of principal component analysis, heat maps and gene ontology assessments, we demonstrate that ROR1e LECs represent a highly purified and large-scale population of lens cells. These data provide a resource for future characterisation of both normal and cataractous human lens biology.

2020-11-27 | E-MTAB-9178 | 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 | ArrayExpress

Single cell RNA-seq of mouse E10.5 progenitor and E14.5 barrelette neurons

Project description:Single cell RNA-seq with 10xGenomics in mouse progenitors and barrelette neurons at embryonic stages E10.5 and E14.5.

2021-01-09 | E-MTAB-8312 | ArrayExpress

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
GPMDB
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub Seek

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data