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In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells (10X Genomics scRNA-seq)

ABSTRACT: Single-cell RNA-seq (10X Genomics Chromium) to profile of cardiac progenitor cells, comparing the transcriptomes of freshly isolated and cultured cardiac progenitor cells

ORGANISM(S): Mus musculus

PROVIDER: GSE114278 | GEO | 2018/09/12

REPOSITORIES: GEO

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In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells (Smart-Seq2 scRNA-seq)

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2018-09-12 | GSE114279 | GEO

In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells (10X Genomics scRNA-seq)

Project description:In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells (10X Genomics scRNA-seq)

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In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-09-12 | GSE114280 | GEO

In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells.

Project description:Regenerative therapeutic approaches for myocardial diseases often involve delivery of stem cells expanded ex vivo. Prior studies indicate that cell culture conditions affect functional and phenotypic characteristics, but relationship(s) of cultured cells derived from freshly isolated populations and the heterogeneity of the cultured population remain poorly defined. Functional and phenotypic characteristics of ex vivo expanded cells will determine outcomes of interventional treatment for disease, necessitating characterization of the impact that ex vivo expansion has upon isolated stem cell populations. Single-cell RNA-Seq profiling (scRNA-Seq) was performed to determine consequences of culture expansion upon adult cardiac progenitor cells (CPCs) as well as relationships with other cell populations. Bioinformatic analyses demonstrate that identity marker genes expressed in freshly isolated cells become undetectable in cultured CPCs while low level expression emerges for thousands of other genes. Transcriptional profile of CPCs exhibited greater degree of similarity throughout the cultured population relative to freshly isolated cells. Findings were validated by comparative analyses using scRNA-Seq datasets of various cell types generated by multiple scRNA-Seq technology. Increased transcriptome diversity and decreased population heterogeneity in the cultured cell population may help account for reported outcomes associated with experimental and clinical use of CPCs for treatment of myocardial injury.

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In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells

Project description:In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells

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Tetraploidy in Rodent Cardiac Stem Cells Confers Enhanced Biological Properties

Project description:Single-cell RNA-seq (10X Genomics Chromium) to profile of cardiac progenitor cells, comparing the transcriptomes of diploid and tetraploid cardiac progenitor cells

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Single cell RNA-sequencing of Spike-ins and Control RNA using 10x Genomics Chromium system

Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. In this dataset, we assess the RNA detection rates using high-throughput 10x Genomics Chromium system. We mix equal volume of Control Brain RNA (3ul; FirstChoice Total Brain RNA; #AM7962) and ERCC spikes (3ul 1:4 dilution; #4456653) to make a '2x Control RNA+ERCC' master mix. The '2x Control RNA+ERCC' master mix is diluted with equal volume nuclease-free water to make '1x Control RNA+ERCC' master mix. 3ul of '1x Control RNA+ERCC' master mix is added to Chromium single cell suspension and processed as per Chromium guidelines. The sample-data relationship format (SDRF) file for this submission contains only a high-level representation of the sample, library and run information per flow cell, and not per cell. For meta-data at the level of individual cells, please refer to the supplementary file called single_cells_list.txt, which is included as part of this ArrayExpress submission.

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