scRNA-Seq of in vitro "induced sinoatrial bodies" and ex vivo sinoatrial node region

For scRNA-Seq, iSABs were dissociated using the Primary Cardiomyocyte Isolation Kit (Thermo Fisher Scientific) before library preparation was performed using the 10xGenomics system with subsequent sequencing on the HighSeq4000 (Illumina). The mouse-SAN scRNA-Seq protocol is described in Goodyer et al. Preprocessing of raw sequencing data from iSABs relied on tools of the Cell Ranger Software (v.6.1.0) as was the procedure in Goodyer et al. Downstream analyses were conducted similar for both datasets using Seurat (v.3.2.2). Plotting the %mtRNA we found that all pacemaker subpopulations in the iSABs dataset had values above the standard 5%-threshold. Automatically filtering with this quality control parameter causes a strong bias and loss of these data. The SAN cluster of Goodyer revealed similar %mtRNA values exposing them to the same bias.

SEEK ID: https://fairdomhub.org/assays/1438

Modelling Analysis

Anne-Marie Galow

Projects: iRhythmics

Investigation: hidden item

Study: Quality control in scRNA‑Seq can discriminate pacemaker cells: the mtRNA bias

Assay position:

Biological problem addressed: Gene Expression

Organisms: No organisms

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Created: 21st Apr 2021 at 08:24

Last updated: 3rd Sep 2021 at 07:46

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