Developmentally Conserved CDX2 Cells from Human Term Placenta Drive Cardiovascular Regeneration

Description

scRNA seq raw data files of freshly isolated placental CDX2 cells and the expanded CDX2 cells

Steps to reproduce

Human CDX2mCherry cell samples, both freshly isolated (n=2) and expanded at passage 3 (n=3), were thawed for analysis (total n=5). Cell counts were assessed using the Cellaca Cell Counter (Nexcelom Bioscience, Lawrence, MA, USA) in conjunction with NucBlue for staining cell nuclei and propidium iodide (PI) for identifying dead cells. Samples were then processed with the Chromium X platform (10x Genomics, Pleasanton, CA, USA), following the manufacturer’s protocols, to target the capture of approximately 3,000 cells per sample for downstream analysis. Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Gene Expression Kit. Library quality was assessed using the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified via Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Additional quantification was performed using quantitative PCR (qPCR) (Applied Biosystems, Carlsbad, CA, USA) prior to sequencing on an Illumina platform, following 10x Genomics' recommended sequencing configurations. Raw sequencing data, in the form of .bcl files generated by Illumina, were converted into FASTQ files and demultiplexed using the 10x Genomics Cell Ranger mkfastq pipeline. QC was carried out by removing doublets from analysis, excluding cells that showed> 8,000 feature counts (potential multiplets) or mitochondrial genes at>50% or hemoglobin genes at greater than 5%. Differential gene expression analysis was conducted interactively using the 10x Genomics Loupe Browser for data visualization and interpretation. Cell annotation was performed using cell marker identification based on classical trophoblast gene markers and the upregulated gene expression profiles from our dataset. A total of 19,594 filtered CDX2 cells were analyzed in this study.

Institutions

• Icahn School of Medicine at Mount Sinai

  NY, New York

Categories

Funders

• National Institutes of Health

  Maryland, United States

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