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Gudiseva HV, Vrathasha V, He J, et al. Single Cell Sequencing of Induced Pluripotent Stem Cell Derived Retinal Ganglion Cells (iPSC-RGC) Reveals Distinct Molecular Signatures and RGC Subtypes. Genes (Basel). 2021;12(12)doi: 10.3390/genes12122015.
Gudiseva, H. V., Vrathasha, V., He, J., Bungatavula, D., O'Brien, J. M., & Chavali, V. R. M. (2021). Single Cell Sequencing of Induced Pluripotent Stem Cell Derived Retinal Ganglion Cells (iPSC-RGC) Reveals Distinct Molecular Signatures and RGC Subtypes. Genes, 12(12), . https://doi.org/10.3390/genes12122015
Gudiseva, Harini V, et al. "Single Cell Sequencing of Induced Pluripotent Stem Cell Derived Retinal Ganglion Cells (iPSC-RGC) Reveals Distinct Molecular Signatures and RGC Subtypes." Genes vol. 12,12 (2021). doi: https://doi.org/10.3390/genes12122015
Gudiseva HV, Vrathasha V, He J, Bungatavula D, O'Brien JM, Chavali VRM. Single Cell Sequencing of Induced Pluripotent Stem Cell Derived Retinal Ganglion Cells (iPSC-RGC) Reveals Distinct Molecular Signatures and RGC Subtypes. Genes (Basel). 2021 Dec 18;12(12). doi: 10.3390/genes12122015. PMID: 34946963; PMCID: PMC8702079.
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Genes (Basel). 2021 Dec 18;12(12). doi: 10.3390/genes12122015.

Single Cell Sequencing of Induced Pluripotent Stem Cell Derived Retinal Ganglion Cells (iPSC-RGC) Reveals Distinct Molecular Signatures and RGC Subtypes.

Genes

Harini V Gudiseva, Vrathasha Vrathasha, Jie He, Devesh Bungatavula, Joan M O'Brien, Venkata R M Chavali

Affiliations

  1. Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.

PMID: 34946963 PMCID: PMC8702079 DOI: 10.3390/genes12122015

Abstract

We intend to identify marker genes with differential gene expression (DEG) and RGC subtypes in cultures of human-induced pluripotent stem cell (iPSC)-derived retinal ganglion cells. Single-cell sequencing was performed on mature and functional iPSC-RGCs at day 40 using Chromium Single Cell 3' V3 protocols (10X Genomics). Sequencing libraries were run on Illumina Novaseq to generate 150 PE reads. Demultiplexed FASTQ files were mapped to the hg38 reference genome using the STAR package, and cluster analyses were performed using a cell ranger and BBrowser2 software. QC analysis was performed by removing the reads corresponding to ribosomal and mitochondrial genes, as well as cells that had less than 1X mean absolute deviation (MAD), resulting in 4705 cells that were used for further analyses. Cells were separated into clusters based on the gene expression normalization via PCA and TSNE analyses using the Seurat tool and/or Louvain clustering when using BBrowser2 software. DEG analysis identified subsets of RGCs with markers like

Keywords: FACS analysis; RGC subtypes; clustering; glaucoma; iPSC-RGCs; iPSCs; marker genes; retinal ganglion cells; single cell sequencing; transcriptome

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