Welcome!

Welcome to the MORL single-cell (sc) RNA sequencing (scRNA-seq) Database for the cochlear lateral wall (stria vascularis cells).
This database contains scRNA-seq datasets generated in the Molecular Otolaryngology and Renal Research Laboratories (MORL) at the University of Iowa.
The currently available dataset for clustering contains 172 single-cell samples from WT (129S6) mice cochlear stria vascularis:
Intermediate Cells (IMC) (n=107), Spindle Cells (SC) (n=51), Marginal Cells (MC) (n=14).
In addition, 69 cells were extracted from the Pendrin Knockout Mice (PDSKO) and 40 more cells from the Heterozygous Knockout Mice (PDSHET).
Differentially expressed genes were identified in a cell-type specific manner.
The samples available here are from the P22-44 timepoint.

This app utilizes Seurat (https://satijalab.org/seurat) and SCDE (https://hms-dbmi.github.io/scde) single-cell RNA-Seq analysis packages for R.

Stria Vascularis of Cochlea Clustering

Choose your gene of interest and press Submit

The four genes below are set to default.
Press the ''Submit'' button to check expression of selected genes of interest.
Then press 'Backspace' on your keyboard to change the gene of interest.
And choose your gene of interest from the list.
You can select as many genes as you want from one.
Press the ''Submit'' button again to check expression of changed gene of interest.


Violin Plots of cluster-defining genes

Choose your gene of interest and press Submit

The three genes below are set to default.
Press the ''Submit'' button to check expression of selected genes of interest.
Then press 'Backspace' on your keyboard to change the gene of interest.
And choose your gene of interest from the list.
You can select as many genes as you want from one.
Press the ''Submit'' button again to check expression of changed gene of interest.




InterMediate Cells (IMC) of Stria Vascularis Cluster-Defining Genes



Cluster-Defining Genes were obtained using Seurat R package.


Spindle Cells (SC) of Stria Vascularis Cluster-Defining Genes



Cluster-Defining Genes were obtained using Seurat R package.


Marginal Cells (MC) Cluster-Defining Genes



Cluster-Defining Genes were obtained using Seurat R package.


Heatmap of Differential Expression Analysis between Genotype of IMC (InterMediate Cells)

Choose your gene of interest and press Submit

The five genes below are set to default.
Press the ''Submit'' button to check expression of selected genes of interest.
Then press 'Backspace' on your keyboard to change the gene of interest.
And choose your gene of interest from the list.
You can select as many genes as you want from one.
Press the ''Submit'' button again to check expression of changed gene of interest.



Heatmap of Differential Expression Analysis between Genotype of Spindle Cells (SC)

Choose your gene of interest and press Submit

The five genes below are set to default.
Press the ''Submit'' button to check expression of selected genes of interest.
Then press 'Backspace' on your keyboard to change the gene of interest.
And choose your gene of interest from the list.
You can select as many genes as you want from one.
Press the ''Submit'' button again to check expression of changed gene of interest.



Differential Expression Analysis between Genotype of of MC (Marginal Cells)

Choose your gene of interest and press Submit

The three genes below are set to default.
Press the ''Submit'' button to check expression of selected genes of interest.
Then press 'Backspace' on your keyboard to change the gene of interest.
And choose your gene of interest from the list.
You can select as many genes as you want from one.
Press the ''Submit'' button again to check expression of changed gene of interest.



IMC (InterMediate Cells) Differentially Expressed Genes of PDSKO vs WT



Differentially Expressed Genes of PDSKO vs WT were obtained using SCDE (Single-Cell Differential Expression) R package.


IMC (InterMediate Cells) Differentially Expressed Genes of PDSHET vs WT



Differentially Expressed Genes of PDS_HET vs WT were obtained using SCDE (Single-Cell Differential Expression) R package.


IMC (InterMediate Cells) Differentially Expressed Genes of PDSHET vs PDSKO



Differentially Expressed Genes of PDS_HET vs PDSKO were obtained using SCDE (Single-Cell Differential Expression) R package.


SC (Spindle Cells) Differentially Expressed Genes of PDSKO vs WT



Differentially Expressed Genes of PDSKO vs WT were obtained using SCDE (Single-Cell Differential Expression) R package.


SC (Spindle Cells) Differentially Expressed Genes of PDSHET vs WT



Differentially Expressed Genes of PDS_HET vs WT were obtained using SCDE (Single-Cell Differential Expression) R package.


SC (Spindle Cells) Differentially Expressed Genes of PDSHET vs PDSKO



Differentially Expressed Genes of PDS_HET vs PDSKO were obtained using SCDE (Single-Cell Differential Expression) R package.

Releases and Contributors

Version 3.0 (09-02-2021)
Jin-Young Koh: Final layout of database
William (Daniel) Walls: VM system upgrade and update

Version 2.0 (11-10-2020)
Jin-Young Koh: Data analysis (Seurat 3.0.2) and database update
Cody West: Additional data collection from HET mice

Version 1.0 (06-28-2018)
Jin-Young Koh: Data collection of cochlear stria vascularis cells and analysis (Seurat 2.3.4)
Paul Ranum: Initial layout and idea