Gene Atlas of Reversible Unilateral Ureteric Obstruction Model (rUUO)

Single Cell Analysis
Bulk Gene Analysis

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Single Cell RNA sequencing (sc-RNAseq) was performed on the reversible unilateral ureteric obstruction (rUUO) murine model. Unilateral Ureteric Obstruction (UUO) was performed on day 0, with culls performed at day 2 and day 7. In the rUUO group, ureteric re-implantation was performed at day 7 and cull was performed following 14 days reversal.

Single cell libraries were prepared using a high-throughput droplet-based library preparation workflow (10x). Sequencing was performed on a NextSeq 550 High Output Kit v2 2x150bp PE configuration and 8bp index reads (Illumina), resulting in a read depth of approximately 100,000 reads per transcriptome.

For further details, please see the manuscript below

TSNE plots

TSNE plots of 17136 cells (global)/2956 pooled myeloid cell ( myeloid) from pooled libraries coloured by shared nearest neighbour (SNN) allocated cluster, colours indicate classification by cell type or timepoint.

Feature plots

In the feature plots the expression of selected marker genes characteristic of each classification projected onto TSNE plot.

Violin plots

The violin plots show the Log10 expression of gene expression.

For further details, please see the manuscript below

Funding

This project has been generously funded by Kidney Research UK (KRUK).

Contact Us

Please contact Laura Denby or Bryan Conway for general questions regarding the project if not addressed in the manuscript.

laura.denby@ed.ac.uk

bryan.conway@ed.ac.uk

eoin.osullivan@ed.ac.uk

For bugs relating to the shiny app, please contact katie.connor@ed.ac.uk

Bryan R Conway, Eoin D O'Sullivan, Carolynn Cairns, James O'Sullivan, Daniel J Simpson, Angela Salzano, Katie Connor, Peng Ding, Duncan Humphries, Kevin Stewart, Oliver Teenan, Riinu Pius, Neil C Henderson, Cécile Bénézech, Prakash Ramachandran, David Ferenbach, Jeremy Hughes, Tamir Chandra, Laura Denby

Single cell transcriptomics and paired blood exchange reveal myeloid cell heterogeneity and kinetics in progression and regression of kidney disease. JASN, 2020

PMID: 32978267

DOI: 10.1681/ASN.2020060806

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Type in mouse gene name:

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To identify the pathways activated in the injury and repair phases, we applied RNA sequencing to bulk renal cortical tissue from sham, UUO (at time-points day 2 and 7 post UUO) and R-UUO kidneys (1, 2 and 4 weeks post-reversal).

For further details, please see the manuscript below

Plots

Profile of the selected gene expression (FPKM) in the rUUO model

Profile Clusters

To identify the pathways activated in the injury and repair phases, we applied RNA sequencing to bulk renal cortical tissue from sham, UUO (at time-points day 2 and 7 post UUO) and R-UUO kidneys (1, 2 and 4 weeks post-reversal). Analysis of unbiased clustering from the time course for each each cluster’s FPKM expression.

Table

The differential expression profile of selected genes in bulk RNA-seq data. Differential expression analysis was performed by DESeq2 for all of the possible comparisons. A logFC of 1.5 and p.adjusted value < 0.05 was considered significant.

For further details, please see the manuscript below

Funding

This project has been generously funded by Kidney Research UK (KRUK).

Contact Us

Please contact Laura Denby or Bryan Conway for general questions regarding the project. For questions regarding the single cell methodology contact Eoin O'Sullivan

laura.denby@ed.ac.uk

bryan.conway@ed.ac.uk

eoin.osullivan@ed.ac.uk

For bugs relating to the shiny app, please contact katie.connor@ed.ac.uk

Bryan R Conway, Eoin D O'Sullivan, Carolynn Cairns, James O'Sullivan, Daniel J Simpson, Angela Salzano, Katie Connor, Peng Ding, Duncan Humphries, Kevin Stewart, Oliver Teenan, Riinu Pius, Neil C Henderson, Cécile Bénézech, Prakash Ramachandran, David Ferenbach, Jeremy Hughes, Tamir Chandra, Laura Denby

Single cell transcriptomics and paired blood exchange reveal myeloid cell heterogeneity and kinetics in progression and regression of kidney disease. JASN, 2020

PMID: 32978267

DOI: 10.1681/ASN.2020060806

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Gene Atlas of Reversible Unilateral Ureteric Obstruction Model (rUUO)

Select Variables

For further details, please see the manuscript below

TSNE plots

TSNE plots of 17136 cells (global)/2956 pooled myeloid cell ( myeloid) from pooled libraries coloured by shared nearest neighbour (SNN) allocated cluster, colours indicate classification by cell type or timepoint.

Feature plots

In the feature plots the expression of selected marker genes characteristic of each classification projected onto TSNE plot.

Violin plots

The violin plots show the Log10 expression of gene expression.

For further details, please see the manuscript below

Funding

This project has been generously funded by Kidney Research UK (KRUK).

Contact Us

Please contact Laura Denby or Bryan Conway for general questions regarding the project if not addressed in the manuscript.

laura.denby@ed.ac.uk

bryan.conway@ed.ac.uk

eoin.osullivan@ed.ac.uk

For bugs relating to the shiny app, please contact katie.connor@ed.ac.uk

Single cell transcriptomics and paired blood exchange reveal myeloid cell heterogeneity and kinetics in progression and regression of kidney disease. JASN, 2020

PMID: 32978267

DOI: 10.1681/ASN.2020060806

Select Variables

To identify the pathways activated in the injury and repair phases, we applied RNA sequencing to bulk renal cortical tissue from sham, UUO (at time-points day 2 and 7 post UUO) and R-UUO kidneys (1, 2 and 4 weeks post-reversal).

For further details, please see the manuscript below

Plots

Profile of the selected gene expression (FPKM) in the rUUO model

Profile Clusters

Table

The differential expression profile of selected genes in bulk RNA-seq data. Differential expression analysis was performed by DESeq2 for all of the possible comparisons. A logFC of 1.5 and p.adjusted value < 0.05 was considered significant.

For further details, please see the manuscript below

Funding

This project has been generously funded by Kidney Research UK (KRUK).

Contact Us

Please contact Laura Denby or Bryan Conway for general questions regarding the project. For questions regarding the single cell methodology contact Eoin O'Sullivan

laura.denby@ed.ac.uk

bryan.conway@ed.ac.uk

eoin.osullivan@ed.ac.uk

For bugs relating to the shiny app, please contact katie.connor@ed.ac.uk

Single cell transcriptomics and paired blood exchange reveal myeloid cell heterogeneity and kinetics in progression and regression of kidney disease. JASN, 2020

PMID: 32978267

DOI: 10.1681/ASN.2020060806