/
index.Rmd
118 lines (92 loc) · 4.67 KB
/
index.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
---
# Single cell analysis reveals congruence between kidney organoids and human fetal kidney
**Website and code:** [![DOI](https://zenodo.org/badge/148580527.svg)][doi]
This site contains the results of the analysis presented in the Combes kidney
organoid scRNA-seq paper. Follow the links below to see the different parts of
the analysis. If you want to reproduce the analysis please have a look at the
[Getting started](getting_started.html) page.
Abstract
--------
### Background:
Human kidney organoids hold promise for studying development, disease modelling
and drug screening. However, the utility of stem cell-derived kidney tissues
will depend on how faithfully these replicate normal fetal development at the
level of cellular identity and complexity.
### Results:
Here we present an integrated analysis of single cell datasets from human kidney
organoids and human fetal kidney to assess similarities and differences between
the component cell types. When overlaid, individual cell clusters contained
cells from both organoid and fetal kidney with transcriptional congruence for
key stromal, endothelial and nephron cell-type specific markers. Organoid
enriched neural, glial and muscle progenitor populations are also evident. Major
transcriptional differences between organoid and human tissue were likely
related to technical artefacts. Cell type-specific comparisons revealed
differences in stromal, endothelial, and nephron progenitor cell types including
expression of WNT2B in the human fetal kidney stroma but not in the organoids.
### Conclusions:
This study supports the fidelity of kidney organoids as models of the developing
kidney and affirms their potential in disease modelling and drug screening.
Authors
-------
Alexander N. Combes^#1,2+^, Luke Zappia^#2,3^, Pei Xuan Er^2^, Jessica M.
Vanslambrouck^2^, Alicia Oshlack^2,3^, Melissa H. Little^1,2,3,4,+^
^1^ Department of Anatomy & Neuroscience, University of Melbourne, VIC,
Australia ^2^ Murdoch Children's Research Institute, Flemington Rd, Parkville,
VIC, Australia ^3^ School of Biosciences, The University of Melbourne, VIC,
Australia ^4^ Department of Paediatrics, The University of Melbourne, VIC,
Australia
^#^ Equal contribution
^+^ Corresponding authors
Analysis
--------
* Quality control
* [Organoid Batch 1](01_Organoid123_QC.html) - Quality control of the first
batch of organoids containing three samples
* [Organoid 4](02_Organoid4_QC.html) - Quality control of the second batch
of organoids containing a single sample
* [Fetal kidney](05_Lindstrom_QC.html) - Quality control of the Lindstrom
fetal kidney dataset
* Organoids analysis
* [Integration](03_Organoids_Integration.html) - Integration of the four
organoid samples
* [Clustering](04_Organoids_Clustering.html) - Clustering of the organoid
samples
* [Nephron re-clustering](04B_Organoids_Nephron.html) - Re-clustering of the
organoid nephron lineage
* [Nephron trajectory](04C_Organoids_Trajectory.html) - Trajectory analysis
of the organoids nephron lineage
* [Figures](04D_Organoids_Figures.html) - Figures for the organoids analysis
presented in the paper
* Combined analysis
* [Integration](06_Combined_Integration.html) - Integration of the organoids
datasets and the Lindstrom fetal kidney dataset
* [Clustering](07_Combined_Clustering.html) - Clustering of the combined
dataset
* [Nephron re-clustering](07B_Combined_Nephron.html) - Re-clustering of the
nephron lineage in the combined dataset
* [Figures](07D_Combined_Figures.html) - Figures for the combined analysis
presented in the paper
* [Clustering crossover](08_Crossover.html) - Overlap in samples between
clusters from different parts of the analysis
* [Methods](99_Methods.html) - Methods describing the analysis
Licenses
--------
The code in this analysis is covered by the [MIT license][mit] and the written
content on this website is covered by a [Creative Commons CC-BY][cc] license.
The associated publication and the datasets used are covered by their respective
licenses and usage agreements. Please refer to those sources for details.
Citations
---------
This website and the analysis code can be cited as:
> Zappia, Luke, Combes, Alexander N., Er, Pei Xuan, Vanslambrouck, Jessica M.,
> Oshlack, Alicia, & Little, Melissa H. Combes organoid paper analysis code.
> Zenodo. http://doi.org/10.5281/zenodo.1960044
[doi]: https://zenodo.org/badge/latestdoi/148580527 "DOI"
[mit]: https://choosealicense.com/licenses/mit/ "MIT License"
[cc]: https://creativecommons.org/licenses/by/4.0/ "CC-BY License"