Chapter 27 Chimeric embryo 10X dataset

27.1 Introduction

This performs an analysis of the (???) dataset on mouse gastrulation. Here, we examine chimeric embryos at the E7.5 stage of development where td-Tomato-positive embryonic stem cells (ESCs) were injected into a wild-type blastocyst.

27.2 Analysis code

27.2.1 Data loading

## class: SingleCellExperiment 
## dim: 29453 20935 
## metadata(0):
## assays(1): counts
## rownames(29453): ENSMUSG00000051951 ENSMUSG00000089699 ...
##   ENSMUSG00000095742 tomato-td
## rowData names(2): ENSEMBL SYMBOL
## colnames(20935): cell_9769 cell_9770 ... cell_30702 cell_30703
## colData names(10): cell barcode ... closest.cell doub.density
## reducedDimNames(2): pca.corrected.E7.5 pca.corrected.E8.5
## spikeNames(0):
## altExpNames(0):

27.2.3 Quality control

Quality control on the cells has already been performed by the authors, so we will not repeat it here. We additionally remove cells that are labelled as stripped nuclei or doublets.

27.2.4 Normalization

We use the pre-computed size factors in sce.chimera.

27.2.5 Variance modelling

Retaining all genes with any positive biological component, to preserve as much signal as possible across many samples.

27.2.8 Dimensionality reduction

We use an external algorithm to compute nearest neighbors for greater speed.

27.3 Results

27.3.2 Batch correction

##             5        6        7        8       9      10
## [1,] 0.00e+00 0.020440 0.00e+00 0.016946 0.00000 0.00000
## [2,] 0.00e+00 0.000739 0.00e+00 0.000442 0.00000 0.01547
## [3,] 3.09e-02 0.000000 2.01e-02 0.000000 0.00000 0.00000
## [4,] 9.03e-05 0.000000 8.27e-05 0.000000 0.01805 0.00000
## [5,] 4.32e-03 0.007251 4.12e-03 0.007828 0.00383 0.00778

27.3.3 Clustering

## 
##    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
##  952  113  863  680  507 1875  929  420 1260  104  727 1034   58  872  431 
##   16   17   18   19   20   21   22   23   24   25 
##  982  699  211 1256  160  156 1993  564  435 2145