Sample #231 Bladder tumor

Overview of tissue

 

Overview


This sample was a tiny tissue piece that had dried in the -70°C freezer. Attempts were made to rehydrate the tissue prior to sectioning in the cryotome. The reason for this deviation from the standard protocol was that a matching lymph node (in good condition) was available. Consequently thicker slices had to be taken. 9 microtome slices, of 20 μm thickness were obtained, where  4 slices were subjected to laser capture microdissection (LCMD). The same grid of 96 (~25000 μm2) circles was used as a template for the laser capture microdissection on each slide. Pictures of slices and LCMD cuts can be found at the following link.

 

Descriptive statistics of mutant fraction found in each LCMD sample.

Comparison MF

 P2F6 (M1)  
P5F6 (M2)
N286228
Min (%)1.54.4
Max (%)93.893.7
Mean (%)25.535.1
First Quantile (%)8.249.7
Median (%)11.518.7
Third Quantile (%)25.059.3

Links to 3 different approaches to visualizing the mutant fraction in the 3D volume.

 

Isosurface of a random spread of homoplasmic cells (wild-type and/or mutant) in each LCMD volumes.

P2F6 (M1)Non-mutatedMutated
P5F6 (M2)Non-mutatedMutated

 

Isosurfaces of mutant fractions from 0% to 100% in 5% points increments.

ISO MF90

 

3D bubble plot of wild-type and mutant fractions.

Marker 1 (P2F6)

Bubble plot M1

Marker 2 (P5F6)

Bubble marker 2