Does single cell data typically have the following meta-data: the "coordinates" (e.g. on a tissue, adjacent tissues) saying where each cell in the sample was located relative to other cells? If not, is it possible to reconstruct this with other meta-data on the cells?
With the ultimate goal of working hands on with such location-tagged data, I am hoping for suggestions on the correct terms to search for, and even references to previous studies and/or easy to use public datasets.
For visual reference of the idea I have in mind, consider this picture:
I expect expression of any given gene in the skin cells in Condition 1 to be very different according to the location of the cell. For condition 2, I wouldn't expect the expression of a gene in the skin cells to be overly different, if at all. I want to see if I can formalize this idea using data mining techniques that were created for other purposes, but first I need the proper data.
edit: Here is an example of the format I eventually hope to work with.
Fake table 1: Each row represents measurements taken for a unique cell, while the last three columns have coordinates for its location. \begin{array}{r|lllllllll} \hline cell & phenotype1 & phenotype2 & \dots & gene1.expr & gene2.expr & \dots & x.loc.coord & y.loc.coord & z.loc.coord \\ \hline 1 & 0.69 & 1.34 & \dots & 1.91 & 0.21 & \dots & 1.12 & 0.05 & 1.09 \\ 2 & 0.34 & 0.92 & \dots & 1.74 & 2.03 & \dots & 0.57 & 0.46 & 0.24 \\ \vdots & \vdots & \vdots & \vdots & \vdots & \vdots & \vdots & \vdots & \vdots & \vdots \\ n & 1.97 & 1.3 & 0.96 & 0.19 & 0.66 & \dots & 0.25 & 0.02 & 1.27 \\ \hline \end{array}
Alternatively, if the (x,y,z) coordinates of Fake Table 1 are unavailable or not reconstructable, are there datasets which help us construct an adjacency list of cell pairs according to their location, such as Fake Table 2?
Fake Table 2: An adjacency table with pairs of cells which were next to each other when the measurement was taken. \begin{array}{r|cc} \hline pair & cell1 & cell2 \\ \hline 1 & 1 & 2 \\ 2 & 1 & 3 \\ 3 & 1 & 4 \\ 4 & 2 & 3 \\ 5 & 2 & 4 \\ \vdots & \vdots & \vdots \\ m-1 & n & n-2 \\ m & n & n-1 \\ \hline \end{array}
I come from a statistics background with a basic understanding of this type of data from talks I've attended, but not hands on experience. I mostly just want to explore this type of data to inform my future work. I am open to any type of scRNA-seq data with cell location "coordinates," if that's the correct thing to ask.