how many genes are expressed at each stage? are there overlaps?

[mgavery]

There are 3 types of libraries we made

1. cleavage pool (3 replicate libraries) - 7658 cells
2. blastula (1 library) - 2836 cells
3. gastrula (4 replicate libraries) - 18511 cells

The cleavage pool and blastula samples are part of the same "experiment" so they are combined below in a file called "CPbla"

I downloaded a table that has the "number of cells expressed" for each gene for each of these 3 types of libraries. We can use this to see what proportion of all genes are expressed at each stage and to look for overlaps/differences in genes expressed in each cluster.

As a note - these libraries all have different sequencing "saturation" meaning it might not mean much if a gene is expressed lowly in only a few cells in one stage and not the other. We probably need some kind of cutoff for that (e.g. only counted if genes expressed in >50 or >100 cells) cleavage_geneBYcellsexpressed.txt gastrula_geneBYcellsexpressed.txt blastula_geneBYcellsexpressed.txt CPbla_geneBYcellsexpressed.txt .

[mgavery]

maybe a more fair way to make a cut off would be something like: must be expressed in at least 5% of the cells for a given developmental stage (this would acct for diffs in the number of cells sequenced for each type of library)

[sr320]

New file at early dev https://github.com/RobertsLab/project-sc-RNAseq/files/9262721/CPbla_geneBYcellsexpressed.txt

[mgavery]

There are 10,494 cells in the early dev samples