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C-intestinalis-datasets-normalized.xlsx
readme.txt

readme.txt

Primary data available at ANISEED database: http://www.aniseed.cnrs.fr/. For explanation of methods, please see: Tassy et.al, Genome Research, 20, 1459-1468 (2010).'

Secondary data repository located at: https://drive.google.com/open?id=0B7RsqJbITXXAfkdDUFZ2Q0VFS1BOUXRVNE5RUk9HNmlxZURzd0V3ZDNkdUZFbTZaU042Qlk

Available Constructs: 

1) volume (summation) -- total get slightly smaller as cell stage increases.

2) cell volume/embryo volume -- percentage of cell size vs. entire embryo.

3) functional volume -- summation of all cell volumes, not acccounting for interstitial space (decreases with increase in number of stage?).

Notes on construct #3:
* each set of observations (cell stages) include all cells in observed embryo plus duplicates neccessary to align dataset to 112-cell stage. Cell Volume: Embryo Volume variable is close to 100 for the 112-cell stage (save for 4 missing cells). All others 
add up to >100% due to duplicated cells.

* each "set" are two adjacent time-points aligned for the larger cell stage. The "mother" cell (smaller cell stage) produces two daughter cells (or in one case produces two daughter cells and maintains its own identity through two division events). The error and asymmetry can be calculated on these pairs.

Ascidian Differentiation Tree Analysis notes:

* many sets of embryo observation (e.g. 24-cell, 32-cell) had multiple replicates. All of these exist in the locked-down version of the file (full-original). For (normalized), I simply chose one replicate and used this one, as averaging will wash out the cell size/volume differences.

* create three variables: difference in size between cell pairs (A7.4, A7.4*); difference in size between pairs (A7.4/A7.4*, A7.3/A7.3*); difference in cell size between developmental stage (A7.4 4-cell version, A7.4 8-cell version).

* calculated size of whole embryo according to summation of individual cells measured at each stage. 

* Nomenclature for cells in development:

2-cell stage = AB2, AB2* (establishment of all lineages)

4-cell stage = establishment of animal and vegetal poles of embryo (A3 and B3, respectively).

8-cell stage = establishment of A-line and B-line blastomeres (animal and vegetal poles, respectively).

8-cell stage = establishment of a-line and b-line blastomeres (animal and vegetal poles, respectively).

* in general, A-line (anterior, animal), B-line (posterior, vegetal), a-line (anterior, animal), b-line (posterior, animal).

* A-line descendents come from A4.1 pair (8-cell stage).

* B-line descendents come from B4.1 pair (8-cell stage).
* a-line descendents come from a4.2 pair (8-cell stage). 

* b-line descendents come from b4.2 pair (8-cell stage).

MUSCLE lineage: Development, 108(4), 559-568 (1990) -- B-line = autonomous development of muscle-specific enzymes (primary), A-line, b-line = cannot produce muscle-specific enzymes in isolation (secondary).

FLEXIBILITY in Mosaic development: observed betwween species C. intestinalis and H. roretzi (Biol. Cell, 100(5), 265-277 -- 2008).

Contact Area between pairwise comparisons of cells:


* 7809/63119 cells have countable contact area (adjacent in embryo at same developmental stage).