This folder contains:


FINAL DATASETS

Turtle and lizard single cell datasets as Seurat objects generated with the Seurat package in R. Each of these includes a raw gene/cell matrix, metadata, the normalised and batch-corrected data, PCA and tSNE projections, and cluster information. Refer to the Seurat tutorials at http://satijalab.org/seurat/ for more information on the Seurat package. Please note that these files were generated with the Seurat version 1.4 (October 2016). 

- turtle.all.cells.Robj : dataset with all the 18828 single cells (neuronal and non-neuronal) sequenced from the turtle pallium

- turtle.neurons.Robj : dataset with the 5901 neurons sampled from the turtle pallium

- lizard.all.cells.obj : dataset with all the 4187 single cells (neuronal and non-neuronal) sequenced from the lizard pallium

- lizard.neurons.Robj : dataset with the 1160 neurons sampled from the lizard pallium



GENOME ANNOTATION FILES 

RefFlat files with the extended annotations (3’ extension based on MACE results). 

- annChrPicBel_19Apr2016.refFlat	(turtle)
- lizard_annotation.refFlat		(lizard)



EGGNOG FUNCTIONAL ANNOTATIONS 

Files: 

- chrysemys_eggnog_pruned.txt	(turtle)
- pogona_eggnog_pruned.txt	(lizard)
- mus_eggnog_pruned.txt		(mouse)
- homo_eggnog_pruned.txt	(human)

These files were generated from the functional annotations of turtle, lizard, mouse and human genes produced by EggNOG Mapper (see http://eggnogdb.embl.de/). The original EggNOG Mapper annotations were pruned to remove ambiguous terms (e.g. one-to-many assignments). Matching functional annotations were used to identify one-to-one orthologs across species.



TRANSCRIPTION FACTORS LIST

- 170712_TFs_list_ensembl.txt
List of human transcription factors, annotated in ENSEMBL under the GO terms GO:0003700 (transcription factor activity), GO:0003702 (RNA polymerase II transcription factor activity), GO:0003709 (RNA polymerase III transcription factor activity), GO:0016563 (transcriptional activator activity) and GO:0016564 (transcriptional repressor activity).