---------------------------------------------------------
GENERAL INFORMATION
---------------------------------------------------------

1. Title of Dataset 

README file : SNAREs in giant viruses

2. Author Information

Principal Investigator Contact Information
Name: FASSHAUER DIRK
Institution: Department of Computational Biology
Address: Génopode - CH - 1015 Lausanne - Switzerland
Email: dirk.fasshauer@unil.ch

Associate Contact Information
Name: KHALIFEH DANY
Institution: Department of Fundamental Neurosciences 
Address: Rue du Bugnon 9 - CH - 1005 Lausanne - Switzerland
Email: dany.khalifeh@unil.ch

3. Method section 

a) Tris-Tricine-SDS gel 15% (for 4 gels):

Resolving (15%):
H2O = 6 780 μl
AMBA (40%) = 9 000 μl
Gel Buffer (3X) Schägger = 8 000 μl
TEMED = 20 μl
10% APS = 200 μl
Total = 24 000 μl

Stacking (3,75%) :
H2O = 4 495 μl
AMBA (40%) = 750 μl
Gel Buffer (3X) Schägger = 2 667 μl
TEMED = 8 μl
10% APS = 80 μl
Total = 8 000 μl

AMBA (40%) from serva, 37.5:1 REF#10681
Gel Buffer (3X) Schäfer : 3M Tris pH 8.45 + 0.3% SDS

Running Buffer 10X :
Anode Buffer 10X (outside): 1M tris pH8.9
Cathode Buffer 10X (inside): 1M tris + 1% SDS + 1M tricine (pH should be ~ 8.25 but do not adjust the pH)

Firstly, the tris-tricine-SDS gel was run at around 40V constant until the end of the stacking. Then the native gels was run at around 130V constant in running buffer.

b) Native gel 10% (for 4 gels):

Resolving (10%):
H2O = 9 780 μl
AMBA (30%) = 8 000 μl
Native lower tris (4X) = 6 000 μl
TEMED = 20 μl
10% APS = 200 μl
Total = 24 000 μl

Stacking (3,75%) :
H2O = 4 912 μl
AMBA (40%) = 1 000 μl
Native Upper tris (4X) = 2 000 μl
TEMED = 8 μl
10% APS = 80 μl
Total = 8 000 μl

AMBA (30%) from Roth, 37.5:1 REF#3029
Native Lower tris (4X) : 1,5M Tris pH 8.8
Native Upper tris (4X) : 0,5M Tris pH 6.8

Running Buffer 10X :
1,92 M glycine + 0,25 M tris (NEVER adjust pH of running buffer)

Firstly, the native gels will run at around 40V constant until the end of the stacking then the native gels will run at around 130V constant in running buffer.

c) Phylogenetic analysis

The sequences for the DNA polymerase were initially collected from the publication Guglielmini J, Woo AC, Krupovic M, Forterre P, Gaia M. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19585-19592. doi: 10.1073/pnas.1912006116. Epub 2019 Sep 10. PMID: 31506349; https://doi.org/10.1073/pnas.1912006116
The alignments were made using Muscle as described.
The trees are computed using IQ-TREE following the method described in the publication (see *Method*) 
---------------------------------------------------------
DATA & FILE OVERVIEW : date,N°, type
---------------------------------------------------------

1. Gel (.png)
- scan of the gel after Coomassie Blue-staining

2018_09_12_2 native
2018_09_13_2 native
2018_09_14_2 native
2017_10_26_2 SDS

1. List of sequences used

ListDNAPolymeraseFromGuil2019.csv

2. Alignments
  .fasta format

DNAPol_Aligned_trimmed_30pc.fasta

3. Tree

 DNAPol_.tree