Similar protocols

Pipeline publication

[…] b'(MGI:95931), H2-Q4 (MGI:95933), H2-Q6 (MGI:95935), H2-Q7 (MGI:95936), H2-Q10 (MGI:95929), H2-T24 (MGI:95958), H2-T23 (MGI:95957), H2-T22 (MGI:95956), H2-T17 (MGI:95949), H2-M10.1 (MGI:1276522), H2-T10 (MGI:95942), H2-T3 (MGI:95959), H2-M10.2 (MGI:1276525), H2-M10.4 (MGI:1276527), H2-M1 (MGI:95913), H2-M9 (MGI:1276570), H2-M10.3 (MGI:1276524), H2-M11 (MGI:2676637), H2-M10.5 (MGI:1276526), H2-M5 (MGI:95917), H2-M3 (MGI:95915), H2-M2 (MGI:95914), Mill1 (MGI:2179988), Cd1d1 (MGI:107674), B2m (MGI:88127), Mr1 (MGI:1195463), Azgp1 (MGI:103163), Mill2 (MGI:2179989), Fcgrt (MGI:103017), Cd1d2 (MGI:107675), H2-Q8 (MGI:95937), H2-Q9 (MGI:95938) and H2-T9 (MGI:95965). Alignment was performed using the Muscle tool [], the best model to construct the phylogenetic tree was assessed using Prottest [], and the phylogenetic tree was constructed in PhyML [] using the JTT substitution model., Luciferase reporter plasmids were created by replacing the MluI\xe2\x80\x94BglII fragment spanning the HLA-DRA SXY region in the pDRAprox plasmid [] with the corresponding H2-K, H2-Eb1 and hybrid SXY regions. The pGL3-min plasmid containing only the HLA-DRA core promoter (from \xe2\x88\x9260 to +10) in the same reporter plasmid was used as negative control. DNA fragments corresponding to the SXY regions were generated using partially complementary primers that were annealed and amplified by PCR using GoTaq polymerase (Promega). Primer sequences used are listed below. Extensions containing the MluI and BglII restriction sites (underlined) used for cloning are indicated i' […]

Pipeline specifications

Software tools MUSCLE, ProtTest, PhyML
Organisms Mus musculus