#Passing Flanks - A first look at population differences at qPCR primer sites Plate 1 (`samwhite_112381`) included, BMP2, CARM, HSPb11, and PGEEP4. At the bottom is a full list of qPCR primers. ### BMP2 Limited coverage ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39C15A.png) ### CARM Better coverage ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39C23F.png) conflicts were ambigs (ie S,W,R) ### HSPb11 Missed qPCR primer (R did not seem to work) ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39C3CA.png) ### PGEEP4 Nothing assembled - everything under 100 bp. --- Plate 2 (`samwhite_112404`) included, H2A, H2AV, p291N, CRAF, GABABR, GRB2, H3-3 ### H2A `comp23253_c0_seq1` One primer not covered ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39C826.png) ### H2AV `comp25000_c0_seq1` Not much coverage ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39C99F.png) ### p291N `comp22144_c0_seq1` Not much coverage ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39CB03.png) ### CRAF `comp25313_c0_seq1` Decent coverage, only conflict = ambig, SNP! ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39CC30.png) **SNP** ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39D125.png) ### GABABR `comp19002_c0_seq1` Great coverage, did find some SNPs. Missed qPCR primer ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39CDCF.png) **SNPs** ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39CD60.png) ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39CD9F.png) ### GRB2 `comp10127_c0_seq1` Not great coverage ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39CEEF.png) ### H3-3 `comp19571_c0_seq1` ![](http://eagle.fish.washington.edu/cnidarian/skitch/CLC_Genomics_Workbench_8_0_1_-_Evaluation_1B39D08C.png) --- # List of QPCR Primers | QPCR Primer | sequence | Protein | |--------------|----------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------| | HSP70c_FWD | AGGAAAGGTCGGGAGAGGAA | Heat shock 70 kDa protein 12A | HSP70c_REV | ACCTCGGACTTTGGACGAAC | Heat shock 70 kDa protein 12A | | p29ING4_FWD | TACCTTTGGGCTTCACCGTC | Inhibitor of growth protein 4 (p29ING4) | | p29ING4_REV | GTCCATCACACACCCCTCAG | Inhibitor of growth protein 4 (p29ING4) | | CerS2_FWD | TTGTCGGTCTCCTCCTGCTA | Ceramide synthase 2 (CerS2) (LAG1 longevity assurance homolog 2) | | CerS2_REV | CCGTCTTCTGAGCCATCGTT | Ceramide synthase 2 (CerS2) (LAG1 longevity assurance homolog 2) | | GABABR1_FWD | CCGAGGAGGACACGAAACTC | Gamma-aminobutyric acid type B receptor subunit 1 (GABA-B receptor 1) (GABA-B-R1) (GABA-BR1) (GABABR1) (Gb1) | | GABABR1_REV | CGGACAGGTTCTGGATTCCG | Gamma-aminobutyric acid type B receptor subunit 1 (GABA-B receptor 1) (GABA-B-R1) (GABA-BR1) (GABABR1) (Gb1) | | HSP70d_FWD | TTTGTCTCACCGGCTTTGTG | Heat shock 70 kDa protein 6 (Heat shock 70 kDa protein B') | | HSP70d_REV | GACATGAGACCAAAGACGCC | Heat shock 70 kDa protein 6 (Heat shock 70 kDa protein B') | | THRa_FWD | GACACTATCCTCACTCGGCG | Thyroid hormone receptor alpha (Nuclear receptor subfamily 1 group A member 1) | | THRa_REV | GGGTGCCGAGTAAACAAGGA | Thyroid hormone receptor alpha (Nuclear receptor subfamily 1 group A member 1) | | Defensin_FWD | TCTAGCGGAGTTTGTTGGGG | Big defensin | | Defensin_REV | ATGGCTGTCGGAGGAGGATT | Big defensin | | GRB2_FWD | AACTTTGTCCACCCAGACGG | Growth factor receptor-bound protein 2 (Adapter protein GRB2) (Protein Ash) (SH2/SH3 adapter GRB2) | | GRB2_REV | CCAGTTGCAGTCCACTTCCT | Growth factor receptor-bound protein 2 (Adapter protein GRB2) (Protein Ash) (SH2/SH3 adapter GRB2) | | H3.3_FWD | CACGCTCTCCTCGAATCCTC | Histone H3.3 | | H3.3_REV | AAGTTGCCTTTCCAGCGTCT | Histone H3.3 | | H2A.V_FWD | TGCTTTCTGTGTGCCCTTCT | Histone H2A.V (H2A.F/Z) (Fragment) | | H2A.V_REV | TATCACACCCCGTCACTTGC | Histone H2A.V (H2A.F/Z) (Fragment) | | H2A_FWD | GCTGGGGTTTTTCTGGGTCT | Histone H2A | | H2A_REV | GGAACTACGCCGAGAGAGTG | Histone H2A | | Hspb11_FWD | ATGTTTCCTGGTCTCCGTCA | Heat shock protein beta-11 (Hspb11) (Placental protein 25) (PP25) | | Hspb11_REV | CATCAACGCCAGGGGAACTT | Heat shock protein beta-11 (Hspb11) (Placental protein 25) (PP25) | | GDF-8_FWD | CCGTGGATGTCGCAGAAAGA | Growth/differentiation factor 8 (GDF-8) (Myostatin) (Myostatin-1) (zfMSTN-1) (Myostatin-B) | | GDF-8_REV | CTGCTTTCTCCGTCCCCTTT | Growth/differentiation factor 8 (GDF-8) (Myostatin) (Myostatin-1) (zfMSTN-1) (Myostatin-B) | | HSP70b_FWD | AAGTACCTTGGGGAGCTTGC | Heat shock 70 kDa protein 12B | | HSP70b_REV | TCCACAGACTTTCCTCCCCA | Heat shock 70 kDa protein 12B | | GRP-78_FWD | GAGAAACCACGCAGGGAGAA | 78 kDa glucose-regulated protein (GRP-78) (Heat shock 70 kDa protein 5) (Immunoglobulin heavy chain-binding protein) (BiP) | | GRP-78_REV | CATCAGCATCGAAGGCAACG | 78 kDa glucose-regulated protein (GRP-78) (Heat shock 70 kDa protein 5) (Immunoglobulin heavy chain-binding protein) (BiP) | | CARM1_FWD | TGGTTATCAACAGCCCCGAC | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-) (EC 2.1.1.125) (Coactivator-associated arginine methyltransferase 1) (Protein arginine N-methyltransferase 4) | | CARM1_REV | GTTGTTGACCCCAGGAGGAG | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-) (EC 2.1.1.125) (Coactivator-associated arginine methyltransferase 1) (Protein arginine N-methyltransferase 4) | | BMP-2_FWD | TGAAGGAACGACCAAAGCCA | Bone morphogenetic protein 2 (BMP-2) (Bone morphogenetic protein 2A) (BMP-2A) | | BMP-2_REV | TCCGGTTGAAGAACCTCGTG | Bone morphogenetic protein 2 (BMP-2) (Bone morphogenetic protein 2A) (BMP-2A) | | PGE/EP4_FWD | ACAGCGACGGACGATTTTCT | Prostaglandin E2 receptor EP4 subtype (PGE receptor EP4 subtype) (PGE2 receptor EP4 subtype) (Prostanoid EP4 receptor) | | PGE/EP4_REV | ATGGCAGACGTTACCCAACA | Prostaglandin E2 receptor EP4 subtype (PGE receptor EP4 subtype) (PGE2 receptor EP4 subtype) (Prostanoid EP4 receptor) | | CRAF1_FWD | AGCAGGGCATCAAACTCTCC | TNF receptor-associated factor 3 (EC 6.3.2.-) (CD40 receptor-associated factor 1) (CRAF1) (TRAFAMN) | | CRAF1_REV | ACAAGTCGCACTGGCTACAA | TNF receptor-associated factor 3 (EC 6.3.2.-) (CD40 receptor-associated factor 1) (CRAF1) (TRAFAMN) | | NFKBina_FWD | GATGGCGGTGCATGTGTTAG | NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkB-alpha) (IkappaBalpha) (REL-associated protein pp40) | | NFKBina_REV | CGAGGAGAACCTTGTGCAGT | NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkB-alpha) (IkappaBalpha) (REL-associated protein pp40) | | PGRP-S_FWD | GAGACTTCACCTCGCACCAA | Peptidoglycan recognition protein 1 (Peptidoglycan recognition protein short) (PGRP-S) | | PGRP-S_REV | AACTGGTTTGCCCGACATCA | Peptidoglycan recognition protein 1 (Peptidoglycan recognition protein short) (PGRP-S) | | TLR2.1_FWD | ACAAAGATTCCACCCGGCAA | Toll-like receptor 2 type-1 | | TLR2.1_REV | ACACCAACGACAGGAAGTGG | Toll-like receptor 2 type-1 | | GDF-8b_FWD | AACTGATTCTGCTCGTCGCA | Growth/differentiation factor 8 (GDF-8) (Myostatin) | | GDF-8b_REV | TGTTCTTCCACCCACCACTG | Growth/differentiation factor 8 (GDF-8) (Myostatin)