Posted by & filed under Ostrea lurida.

In selecting qPCR targets from the Oly transcriptome (version 3) I came up with the following list. In general this was done by first focusing on stress response GO slim terms, followed by simple word searches.

The table is available for download here

The next step would be some joining & file converting to pull sequences to design primers. In reality this could be done either in bulk or single gene cut and pastes.

ID evalue Gene Sp score SPID GO GO term goslim aspect
comp9638_c0_seq1 6.00E-39 Heat shock protein beta-11 (Hspb11) (Placental protein 25) (PP25) Homo sapiens (Human) 144 Q9Y547 GO:0006950 response to stress stress response P
comp9524_c1_seq1 2.00E-28 Growth/differentiation factor 8 (GDF-8) (Myostatin) (Myostatin-1) (zfMSTN-1) (Myostatin-B) Danio rerio (Zebrafish) (Brachydanio rerio) 374 O42222 GO:0007517 muscle organ development developmental processes P
comp9280_c0_seq1 2.00E-103 Heat shock 70 kDa protein 12B Homo sapiens (Human) 686 Q96MM6 GO:0000166 nucleotide binding other molecular function F
comp8243_c0_seq1 0 78 kDa glucose-regulated protein (GRP-78) (Heat shock 70 kDa protein 5) (Immunoglobulin heavy chain-binding protein) (BiP) Gallus gallus (Chicken) 652 Q90593 GO:0008303 caspase complex cytosol C
comp7220_c0_seq2 0 Histone-arginine methyltransferase CARM1 (EC 2.1.1.-) (EC (Coactivator-associated arginine methyltransferase 1) (Protein arginine N-methyltransferase 4) Danio rerio (Zebrafish) (Brachydanio rerio) 588 Q6DC04 GO:0003713 transcription coactivator activity transcription regulatory activity F
comp7183_c0_seq1 2.00E-93 Bone morphogenetic protein 2 (BMP-2) (Bone morphogenetic protein 2A) (BMP-2A) Homo sapiens (Human) 396 P12643 GO:0001666 response to hypoxia stress response P
comp6939_c0_seq1 1.00E-50 Prostaglandin E2 receptor EP4 subtype (PGE receptor EP4 subtype) (PGE2 receptor EP4 subtype) (Prostanoid EP4 receptor) Mus musculus (Mouse) 513 P32240 GO:0050728 negative regulation of inflammatory response stress response P
comp25313_c0_seq1 3.00E-145 TNF receptor-associated factor 3 (EC 6.3.2.-) (CD40 receptor-associated factor 1) (CRAF1) (TRAFAMN) Mus musculus (Mouse) 567 Q60803 GO:0050688 regulation of defense response to virus stress response P
comp24195_c0_seq1 5.00E-36 NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkB-alpha) (IkappaBalpha) (REL-associated protein pp40) Gallus gallus (Chicken) 318 Q91974 GO:0034142 toll-like receptor 4 signaling pathway stress response P
comp24065_c0_seq1 2.00E-42 Peptidoglycan recognition protein 1 (Peptidoglycan recognition protein short) (PGRP-S) Homo sapiens (Human) 196 O75594 GO:0045087 innate immune response stress response P
comp23747_c0_seq1 8.00E-29 Toll-like receptor 2 type-1 Gallus gallus (Chicken) 793 Q9DD78 GO:0034142 toll-like receptor 4 signaling pathway signal transduction P
comp23265_c1_seq1 5.00E-39 Growth/differentiation factor 8 (GDF-8) (Myostatin) Coturnix coturnix (Common quail) (Tetrao coturnix) 375 Q8AVB2 GO:0005615 extracellular space non-structural extracellular C
comp22403_c0_seq1 7.00E-114 Heat shock 70 kDa protein 12A Mus musculus (Mouse) 675 Q8K0U4 GO:0008150 biological_process other biological processes P
comp22144_c0_seq1 6.00E-42 Inhibitor of growth protein 4 (p29ING4) Mus musculus (Mouse) 249 Q8C0D7 GO:0006978 “DNA damage response signal transduction by p53 class mediator resulting in transcription of p21 class mediator””” stress response P
comp20292_c2_seq1 4.00E-25 Ceramide synthase 2 (CerS2) (LAG1 longevity assurance homolog 2) Bos taurus (Bovine) 380 Q3ZBF8 GO:0003700 transcription factor activity transcription regulatory activity F
comp19002_c0_seq1 1.00E-27 Gamma-aminobutyric acid type B receptor subunit 1 (GABA-B receptor 1) (GABA-B-R1) (GABA-BR1) (GABABR1) (Gb1) Mus musculus (Mouse) 960 Q9WV18 GO:0060124 positive regulation of growth hormone secretion transport P
comp16752_c2_seq1 2.00E-27 Heat shock 70 kDa protein 6 (Heat shock 70 kDa protein B’) Homo sapiens (Human) 643 P17066 GO:0008180 signalosome nucleus C
comp16251_c0_seq1 8.00E-104 Thyroid hormone receptor alpha (Nuclear receptor subfamily 1 group A member 1) Hippoglossus hippoglossus (Atlantic halibut) (Pleuronectes hippoglossus) 416 Q9W6N4 GO:0003700 transcription factor activity transcription regulatory activity F
comp10930_c0_seq1 1.00E-23 Big defensin Tachypleus tridentatus (Japanese horseshoe crab) 117 P80957 GO:0050829 defense response to Gram-negative bacterium stress response P
comp10127_c0_seq1 1.00E-83 Growth factor receptor-bound protein 2 (Adapter protein GRB2) (Protein Ash) (SH2/SH3 adapter GRB2) Rattus norvegicus (Rat) 217 P62994 GO:0031623 receptor internalization transport P
comp19571_c0_seq1 2.00E-90 Histone H3.3 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) 136 Q6P823 GO:0006334 nucleosome assembly cell organization and biogenesis P
comp25000_c0_seq1 5.00E-64 Histone H2A.V (H2A.F/Z) (Fragment) Strongylocentrotus purpuratus (Purple sea urchin) 125 P08991 GO:0000786 nucleosome other cellular component C
comp23253_c0_seq1 2.00E-49 Histone H2A Sipunculus nudus (Marine worm) 124 P02270 GO:0006334 nucleosome assembly cell organization and biogenesis P

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