RBC2 unique Gene FC P FDR   actin, alpha 1 , skeletal muscle (ACTA1) (array address 5, 13, 2) -2.84 0.0002 0.0496   actin, alpha 1 (ACTA1) (array address 5, 16, 8) -3.12 0.0002 0.0496   ATPase, Ca++ transporting, cardiac muscle, fast  twitch 1 (ATP2A1) -2.23 0.0002 0.0496   CDC28 protein kinase regulatory subunit 2 (CKS2) -2.06 0.0001 0.0496   collagen pro-alpha-1 (COL1AI) -2.65 0.0002 0.0496   glycosyltransferase 8 domain containing 1 (GLT8D1) -1.52 0.0002 0.0496   lamin B2 (LMNB2) -1.63 0.0002 0.0496   maternal embryonic leucine zipper kinase (MELK) -2.00 0.0001 0.0496   P311 POU, neuronal protein 3.1 (C5orf13) -2.34 0.0000 0.0224   proteoglycan (PRG) -2.02 0.0000 0.0255   serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 (SERPINE2) -1.89 0.0001 0.0496   small nucleolar RNA host gene* 1.87 0.0002 0.0496   tubulin, alpha (TUBA) -1.81 0.0002 0.0496   tubulin, beta 2B (TUBB2B) -1.92 0.0001 0.0496 F Unique           actin, alpha 2, smooth muscle, aorta (ACTA2) -1.92 0.0001 0.0354   cardiac C-protein (MYBPC3) 1.75 0.0002 0.0498   cysteine and glycine-rich protein 3  (cardiac LIM protein) (CSRP3) 2.49 0.0000 0.0183   FRA10AC1 protein (C10orf4) 1.67 0.0001 0.0351   Leber congenital amaurosis 5-like (LCA5L) 2.44 0.0001 0.0354   microphthalmia-associated transcription factor (MITF) 1.76 0.0002 0.0470   similar to nexilin isoform s 2.36 0.0000 0.0145   unknown 1.58 0.0002 0.0470   unknown protein 1.91 0.0002 0.0498 Shared Gene Line FC P Value FDR   actin, alpha RBC2 -3.12 0.0000 0.0083     F -2.49 0.0000 0.0183   CD74 molecule, major histocompatibility complex, class II invariant chain (CD74) RBC2 2.43 0.0000 0.0195     F 2.15 0.0000 0.0237   family with sequence similarity 134, member B (FAM134B) RBC2 1.72 0.0001 0.0496     F 1.71 0.0001 0.0354   Kazal-type serine peptidase inhibitor domain 1 (KAZALD1) RBC2 -1.59 0.0001 0.0496     F -1.79 0.0000 0.0237   Kelch domain containing 3 (KLHDC3) RBC2 -1.62 0.0002 0.0496     F -1.68 0.0001 0.0354   myosin regulatory light chain 2B, cardiac muscle isoform RBC2 2.00 0.0001 0.0496     F 2.72 0.0000 0.0183   myotilin (MYOT) (array address 4, 7, 4) RBC2 3.80 0.0000 0.0083     F 4.15 0.0000 0.0061   myotilin (MYOT) (array address 22, 9, 6) RBC2 3.30 0.0000 0.0097     F 2.50 0.0000 0.0207   similar to nebulin (LOC771699) RBC2 2.32 0.0001 0.0496     F 2.68 0.0001 0.0331   TNNI1 troponin I type 1 (skeletal) (array address 9,2,8) RBC2 -2.70 0.0000 0.0223     F -2.23 0.0001 0.0351   TNNI1 troponin I slow skeletal muscle isoform (array address 11, 1, 10) RBC2 -2.13 0.0000 0.0195     F -1.97 0.0000 0.0237   TNNI1 troponin I type 1 (skeletal, slow) (array address 18, 1, 14) RBC2 -1.68 0.0001 0.0496     F -1.85 0.0001 0.0331   tropomyosin, alpha (TPMI) RBC2 -1.53 0.0002 0.0496     F -3.80 0.0001 0.0412   unknown RBC2 2.55 0.0002 0.0496     F 3.08 0.0001 0.0354 *this gene contains four snoRNAs as introns

Table 2: Genes showing differential expression between developmental stages within genetic lines (RBC2 and F) as measured with the TSKMLO microarray. Genes in the Shared group were differentially expressed in both genetic lines. For each gene the directional fold change (FC; 16 wk versus 1 dph), P value, and false discovery rate(FDR) are given.