Table 2.
Differential gene expression in 10-dpf NBH and SC embryos as measured by RNA-Seq.
| Gene | SC-DMSO | SC-PCB | NBH-DMSO | NBH-PCB |
|---|---|---|---|---|
| UnAn_29411_6378* (CYP1B1) # | 0 | 66 | 0 | 0 |
| Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)_1115 # | 0 | 4987 | 0 | 3 |
| T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)_3770 # | 0 | 0 | 0 | 0 |
| UnAn_27910_5543* (CYP1B1) # | 0 | 66 | 0 | 0 |
| Tubulointerstitial nephritis antigen-like precursor (Androgen-regulated gene protein 1) (Adrenocortical zonation factor 1) (AZ-1) (Tubulointersititial nephritis antigen-related protein) (TARP)_4042 # | 1 | 0 | 3 | 6 |
| UnAn_29159_6257** (apolipoprotein E) # | 41 | 177 | 52 | 37 |
| UnAn_28041_5632** (apolipoprotein E) # | 41 | 177 | 52 | 37 |
| Acidic phosphoprotein precursor (50 kDa antigen)_277 # | 0 | 0 | 0 | 0 |
| UnAn_23610r_4780** (apolipoprotein E) # | 41 | 177 | 52 | 37 |
| UnAn_21996_4295 # | 0 | 0 | 0 | 0 |
| Apomucin (Mucin core protein) (Fragment)_492 # | 18 | 31 | 8 | 10 |
| C61 protein [Mus musculus]_684 # | 0 | 0 | 0 | 2 |
| WAP four-disulfide core domain protein 3 precursor (Putative protease inhibitor WAP14)_6790 # | 0 | 0 | 0 | 0 |
| Tyrosine aminotransferase (EC 2.6.1.5) (L-tyrosine:2-oxoglutarate aminotransferase) (TAT)_4064 # | 0 | 0 | 0 | 0 |
| MHC class II transactivator (CIITA)_2363 # | 0 | 0 | 0 | 0 |
| UnAn_23121_4564 # | 2 | 0 | 3 | 0 |
| Troponin C, slow skeletal and cardiac muscles (TN-C)_3995 | 13 | 26 | 22 | 14 |
| Epsin-4 (Epsin-related protein) (EpsinR) (Enthoprotin)_1384 # | 0 | 0 | 0 | 0 |
| UnAn_27985_5592 # | 19 | 10 | 14 | 11 |
| AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M)_431 # | 0 | 0 | 0 | 0 |
| UnAn_29343_6349 # | 134 | 179 | 92 | 137 |
| UnAn_29849_6655 | 2 | 0 | 0 | 0 |
| Cathepsin D precursor (EC 3.4.23.5)_755 | 0 | 0 | 1 | 0 |
| UnAn_22785_4432 | 129 | 103 | 77 | 135 |
| UnAn_20648_4152 | 5 | 0 | 9 | 8 |
| Mitogen-activated protein kinase kinase 1 interacting protein 1 (MEK binding partner 1) (Mp1)_2424 | 11 | 7 | 5 | 13 |
| Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione peroxidase-like protein) (EGLP)_1378 | 3 | 4 | 0 | 1 |
| Muted protein homolog_2461 | 22 | 5 | 4 | 7 |
| UnAn_22879_4456 | 50 | 35 | 42 | 32 |
| UnAn_22354_4332 | 12 | 22 | 32 | 25 |
| Type II antifreeze protein precursor (AFP)_4059 | 2 | 1 | 2 | 0 |
| T-cell surface glycoprotein CD8 beta chain precursor (CD8 antigen 37 kDa chain) (OX-8 membrane antigen)_3771 | 11 | 9 | 13 | 12 |
| UnAn_20957_4180 | 0 | 0 | 1 | 2 |
| Chromobox protein homolog 2 (Modifier 3 protein) (M33)_827 | 0 | 0 | 0 | 0 |
| Beta enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Muscle-specific enolase) (MSE) (Skeletal muscle enolase) (Enolase 3)_620 | 18 | 15 | 18 | 20 |
| UnAn_27466_5284 | 12 | 12 | 14 | 19 |
| Transcription factor PU.1_3890 | 0 | 0 | 0 | 0 |
| UnAn_22873_4452 | 0 | 0 | 0 | 0 |
| RWD domain containing protein 1 (Small androgen receptor-interacting protein)_3458 | 15 | 9 | 10 | 1 |
| Parvalbumin beta_2778 | 49 | 44 | 40 | 60 |
The probe sequences representing genes with significant differences in pairwise comparisons in the 10-dpf samples (see Table 1) were used in blast searches against a database of the reads from each EST library using BlastStation-Local (version 1.4). The number of reads matching each probe sequence is indicated. The e-value cut-off was approximately 1x10-20, and the percent identity limit was set as 90% or higher. NBH: New Bedford Harbor; SC: Scorton Creek; PCB: PCB-126; DMSO: dimethylsulfoxide. Unannotated genes are denoted by UnAn and a unique number. The probes labeled with asterisks (* or **) belong to the same transcript, and therefore share the same 454 read counts. Some of the unannotated probes were subsequently annotated after extension using the 454 database; see Table S4 (Additional file 6) for details. Probes labeled with "#" are those exhibiting significant induction by PCB in SC embryos but not NBH embryos in the microarray analysis (see Table 1).