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).

Oleksiak et al. BMC Genomics 2011 12:263   doi:10.1186/1471-2164-12-263

Open Data