Regassa et al. BMC Genomics 2011, 12:57 http://www.biomedcentral.com/1471-2164/12/57 Table 1 Pairs of primers that were used for validation of array data Gene name Accession number Forward (5’ - 3’) Reverse (3’ - 5’) Page 6 of 20 Annealing temperature (°C) Product length (bp) GDF9 MSX1 IRF6 SPARC HPSE DGAT2 SOX2 HAS2 PTX3 IGF2BP3 ADAMTS1 PDK4 CCRK FOSB POU5F1 VEGFA 18S GPT DAPL1 IRF7 GADD45A DPP4 IFI6 ADAMTS4 CASP1 IFIT5 DDX39 GTF2A2 TSSC1 FSHR GPT PLAUR CA2 NM_174681 NM_174798 NM_001076934 NM_174464 NM_1744082 NM_205793 NM_001105463 NM_174079 NM_001076259 XM_588560 NM_001101080 XM_583960 XM_879150 XM_880646 NM_174580 NM_174216 NR_003286 XM_585516 NM_001025346 NM_001105040 NM_001034247 NM_174039 NM_001075588 NM_181667 XM_592026 NM_001075698 NM_001034752 NM_001037619 XM_001789233 NM_174061 NM_001083740 NM_174423 NM_178572 AGCGCCCTCACTGCTTCTATAT AAGGTATCCACAGTCCCCAGC GGACTCCAAACGCTTCCAGA CGATGATGGTGCTGAGGAAA ATGGGCATAGAAGTGGTGATGA TGAACCGGGACACCATAGACTA GCGGCAACCAGAAGAACAG CCAAATGAAATGCCAAAGGAA TTTATTCCCCATGCGTTCCA GACGCGAAAGTGAGGATGGT TCGTCATACAGCTCCCCTCC ATTTTTGCGACAAGAGTTGCCT GGCCCCACTCATGGCTACTT TTCCTGAATCTCTCCCGCC AGAAGGGCAAACGATCAAGC GGTTTCGGGAACCAGACGT GTGCCCTTCCGTCAATTCCT CCGATGAGGTGTACCAAGACAA AAATTTCCAGCAGTAGCGCAC CTCCCCGCACTACACCATCTA GACCGAAAGGATGGATAAGGTG CAACTGGGCTACTTACCTTGCA ACGGTGACAAAGCCTTGAGC CCATTGTGGAGGATGATGGG CTCACTCAGAGCATCGGACCT CACAGTGTATCGGCTGGATGA GCAGTTCAAGGACTTCCAGC AGAAAGAGGTTCTGCCCGGA AGCAGCGACAGCAGAGTCATC GCTGGATCTTTGCTTTTGCAGT CCGATGAGGTGTACCAAGACAA GGATTCCACAACAACCACACCT CAAAGCAGTGCTGAAAGATGGA ACACCCTCAGCAGCTTCTTCTC TCTGCCTCTCCTGCAAAGTTC TCCTTGGTGCCATCATACATCA TGGTGGCAAAGAAGTGGCA TGTTTGGTGTTTGTGCAATGAA CACCTCATTCTCCCCAAAGGA GCTTCTCCGTCTCGGACAAA CAACGTCAACCAAGCTTCACA CTCCACCCACCACAAGCATT TGCACTTGACAAATTCTGGAGC ATTGACACACCATTTCCCCTCT GGATTCCTTGTGCCATTGTAGG TCCTGAGGGTGATGCTGGTAA TGCTCACAGCCTCACACTCG GGTGACAGACACCGAGGGAA GGCAATCCAATTCCAAGAGGA ACGAAAGTCGGAGGTTCGAA CCATATTCACCACCTCCACGT AGCTCTCAGACATTCGAGGCA GCCTGTTCCACCTCCATCA TGGATCAGGGTGAAGTGGATCT TTACGTACCCTCCGTATGACCA AGGTCACCATGCCCCAGAA AGGAAGTCAGTGATGAAGCGG GTTTACCCATACCATCCCTTGC GGTTGGGCTGATATCTGGTCC GCTCTGCCACATTCACTTCA CTTATCGGCTGCATTGAAAGC TAGCTCAGGGAGGCGAACAG ATGCGCTTGGCTATCTTGGT CCATATTCACCACCTCCACGT TCGCTTCCAGACATTGATTCAT AAAACACCCACAACAGCCAGTC 57 56 54 53 TD 54-50 55 55 TD 54-50 53 54 TD 57-54 TD 56-52 57 56 TD 57-53 55 55 55 55 TD 58-55 56 56 55 55 57 56 TD 55-52 55 57 54 56 TD 56-52 55 152 180 212 220 202 205 170 237 205 215 220 250 170 205 205 233 184 185 158 245 200 223 158 210 229 200 228 150 229 243 185 204 212 Touch down (TD) = The forward and the reverse primers of a given gene have different annealing temperatures. Removal of oocyte or CCs at GV alters the gene expression of either cell at MII stage In order to investigate transcriptome profile changes when the oocyte matures with or without its companion CCs and when CCs mature with or without their enclosed oocytes, we analyzed their corresponding transcriptome profiles using LIMMA as described previously [56]. The analysis showed that a total of 265 genes are differentially expressed between OO + CCs (number 5) and OO-CCs (number 6) of which 217 and 48 are over expressed in OO + CCs and OO - CCs, respectively (Additional file 12). Similarly, 566 genes are differentially expressed between CCs that were cultured with (CCs + OO) (number 7) or without their enclosed oocytes (CCs - OO) (number 8) of which 320 and 246 are over expressed in CCs + OO and CCs - OO, respectively (Additional file 13). Hierarchical clustering and heat map of the top differentially expressed genes between OO + CCs and OO - CCs and between CCs + OO and CCs - OO, with a fold change of > 4 and 16, are presented in Figures 6 and 7, respectively. We found that 36 and 375 of these genes over expressed in OO + CCs and CCs + OO, respectively, could be assigned to a specific functional group based on the infor- mation in the IPA Knowledge Base. Only 4 of the mapped genes over expressed in OO + CCs group, representing about 1.5% of the total, are classified under the functional group “Carbohydrate metabolism,” which contains genes involved in energy conversion and modulation. Other functional groups, including molecular transport, nucleic acid metabolism, small molecule biochemistry and RNA