- Research article
- Open Access
A mRNA landscape of bovine embryos after standard and MAPK-inhibited culture conditions: a comparative analysis
© Brinkhof et al.; licensee BioMed Central. 2015
- Received: 26 February 2015
- Accepted: 6 March 2015
- Published: 10 April 2015
Genes and signalling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analysed.
Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE, the expression of NANOG, SOX2 and POU5F1 was increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term. Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was down-regulated.
The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent, epiblast-like state. The inability to culture ICM cells as stem cells in the presence of an inhibitor of MAPK activity together with the reported data indicates that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells.
In mammals, early life starts with the formation of a zygote as a result of the fertilization of an oocyte. Sequential cleavage divisions lead to the formation of a morula stage embryo wherein a fluid-filled cavity emerges called the blastocoel. Two differentiated groups of cells can be distinguished in the embryo that is now called a blastocyst. A group of cells adjacent to the blastocoel, the inner cell mass (ICM), is able to contribute to all cells of the three germ layers and is therefore referred to as being pluripotent. The other group of cells, called the trophectoderm (TE), forms an epithelium surrounding the blastocoel and the ICM and is important for implantation within the uterus and contributes to the non-maternal part of the placenta. In the ICM further differentiation occurs by the formation of the epiblast, that will form the foetus, and the formation of extra-embryonic primitive endoderm (PE) contributing to the yolk sac.
Studies with mouse embryos have advanced our understanding of how a pluripotent cell population is established during pre-implantation development [1-4]. During the first differentiation, the transcription factors CDX2 and OCT4 are key regulators for the formation of respectively TE and ICM. CDX2 represses the activity of OCT4 in mouse TE  and is virtually absent in ICM cells . OCT4 in turn can counteract CDX2 activity in the inner cells of the morula. The second differentiation is indicated by the expression of either NANOG or GATA6 in ICM cells fated to become the epiblast or PE respectively . Like for CDX2 and OCT4 in the morula, NANOG and GATA6 inhibit each other’s transcription . Whether the same genes and signalling pathways are also involved in the formation of a pluripotent cell population in other mammals remains to be established. Indeed, in contrast to the mouse, OCT4 protein remains present in the TE of bovine blastocysts even after transcription is down-regulated  and its expression is not negatively regulated by CDX2 . In mouse embryos it has been established that GATA6-stimulated fibroblast growth factor (FGF) signalling via the extracellular signal-regulated protein kinase (ERK) is responsible for NANOG repression and thereby the formation of primitive endoderm [2,10-12]. In bovine and human embryos however, although GATA6 expression is specific for primitive endoderm, inhibition of ERK signalling had a more moderate (bovine) or no (human) effect on the numbers of NANOG and GATA6 expressing cells suggesting that in these species other pathways are involved in the formation of the pluripotent cell population [13-15]. These findings suggest species-specific mechanisms active in the specification of ICM, TE, epiblast and PE lineages and that further insight is needed into the molecular basis of cell sorting during the two first differentiation events.
When mouse ICM cells are cultured under defined conditions, their pluripotent character can be maintained [16,17]. However, the establishment of such embryonic stem (ES) cells has only been successful for mice, non-human primates , humans  and rats . Although pluripotency refers to the capacity to give rise to all embryonic and adult cell types, including the germ line, various states of pluripotency have been described. These states are referred to as “naïve” and “primed”, with “primed” being more developmentally restricted . In mammals other than primates and rodents, the correct stages of embryos that contain pluripotent cells and culture conditions that maintain pluripotency have yet to be established .
In order to identify genes that may be important for the acquisition and maintenance of pluripotency in bovine embryos a genome-wide gene expression analysis was performed in morulae, intact blastocysts, TE and ICM. Analyses of gene expression patterns in pre-implantation embryos to distinguish between pluripotent cells of the ICM versus those of the TE have previously made use of cell lines because of the technical difficulties of separating ICM from TE [23,24]. Here we have manually dissected individual ICMs from TE. As the late ICM is composed of both pluripotent epiblast cells and the PE, the pluripotent character of the ICM was enhanced by inhibition of the ERK-pathway resulting in an increased percentage of ICM cells that express NANOG.
Gene expression profile of pre-implantation embryos
Samples were hybridized on a microarray slide containing almost 44,000 probes per array coding for ~ 14,000 gene transcripts indicating that for a subset of genes more than one probe was present. If the position of the probe is nearer to the 3’ end of the corresponding gene, signal intensity is expected to be higher  and chance of incorrect signal by variations in RNA integrity is smaller . Therefore, the expression of the probes corresponding to the most 3’ ends of genes was used for the analysis [27,28]. Gene expression levels in morula, blastocyst, ICM and TE were determined and a hierarchical clustering analysis was performed. The constructed heat map shows clear pairing of the morula, ICM and TE samples (Figure 1F). This is particularly important for the TE and ICM samples since these were manually dissected and confirms the reproducibility of the dissection. We used mechanical isolation of ICM from TE using tungsten needles. A selection of isolated ICMs was stained for CDX2 and GATA6 to identify the contribution of TE cells to the pooled microarray samples. The isolated ICMs contained only ~20% CDX2 positive TE (Figure 1G). Since however some TE cells remained attached to the ICM, throughout the manuscript “ICM” refers to the ICM containing few TE cells. In the TE samples all cells were CDX2 and GATA6 positive (Figure 1H). Blastocyst samples did not pair since their difference with the reference is minimal indicated by a near black appearance in the heat map. A principal component analysis (PCA) further identified four categories according to cell type or developmental stage. In a 2D plot, morula samples separate the farthest from the other samples. TE and ICM samples are clearly separated from each other with the blastocyst replicates in between (Figure 1I).
Genes differentially expressed between morulae and blastocysts
List of the most differentially expressed genes between blastocyst and morula
Entrez Gene name
G antigen family C member 1
prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) (PTGS2), mRNA.
aldehyde dehydrogenase 1 family, member A3
selenoprotein P, plasma, 1 (SEPP1), mRNA
grancalcin, EF-hand calcium binding protein
keratin, type II cytoskeletal 8
KRT18 proteinUncharacterized protein
solute carrier family 23 (ascorbic acid transporter), member 1
Bos taurus alanine-glyoxylate aminotransferase 2-like 1 (AGXT2L1), mRNA.
Lanosterol 14-alpha demethylase
low-density lipoprotein receptor
Heme oxygenase 1
Urokinase-type plasminogen activatorUrokinase-type plasminogen activator long chain AUrokinase-type plasminogen activator short chain AUrokinase-type plasminogen activator chain B
PQ-loop repeat-containing protein 3
Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Bos taurus solute carrier family 35, member G1 (SLC35G1), mRNA.
AgriGO parametric analysis of gene set enrichment (PAGE) analysis (blastocyst versus morula)
lipid metabolic process
RNA metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleic acid binding
transcription regulator activity
pepsin A activity
extracellular region part
integral to membrane
Genes differentially expressed between ICM and TE
List of the most differentially expressed genes between inner cell mass and trophectoderm
Entrez gene name
Homeobox protein NANOG
uridine phosphorylase 1
SRY (sex determining region Y)-box 2
Adenylate kinase isoenzyme 4, mitochondrial
pancreatic trypsin inhibitor-like
agilent:“Bos taurus orthodenticle homeobox 2 (OTX2), mRNA
agilent:“Bos taurus glypican 4 (GPC4), mRNA
hyaluronan synthase 2
solute carrier family 4, sodium bicarbonate cotransporter, member 7
agilent:“Bos taurus hepatocyte nuclear factor 4, alpha (HNF4A), mRNA
CLIC6 chloride intracellular channel 6
DNA-binding protein inhibitor ID-1
fibronectin leucine rich transmembrane protein 3
agilent:“Bos taurus platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), mRNA
Mast/stem cell growth factor receptor
agilent:“Bos taurus gastrin-releasing peptide GRP mRNA, complete cds.
LOC100139916 interleukin 32-like
Transketolase-like protein 1
actin, gamma 2, smooth muscle, enteric
AgriGO parametric analysis of gene set enrichment (PAGE) analysis (inner cell mass versus trophectoderm)
sterol biosynthetic process
sterol metabolic process
steroid metabolic process
cholesterol metabolic process
steroid biosynthetic process
lipid metabolic process
lipid biosynthetic process
isoprenoid metabolic process
alcohol metabolic process
cellular lipid metabolic process
response to metal ion
terpenoid metabolic process
intracellular signaling pathway
enzyme linked receptor protein signaling pathway
nuclear envelope-endoplasmic reticulum network
endoplasmic reticulum membrane
endoplasmic reticulum part
Genes differentially expressed between MAPK-inhibited and control ICMs
AgriGO parametric analysis of gene set enrichment (PAGE) analysis (MAPK inhibited versus control)
extracellular region part
intracellular non-membrane-bounded organelle
List of genes differentially expressed in ICM versus TE and PD treated versus control ICMs
The expression of GATA6 was significantly down-regulated in the ICM after MAPK inhibition, although the difference was less than 2-fold and was not significant in the qRT-PCR analysis. The expression of 26 other ICM-specific genes was significantly down-regulated upon MAPK inhibition suggesting that these genes are involved in primitive endoderm formation (Figure 5 and Table 6). Expression of a number of the genes was also analysed by qRT-PCR showing a similar pattern and validating the microarray data (Figure 5 and Additional file 4: Figure S3). Indeed mouse follistatin, coded by Fst, has been implicated as a marker for primitive endoderm derivatives . Other genes down-regulated in the MAPK inhibited bovine ICMs themselves code for negative regulators of MAPK activity such as DUSP4 and SPRY4.
The 42 shared genes were analyzed for their properties by gene ontology analysis. A PAGE analysis in AgriGO revealed 59 enriched GO-terms of which none had a FDR < 0.1. When the SEA was performed using either ICM up-regulated, PD up-regulated or PD down-regulated genes (Additional file 2: Table S6), a Venn diagram with the enriched terms (FDR < 0.1) revealed 34 enriched GO-terms shared between the up-regulated gene comparisons (Figure 6B, Additional file 2: Table S6).
During bovine pre-implantation development several cell types display a pluripotent character. The failure in generating true pluripotent ES cell lines from Bos taurus embryos however indicates that, compared with murine and human embryos, other genes are involved in maintenance of pluripotency, that the correct embryonic stage with pluripotent cells has not been used, or that the culture conditions employed did not sufficiently inhibit differentiation. Interestingly, induced pluripotent stem (iPS) cells generated from bovine cells also behave differently than mouse iPS cells. Similar to porcine iPS cells, the introduced transgenes are not silenced in the currently used culture conditions but remain expressed in these cells suggesting that other factors are needed for maintenance of pluripotency . We performed a microarray analysis comparing morula, blastocyst, ICM and TE gene expression profiles to identify genes possibly involved in pluripotency. Further enrichment of the pluripotent character of the ICM was achieved by inhibiting the MAPK pathway through exposure to the MEK inhibitor PD0325901 during in vitro culture thereby increasing the percentage of NANOG expressing cells in the ICM/epiblast [13,14].
To obtain samples for the microarray analysis embryos were cultured up to the morula stage or blastocyst stage. Blastocysts were dissected manually to separate ICM and TE. The advantage of this technique is that ICM and TE are isolated from the same embryo, in contrast to for example a technique like immunosurgery. Manually dissecting blastocysts is challenging however and it is unavoidable that few TE cells remain attached to the ICM. We therefore verified that the separation of the two cell types was successful. For separation of ICM from TE, Nagatomo et al. have used either a micromanipulator or mild trypsin treatment to separate ICM . ICMs isolated using the micromanipulator still contained 43.3% TE cells . In our hands the percentage of TE cells remaining in the ICM isolates was ~20% as determined by CDX2 expression, indicating a low contribution of TE cells to the ICM transcriptome. The disadvantage of mild trypsin treatment to isolate ‘pure’ ICM cells, is that TE and ICM cannot be compared from the same embryo and that the trypsin treatment by itself may cause a difference in gene expression. The observation that duplicate samples paired together and that TE and ICM clustered apart from each other together with the expected expression patterns of known TE- and ICM-specific genes in the microarray as well as by qRT-PCR indicates that indeed the separation was specific and reproducible.
Several genes were represented on the array by multiple probes and in those cases we only used the expression data of the most 3’-located probe. Unfortunately, the Bos taurus genome is not completely annotated  and indeed approximately 5% of the probes representing genes differentially expressed between blastocyst and morula could not be identified. The other comparisons could be made with all probes linked to a known differentially expressed gene. For the Gene Ontology analysis genes need to be associated with a GO-term. Not all genes are associated with a GO-term and therefore 3.7% – 5.3% of the genes could not be analysed in the AgriGO gene ontology analysis.
In vitro derived embryos were used as this enabled us to generate the numbers needed for RNA extraction. Particularly for the ICM and TE samples large numbers of embryos were needed to obtain sufficient amounts of RNA for hybridization (Additional file 2: Table S7). Although a significant difference in gene expression between in vitro and in vivo derived embryos has been demonstrated  the birth of healthy animals from in vitro derived embryos indicates that the pathways for pluripotency are functional in these embryos. When gene expression was compared between different stages of in vivo derived bovine embryos most genes were found to be differentially expressed between early development (oocyte-4 cell stage) and later stages (8-cell stage-blastocyst) . Most likely these differences in gene expression are caused by embryonic genome activation around the 8-cell stage [40-42]. A larger number of genes (~1800) was expressed in in vivo derived oocytes compared with in vitro matured oocytes , indicating that in our study with in vitro derived embryos important genes may not have been detected. However, since in vitro derived embryos are commonly used for embryo transfer and give rise to healthy animals, it can be expected that genes important for pluripotency are sufficiently expressed and the pathways for pluripotency are functional in in vitro derived embryos.
We started our analysis by comparing gene expression in blastocysts with that in morulae. This indicated that most differentially expressed genes are expressed at higher levels in the blastocyst but a GO-analysis revealed that most genes expressed at higher levels in morulae are involved in gene transcription. This might be a result of the embryonic genome activation initiated during the 8-16 cell stage in cattle embryos preceding the morula stage [40-42]. Next we tried to identify genes involved in pluripotency by comparing gene expressions in ICM and TE. Mouse and human ES cell pluripotency is regulated by NANOG, SOX2 and OCT4, and these factors enhance each other’s transcription [43-45]. Indeed, their gene expression levels were found higher in the bovine ICM samples compared with TE. Remarkably, in the comparison of the ICM with the TE, expression of genes in the GO-category RNA splicing was specifically up-regulated in the ICM. This indicates a higher transcriptional activity in ICM cells than in TE cells. This is further reflected in the >400 genes up-regulated in ICM compared with TE. Using deep sequencing, Ozawa et al. examined genes differentially expressed between ICM and TE of day 8 in vitro derived embryos . All of 8 ICM-characteristic genes that Ozawa et al. found were also up-regulated in our study, except for ZC3HAV1 and Il6R. Expression of Il6R was indeed significantly up-regulated in the ICM but the difference was below the cut-off used (2-fold). These results confirm the specificity and reliability of the ICM isolation and microarray analysis. Compared with our results Ozawa et al. found more genes (870 versus 497 in our study) to be differentially expressed between ICM and TE, most likely because of the less stringent cut-off value used (1.5 versus 2.0 fold difference in our study) .
By enhancing the overall NANOG expression in the ICM we had anticipated that SOX2 and POU5F1 expression were similarly enhanced. Surprisingly however, in ICMs from embryos cultured in the presence of a MAPK inhibitor, gene expression levels of NANOG were up-regulated while those of POU5F1 and SOX2 remained relatively unchanged. These results suggest that in bovine cells NANOG by itself is not sufficient in maintaining the core pluripotency network.
An unexpected result was the expression of several interferon-coding genes in the ICM. Various reports have described exclusive IFNT expression in trophectoderm or TE derived cell lines [46-48]. We detected IFNT expression in the isolated ICMs at similar levels as in TE however and the expression in the ICM was down-regulated upon MAPK inhibition even to a greater extent than in TE. In ungulates, interferon tau (coded by IFNT) expression by TE is important for maternal pregnancy recognition . In bovine day 7 blastocysts interferon tau has been detected at varying intensity in the TE and was concentrated at the border of the ICM and TE . By dissecting the ICM, part if not all of the interferon tau-positive adjacent cells have been included in the ICM samples accounting for the observed IFNT expression in the ICM samples. Together with CDX2 predominantly expressed in TE cells and capable of increasing IFNT transcription [46,50], this might explain the greater expression reduction found in ICM (20-fold) than in TE (4-fold). Nevertheless, our results and the previously reported location of interferon tau expression  do not exclude IFNT expression in the ICM even though its function in the ICM is unknown.
After exposure to PD0325901 expression of NANOG in the ICM was enhanced as compared to control ICMs. In the mouse more than 3,000 genes have been identified containing NANOG binding sites . Of the 42 genes identified to be differentially expressed in bovine ICMs and after MAPK inhibition, only five were homologous to murine genes containing NANOG binding sites. Of those genes only expression of NANOG was up-regulated after MAPK inhibition. Of the remaining four, CD8B, DUSP4, JAM2 and SPRY4, the expression was enhanced in the ICM but their expression was down-regulated after MAPK inhibition. The role of the glycoprotein CD8B in early embryonic development, and more specifically in the ICM, is unclear. Its expression can be regulated however by MAPK signalling [52,53] possibly accounting for the observed down-regulation after PD0325901 treatment. DUSP4 is suggested to function in the negative feedback control of MAPK signalling specifically dephosphorylating ERK1/2 [54,55]. Also SPRY4 is known for its involvement in the MAPK pathway by interacting with GRB2 and GAP1 and as such inhibiting RAS activation  and antagonizing FGF activity . Therefore, the down regulation of DUSP4 and SPRY4 expression by MAPK inhibition is most likely a direct result of the MAPK inhibition rather than result from the up-regulation of NANOG expression. JAM2 is expressed in both embryonic and adult stem cell lines  and its expression is enhanced in undifferentiated mouse ES cells compared to early stages of differentiation. Since mouse ES cells that genetically lack Jam2 maintain pluripotency however, the function of JAM2 in stem cells remains unknown . In mouse Sertoli cells inhibition of ERK activity did not affect Jam2 transcription , suggesting that the observed reduced JAM2 expression resulted from increased NANOG levels. Interestingly, JAM2 expression was also down-regulated after OCT4 had been exogenously introduced into human cells, suggesting that low levels of JAM2 induce or indicate differentiation . In our bovine ICMs POU5F1 expression was however not significantly up-regulated after enhanced NANOG expression. Surprisingly, no other genes that had been identified as overlapping NANOG putative targets in mouse and human ES cells  appeared to be up- or down-regulated in bovine ICMs with enhanced NANOG expression.
Apart from the core pluripotency markers NANOG, SOX2 and OCT4, other transcription factors are reported to be involved in mouse or human pluripotency. Of all transcription factors differentially expressed between ICM and TE, OTX2 ranked third and was 7.2-fold higher expressed in ICM. In mouse ES cells OTX2 was reported to be required for the transition to a stable epiblast stem cell condition . Recently, it was shown that OTX2 is one of the earliest transcription factors to be activated during exit from a naïve ground state in mES cells . Although the MAPK pathway is important in cell differentiation  and therefore might influence OTX2 expression we did not detect a difference in OTX2 expression in the PD treated bovine ICMs. Together, these findings suggest that the ICMs under investigation were already in a “primed” state.
Transcription factors involved in the LIF or BMP pathway were also amongst the genes with up-regulated expression levels in the ICM. Although BMP4 was not differentially expressed, STAT3 (2.5-fold), ID3 (2.7-fold) and ID1 (6.7-fold) were expressed at higher levels in ICM than in TE. STAT3 is capable of suppressing mesoderm and endoderm commitment whereas ID genes suppress neuroectoderm commitment in mES cells. Fibronectin, with expression levels almost 4-fold higher in ICM, can induce Id expression and also NANOG is capable of activating STAT3 and inducing ID genes . Up-regulated NANOG expression did however not induce STAT3 or ID expression in MAPK inhibited ICMs. Although the level of expression might not be high enough, the increased expression of STAT3, ID1 and ID3 suggests that, although in a primed state, differentiation is not initiated yet in the bovine day 9 ICMs.
The transcription factor PRDM14 is implicated to act as a safeguard for maintaining pluripotency  and is uniquely expressed in mouse compacted morula, ICM, the early epiblast, primordial germ cells and ES cells [66-68]. Indeed, the expression of PRDM14 was found to be up-regulated in bovine morulae compared to blastocysts (2.4-fold; p = 0.00097) and ICM versus TE (2.5-fold; p = 0.0015). It has been reported that in mouse ES cells PRDM14 attenuates FGF-induced differentiation . We did however not observe a difference in levels of PRDM14 expression in MAPK-inhibited ICMs (1.07 fold difference; p = 0.87), suggesting that the FGF- or MAPK-signalling pathways do not repress PRDM14 expression in bovine pluripotent cells. Expression of the ZIC gene family members ZIC2 and ZIC3 was also up-regulated in the ICM (4.3-fold and 2.2-fold, respectively). Zic2 and its orthologues are expressed in frog  and zebrafish , pregastrulation embryos and in mouse E0.5 and ICM of E4.5 embryos . Zic3 is implicated to play an important role in maintaining pluripotency in mouse ES cells  and contains OCT4, NANOG and SOX2 binding sites [34,51]. Indeed, after increased NANOG expression by MAPK inhibition ZIC3 expression increases 1.5 fold (p = 0.038) but ZIC2 expression decreased 2.2-fold (p > 0.05). Other reported genes to safeguard pluripotency such as PARP1 and PARP7  were expressed at higher levels in morula than in blastocyst (PARP7), did not show a differential expression between ICM and TE and were not differentially expressed after MAPK inhibition. All together, these findings indicate that, despite the increased ZIC3 and NANOG expression, MAPK inhibition by PD0325901 is insufficient to maintain a pluripotent state in bovine ICM cells.
We have identified whole genome expression profiles of different stages of bovine embryos and TE and the pluripotent ICM of blastocysts. In addition, the transcriptome of ICMs with enhanced NANOG expression after inhibition of MAPK activity was established. Unfortunately, these expression profiles did not lead to (new) pathways or indications how to maintain pluripotency and possibly generate genuine bovine ES cells. Furthermore, it became apparent that although MAPK inhibition increased NANOG and ZIC3 expression, this is insufficient to maintain pluripotency. Comparing transcription factor expression in the bovine ICMs used in the microarray with known expressions in mouse pluripotent cells indicates a “primed” or epiblast state. Therefore, the data presented in this paper can act as a starting point for further research on bovine pluripotency.
Bovine in vitro embryo culture and mechanical separation
Bovine embryo culture was performed at 39°C in a humidified atmosphere with 5% CO2, unless stated otherwise. Three to eight mm follicles of ovaries, obtained from a local slaughterhouse, were aspirated to retrieve COCs. Groups of 35–60 COCs were incubated for 23 hrs in 500 μl M199 (Life Technologies, Bleiswijk, The Netherlands) supplemented with 0.05 IU/ml recombinant hFSH (Organon, Oss, The Netherlands) and with 1% (v/v) penicillin-streptomycin (Life Technologies). Fertilization was performed as described previously  with modifications as described . In short, matured COCs were transferred to fertilization medium (Fert-TALP) supplemented with heparin at a final concentration of 10 μg/ml (Sigma-Aldrich, Zwijndrecht, The Netherlands), 20 μM D-penicillamine (Sigma-Aldrich), 10 μM hypotaurine (Sigma-Aldrich), and 1 μM epinephrine (Sigma-Aldrich). Frozen-thawed sperm from a bull with proven fertility was centrifuged over a Percoll-gradient (GE Healthcare Europe GmbH, Eindhoven, The Netherlands) and added to the COCs at a final concentration of 1.0 × 106 spermatozoa/ml. Fertilization day was considered as day 0. After incubation for 20 hrs the COCs were denuded by vortexing for 3 min and the cumulus-free oocytes were placed in synthetic oviduct fluid (SOF) medium. The presumptive zygotes were incubated at 39°C in a humidified atmosphere with 7% O2 and 5% CO2. At day 5 either morulae were collected or embryos were transferred to fresh SOF medium, cultured to blastocyst stage embryos and collected on day 9. Embryos were cultured until day 9 of development as this resulted in a higher percentage of hatching and hatched blastocysts [30,76,77], which facilitated ICM from TE separation. To ensure good quality embryos only stage code 7–9 blastocysts with quality code 1 or 2, according to the IETS manual, were collected [78,79]. To obtain ICMs containing a higher percentage of NANOG-expressing cells, SOF medium was supplemented with a final concentration of 0.5 μM PD0325901 (Stemgent, Cambridge, MA, USA) at day 5. Embryo culture for control ICM samples was performed with equal concentrations of the solvent DMSO.
Blastocysts collected to obtain inner cell mass and trophectoderm were placed in wash buffer containing 6.67 mg/ml NaCl (Merck, Schiphol-Rijk, The Netherlands), 0.24 mg/ml KCl (Merck), 0.168 mg/ml NaHCO3 (Sigma-Aldrich), 0.047 mg/ml NaH2PO4 (Merck), 0.217% (v/v) of a 60% sodium lactate solution (Sigma-Aldrich), 2.38 mg/ml HEPES (Sigma-Aldrich), 0.2% (v/v) phenolred (Sigma-Aldrich), 0.39 mg/ml CaCl2 · 2H2O (Sigma-Aldrich), 0.10 mg/ml MgCl2 · 6H2O (Merck), 0.11 mg/ml sodium pyruvate, 100U/ml Penicillin-Streptomycin (Life Technologies) and 6.0 mg/ml bovine serum albumin fraction 5 (MP Biomedicals, Santa Ana, CA, USA), set at an osmolality of 280 osmol/kg and adjusted to pH 7.3.
Sharpened tungsten needles were used to manually separate the trophectoderm from the ICM. This procedure was performed in wash medium under a stereo microscope.
Collected cells and embryos were harvested per tissue type or treatment and stored in 100 μl extraction buffer (Life Technologies) at −80°C until RNA isolation. RNA isolation and on column DNA digestion (Qiagen, Venlo, The Netherlands) was performed using the PicoPure® RNA isolation kit (Life Technologies) according to the manufacturer’s protocol. Total RNA quality and quantity assessment was performed by micro-electrophoresis on a Bioanalyzer 2100 using the RNA 6000 Pico LabChip kit (Agilent Technologies, Amstelveen, The Netherlands) according to manufacturer’s instructions. RNA was stored at −80°C until further use.
Microarray gene expression analysis
Selected total RNA samples were compared in a common reference experiment design using 12 dual channel microarrays (8 for the stage-/cell-specific microarray and 4 for the ERK-inhibition microarray) with each sample hybridized against an identical common reference total RNA sample consisting of a pool of blastocysts total RNA. Within each group of two microarrays for each stage/tissue type/treatment, sample versus common reference hybridizations were performed in balanced dye-swap.
Microarrays used were bovine whole genome gene expression microarrays V2 (Agilent Technologies) representing 43,653 Bos taurus 60-mer oligos in a 4x44K layout.
cDNA synthesis, cRNA double amplification, labelling, quantification, quality control and fragmentation were performed with an automated system (Caliper Life Sciences NV/SA, Teralfene, Belgium), starting with 10–20 ng total RNA from each sample, all as previously described in detail [80,81]. Microarray hybridization and washing was with an HS4800PRO system with QuadChambers (Tecan, Mechelen, Belgie) using 700 ng, 1-2% Cy5/Cy3 labelled cRNA per channel as described . Slides were scanned on an Agilent G2565BA scanner at 100% laser power, 30% PMT. After automated data extraction using Imagene 8.0 (BioDiscovery, Hawthorne, CA, USA), Loess normalization was performed  on mean spot-intensities. Gene-specific dye bias was corrected by a within-set estimate . Data were further analysed by MAANOVA , modelling sample, array and dye effects in a fixed effect analysis. P-values were determined by a permutation F2-test, in which residuals were shuffled 10000 times globally. Gene probes with p < 0.05 after false discovery rate determination (FDR by Benjamini-Hochberg) were considered significantly changed. In cases of multiple probes per gene, the values from the most 3′ probe were used [27,28]. To determine differentially expressed genes a fold change cut-off of 2 fold was used. All microarray gene expression data have been deposited in NCBI’s Gene Expression Omnibus  and are accessible through GEO Series accession number GSE63054 .
Quantitative reverse transcription-PCR
RNA was converted to cDNA using the iScript™ cDNA Synthesis Kit (BioRad, Veenendaal, The Netherlands) according to manufacturer’s instructions. Primers (Life Technologies; Additional file 2: Table S8) for specific Bos taurus mRNA templates  were designed using a Primer3 based platform . Further in silico validation was performed by predicting PCR product folding structures using the Mfold web server [89-91]. For quantitative reverse transcription PCR (qRT-PCR) we used iQ™ SYBR® Green supermix on a MyiQ detection system (Biorad) in a 25 μl reaction volume with a final primer concentration of 400nM according to manufacturer’s instructions. To confirm specificity of primer pairs and establish melting temperatures (Tm) a temperature gradient was performed ranging from 57.0°C – 65.3°C using a 4 times dilution series of cDNA from blastocyst samples. Reactions started with a 5 min enzyme activation cycle at 95°C continued with 45 cycles in which the first step was 20 sec denaturing at 95°C, followed by 30 sec at Tm (Additional file 2: Table S8) for annealing and the third step for 30 sec at 72°C for elongation. To generate a dissociation curve the reaction continued by increasing the temperature from 60°C to 98°C per 0.5°C for 15 sec each step. For expression analysis of the individual samples the primer specific optimal Tm was chosen (Additional file 2: Table S8) and the dissociation curve was generated with 1°C temperature increments per step until 98°C.
ICM, TE and blastocyst samples were collected and fixed in 4% paraformaldehyde (PFA) for 15 min and stored in 1% PFA at 4°C until further use. Samples were permeabilized in PBS + 10%FCS + 0.5% Triton X100 (Sigma Aldrich) for 30 min. Next, a-specific binding was blocked by incubating the samples in PBS + 10% FCS + 0.1% Triton X100 (PBST) for 1 hour before overnight incubation with primary antibodies rabbit anti-GATA6 (Santa Cruz;sc-9055;1:100), mouse anti-CDX2 (Biogenex; CDX2-88; 1:200) or mouse anti-NANOG (eBiosciences; 14-5768-82;1:250) at 4°C. Secondary antibody incubation for 1 hour with appropriate goat anti mouse Alexa647 or goat anti rabbit Alexa 488 dye (Invitrogen, Venlo, The Netherlands) and subsequent nuclear staining using DAPI (Sigma Aldrich) for 5 min preceded Vectashield (Brunschwig Chemie, Amsterdam, The Netherlands) mounting in Grace Bio-Labs SecureSeal™ imaging spacer (Sigma-Aldrich). All incubations were performed at room temperature unless stated otherwise.
Fluorescent images were obtained using an inverted semi-automated confocal microscope (SPE-II – DMI4000; Leica, Son, The Netherlands) and further analysed with Fiji software .
The authors would like to thank Prof. Dr. Frank C.P. Holstege for suggestions on the micro-array analysis. Christine Oei is thanked for help in sample collection. Richard Wubbolts and Esther van ‘t Veld are thanked for their instructions and help with the confocal imaging. Kaveh Mashayekhi is funded by AniStem, Industry-Academia Partnerships and Pathways (IAPP), Project number: PIAPP-GA-2011-286264. Bas Brinkhof is funded by the Dutch Ministry of Economic Affairs.
- Plusa B, Piliszek A, Frankenberg S, Artus J, Hadjantonakis AK. Distinct sequential cell behaviours direct primitive endoderm formation in the mouse blastocyst. Development. 2008;135(18):3081–91.View ArticlePubMed CentralPubMedGoogle Scholar
- Chazaud C, Yamanaka Y, Pawson T, Rossant J. Early lineage segregation between epiblast and primitive endoderm in mouse blastocysts through the Grb2-MAPK pathway. Dev Cell. 2006;10(5):615–24.View ArticlePubMedGoogle Scholar
- Tanaka S, Kunath T, Hadjantonakis AK, Nagy A, Rossant J. Promotion to trophoblast stem cell proliferation by FGF4. Science. 1998;282(5396):2072–5.View ArticlePubMedGoogle Scholar
- Ralston A, Rossant J. Genetic regulation of stem cell origins in the mouse embryo. Clin Genet. 2005;68(2):106–12.View ArticlePubMedGoogle Scholar
- Strumpf D, Mao C, Yamanaka Y, Ralston A, Chawengsaksophak K, Beck F, et al. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development. 2005;132(9):2093–102.View ArticlePubMedGoogle Scholar
- Wallingford MC, Angelo JR, Mager J. Morphogenetic analysis of peri-implantation development. Dev Dyn. 2013;242(9):1110–20.View ArticlePubMedGoogle Scholar
- Zernicka-Goetz M, Morris SA, Bruce AW. Making a firm decision: Multifaceted regulation of cell fate in the early mouse embryo. Nat Rev Gen. 2009;10(7):467–77.View ArticleGoogle Scholar
- Kurosaka S, Eckardt S, McLaughlin KJ. Pluripotent lineage definition in bovine embryos by Oct4 transcript localization. Biol Reprod. 2004;71(5):1578–82.View ArticlePubMedGoogle Scholar
- Berg DK, Smith CS, Pearton DJ, Wells DN, Broadhurst R, Donnison M, et al. Trophectoderm lineage determination in cattle. Dev Cell. 2011;20(2):244–55.View ArticlePubMedGoogle Scholar
- Nichols J, Smith A. Naive and Primed Pluripotent States. Cell Stem Cell. 2009;4(6):487–92.View ArticlePubMedGoogle Scholar
- Yamanaka Y, Lanner F, Rossant J. FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst. Development. 2010;137(5):715–24.View ArticlePubMedGoogle Scholar
- Schrode N, Saiz N, Di Talia S, Hadjantonakis AK. GATA6 levels modulate primitive endoderm cell fate choice and timing in the mouse blastocyst. Dev Cell. 2014;29(4):454–67.View ArticlePubMedGoogle Scholar
- Kuijk EW, van Tol LTA, Van de Velde H, Wubbolts R, Welling M, Geijsen N, et al. The roles of FGF and MAP kinase signaling in the segregation of the epiblast and hypoblast cell lineages in bovine and human embryos. Development. 2012;139(5):871–82.View ArticlePubMed CentralPubMedGoogle Scholar
- Van Der Jeught M, O’Leary T, Ghimire S, Lierman S, Duggal G, Versieren K, et al. The combination of inhibitors of FGF/MEK/Erk and GSK3ß signaling increases the number of OCT3/4-and NANOG-positive cells in the human inner cell mass, but does not improve stem cell derivation. Stem Cells Dev. 2013;22(2):296–306.View ArticlePubMed CentralPubMedGoogle Scholar
- Roode M, Blair K, Snell P, Elder K, Marchant S, Smith A, et al. Human hypoblast formation is not dependent on FGF signalling. Dev Biol. 2012;361(2):358–63.View ArticlePubMed CentralPubMedGoogle Scholar
- Evans MJ, Kaufman MH. Establishment in culture of pluripotential cells from mouse embryos. Nature. 1981;292(5819):154–6.View ArticlePubMedGoogle Scholar
- Martin GR. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc Natl Acad Sci U S A. 1981;78(12):7634–8.View ArticlePubMed CentralPubMedGoogle Scholar
- Thomson JA, Kalishman J, Golos TG, Durning M, Harris CP, Becker RA, et al. Isolation of a primate embryonic stem cell line. Proc Natl Acad Sci U S A. 1995;92(17):7844–8.View ArticlePubMed CentralPubMedGoogle Scholar
- Thomson JA, Itskovitz-Eldor J, Shapiro SS, Waknitz MA, Swiergiel JJ, Marshall VS, et al. Embryonic stem cell lines derived from human blastocysts. Science. 1998;282(5391):1145–7.View ArticlePubMedGoogle Scholar
- Buehr M, Meek S, Blair K, Yang J, Ure J, Silva J, et al. Capture of authentic embryonic stem cells from rat blastocysts. Cell. 2008;135(7):1287–98.View ArticlePubMedGoogle Scholar
- Hackett JA, Surani MA. Regulatory principles of pluripotency: from the ground state up. Cell Stem Cell. 2014;15(4):416–30.View ArticlePubMedGoogle Scholar
- Telugu BPVL, Ezashi T, Roberts RM. The promise of stem cell research in pigs and other ungulate species. Stem Cell Rev Rep. 2010;6(1):31–41.View ArticleGoogle Scholar
- Tanaka TS, Kunath T, Kimber WL, Jaradat SA, Stagg CA, Usuda M, et al. Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity. Genome Res. 2002;12(12):1921–8.View ArticlePubMed CentralPubMedGoogle Scholar
- Hamatani T, Daikoku T, Wang H, Matsumoto H, Carter MG, Ko MSH, et al. Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proc Natl Acad Sci U S A. 2004;101(28):10326–31.View ArticlePubMed CentralPubMedGoogle Scholar
- Auer H, Lyianarachchi S, Newsom D, Klisovic M, Marcucci G, Kornacker K. Chipping away at the chip bias: RNA degradation in microarray analysis. Nat Genet. 2003;35(4):292–3.View ArticlePubMedGoogle Scholar
- Eklund AC, Szallasi Z. Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biol. 2008;9(2):R26.View ArticlePubMed CentralPubMedGoogle Scholar
- Shi L. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotech. 2006;24(9):1151–61.View ArticleGoogle Scholar
- Li Q, Birkbak N, Gyorffy B, Szallasi Z, Eklund A. Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics. 2011;12(1):474.View ArticlePubMed CentralPubMedGoogle Scholar
- Xie D, Chen C, Ptaszek LM, Xiao S, Cao X, Fang F, et al. Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species. Genome Res. 2010;20(6):804–15.View ArticlePubMed CentralPubMedGoogle Scholar
- Madeja Z, Sosnowski J, Hryniewicz K, Warzych E, Pawlak P, Rozwadowska N, et al. Changes in sub-cellular localisation of trophoblast and inner cell mass specific transcription factors during bovine preimplantation development. BMC Dev Biol. 2013;13(1):32.View ArticlePubMed CentralPubMedGoogle Scholar
- Khan DR, Dubé D, Gall L, Peynot N, Ruffini S, Laffont L, et al. Expression of Pluripotency Master Regulators during Two Key Developmental Transitions: EGA and Early Lineage Specification in the Bovine Embryo. PLoS One. 2012;7(3):e34110.View ArticlePubMed CentralPubMedGoogle Scholar
- Ozawa M, Sakatani M, Yao J, Shanker S, Yu F, Yamashita R, et al. Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst. BMC Dev Biol. 2012;12(1):33.View ArticlePubMed CentralPubMedGoogle Scholar
- Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010;38 suppl 2:W64–70.View ArticlePubMed CentralPubMedGoogle Scholar
- Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005;122(6):947–56.View ArticlePubMed CentralPubMedGoogle Scholar
- Ying Q, Wray J, Nichols J, Batlle-Morera L, Doble B, Woodgett J, et al. The ground state of embryonic stem cell self-renewal. Nature. 2008;453(7194):519–23.View ArticlePubMedGoogle Scholar
- Veltmaat JM, Orelio CC, Ward-Van Oostwaard D, Van Rooijen MA, Mummery CL, Defize LHK. Snail is an immediate early target gene of parathyroid hormone related peptide signaling in parietal endoderm formation. Int J Dev Biol. 2000;44(3):297–307.PubMedGoogle Scholar
- Sumer H, Liu J, Malaver-Ortega LF, Lim ML, Khodadadi K, Verma PJ. NANOG is a key factor for induction of pluripotency in bovine adult fibroblasts. J Anim Sci. 2011;89(9):2708–16.View ArticlePubMedGoogle Scholar
- Nagatomo H, Kagawa S, Kishi Y, Takuma T, Sada A, Yamanaka K, et al. Transcriptional wiring for establishing cell lineage specification at the blastocyst stage in Cattle1. Biol Reprod. 2013;88(6):158.View ArticlePubMedGoogle Scholar
- Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009;10(4):R42.View ArticlePubMed CentralPubMedGoogle Scholar
- Kues WA, Sudheer S, Herrmann D, Carnwath JW, Havlicek V, Besenfelder U, et al. Genome-wide expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation development in vivo. Proc Natl Acad Sci U S A. 2008;105(50):19768–73.View ArticlePubMed CentralPubMedGoogle Scholar
- Sirard MA. Factors affecting oocyte and embryo transcriptomes. Reprod Domest Anim. 2012;47(Suppl4):148–55.View ArticlePubMedGoogle Scholar
- Graf A, Krebs S, Heininen-Brown M, Zakhartchenko V, Blum H, Wolf E. Genome activation in bovine embryos: Review of the literature and new insights from RNA sequencing experiments. Anim Reprod Sci. 2014;149(1–2):46–58.View ArticlePubMedGoogle Scholar
- Loh KM, Lim B. A precarious balance: pluripotency factors as lineage specifiers. Cell Stem Cell. 2011;8(4):363–9.View ArticlePubMedGoogle Scholar
- Wang Z, Oron E, Nelson B, Razis S, Ivanova N. Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells. Cell Stem Cell. 2012;10(4):440–54.View ArticlePubMedGoogle Scholar
- Jaenisch R, Young R. Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming. Cell. 2008;132(4):567–82.View ArticlePubMed CentralPubMedGoogle Scholar
- Sakurai T, Sakamoto A, Muroi Y, Bai H, Nagaoka K, Tamura K, et al. Induction of endogenous interferon tau gene transcription by CDX2 and high acetylation in bovine nontrophoblast cells. Biol Reprod. 2009;80(6):1223–31.View ArticlePubMedGoogle Scholar
- Ezashi T, Ghosh D, Roberts RM. Repression of Ets-2-induced transactivation of the tau interferon promoter by Oct-4. Mol Cell Biol. 2001;21(23):7883–91.View ArticlePubMed CentralPubMedGoogle Scholar
- Johnson KM, Alvarez X, Borkhsenious ON, Kubisch HM. Nuclear and cytoplasmic localization of interferon-t in in vitro-produced bovine blastocysts. Reprod Nutr Dev. 2006;46(1):97–104.View ArticlePubMedGoogle Scholar
- Roberts RM. Interferon-tau, a Type 1 interferon involved in maternal recognition of pregnancy. Cytokine Growth Factor Rev. 2007;18(5–6):403–8.View ArticlePubMedGoogle Scholar
- Imakawa K, Kim MS, Matsuda-Minehata F, Ishida S, Iizuka M, Suzuki M, et al. Regulation of the ovine interferon-tau gene by a blastocyst-specific transcription factor, Cdx2. Mol Reprod Dev. 2006;73(5):559–67.View ArticlePubMedGoogle Scholar
- Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet. 2006;38(4):431–40.View ArticlePubMedGoogle Scholar
- D’Souza WN, Chang CF, Fischer AM, Li M, Hedrick SM. The Erk2 MAPK regulates CD8 T cell proliferation and survival. J Immunol. 2008;181(11):7617–29.View ArticlePubMed CentralPubMedGoogle Scholar
- Wilkinson B, Kaye J. Requirement for sustained MAPK signaling in both CD4 and CD8 lineage commitment: A threshold model. Cell Immunol. 2001;211(2):86–95.View ArticlePubMedGoogle Scholar
- Kondoh K, Nishida E. Regulation of MAP kinases by MAP kinase phosphatases. Biochim Biophys Acta Mol Cell Res. 2007;1773(8):1227–37.View ArticleGoogle Scholar
- Chu Y, Solski PA, Khosravi-Far R, Der CJ, Kelly K. The mitogen-activated protein kinase phosphatases PAC1, MKP-1, and MKP-2 have unique substrate specificities and reduced activity in vivo toward the ERK2 sevenmaker mutation. J Biol Chem. 1996;271(11):6497–501.View ArticlePubMedGoogle Scholar
- Casci T, Vinós J, Freeman M. Sprouty, an intracellular inhibitor of Ras signaling. Cell. 1999;96(5):655–65.View ArticlePubMedGoogle Scholar
- Fürthauer M, Reifers F, Brand M, Thisse B, Thisse C. Sprouty4 acts in vivo as a feedback-induced antagonist of FGF signaling in zebrafish. Development. 2001;128(12):2175–86.PubMedGoogle Scholar
- Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, Lemischka IR. A stem cell molecular signature. Science. 2002;298(5593):601–4.View ArticlePubMedGoogle Scholar
- Sakaguchi T, Nishimoto M, Miyagi S, Iwama A, Morita Y, Iwamori N, et al. Putative “stemness” gene Jam-B is not required for maintenance of stem cell state in embryonic, neural, or hematopoietic stem cells. Mol Cell Biol. 2006;26(17):6557–70.View ArticlePubMed CentralPubMedGoogle Scholar
- Wang Y, Lui WY. Opposite effects of interleukin-1a and transforming growth factor-ß2 induce stage-specific regulation of junctional adhesion molecule-B gene in sertoli cells. Endocrinology. 2009;150(5):2404–12.View ArticlePubMedGoogle Scholar
- Kim JH, Jee MK, Lee SY, Han TH, Kim BSBS, Kang KS, et al. Regulation of adipose tissue stromal cells behaviors by endogenic Oct4 expression control. PLoS One. 2009;4(9):e7166.View ArticlePubMed CentralPubMedGoogle Scholar
- Acampora D, Di Giovannantonio LG, Simeone A. Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition. Development. 2013;140(1):43–55.View ArticlePubMedGoogle Scholar
- Yang SH, Kalkan T, Morissroe C, Marks H, Stunnenberg H, Smith A, et al. Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency. Cell Rep. 2014;7(6):1968–81.View ArticlePubMed CentralPubMedGoogle Scholar
- Ying QL, Nichols J, Chambers I, Smith A. BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell. 2003;115(3):281–92.View ArticlePubMedGoogle Scholar
- Ma Z, Swigut T, Valouev A, Rada-Iglesias A, Wysocka J. Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates. Nat Struct Mol Biol. 2011;18(2):120–8.View ArticlePubMedGoogle Scholar
- Yamaji M, Seki Y, Kurimoto K, Yabuta Y, Yuasa M, Shigeta M, et al. Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat Genet. 2008;40(8):1016–22.View ArticlePubMedGoogle Scholar
- Kurimoto K, Yabuta Y, Ohinata Y, Ono Y, Uno KD, Yamada RG, et al. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res. 2006;34(5):e42.View ArticlePubMed CentralPubMedGoogle Scholar
- Grabole N, Tischler J, Hackett JA, Kim S, Tang F, Leitch HG, et al. Prdm14 promotes germline fate and naive pluripotency by repressing FGF signalling and DNA methylation. EMBO Rep. 2013;14(7):629–37.View ArticlePubMed CentralPubMedGoogle Scholar
- Kuo JS, Patel M, Gamse J, Merzdorf C, Liu X, Apekin V, et al. opl: A zinc finger protein that regulates neural determination and patterning in Xenopus. Development. 1998;125(15):2867–82.PubMedGoogle Scholar
- Grinblat Y, Sive H. zic gene expression marks anteroposterior pattern in the presumptive neurectoderm of the zebrafish gastrula. Dev Dyn. 2001;222(4):688–93.View ArticlePubMedGoogle Scholar
- Brown L, Brown S. Zic2 is expressed in pluripotent cells in the blastocyst and adult brain expression overlaps with makers of neurogenesis. Gene Expr Patterns. 2009;9(1):43–9.View ArticlePubMedGoogle Scholar
- Lim LS, Loh YH, Zhang W, Li Y, Chen X, Wang Y, et al. Zic3 is required for maintenance of pluripotency in embryonic stem cells. Mol Biol Cell. 2007;18(4):1348–58.View ArticlePubMed CentralPubMedGoogle Scholar
- Roper SJ, Chrysanthou S, Senner CE, Sienerth A, Gnan S, Murray A, et al. ADP-ribosyltransferases Parp1 and Parp7 safeguard pluripotency of ES cells. Nucleic Acids Res. 2014;42(14):8914–27.View ArticlePubMed CentralPubMedGoogle Scholar
- Parrish JJ, Susko-Parrish J, Winer MA, First NL. Capacitation of bovine sperm by heparin. Biol Reprod. 1988;38(5):1171–80.View ArticlePubMedGoogle Scholar
- Izadyar F, Colenbrander B, Bevers MM. In vitro maturation of bovine oocytes in the presence of growth hormone accelerates nuclear maturation and promotes subsequent embryonic development. Mol Reprod Dev. 1996;45(3):372–7.View ArticlePubMedGoogle Scholar
- Rizos D, Gutiérrez-Adán A, Pérez-Garnelo S, De la Fuente J, Boland MP, Lonergan P. Bovine embryo culture in the presence or absence of serum: Implications for blastocyst development, cryotolerance, and messenger RNA expression. Biol Reprod. 2003;68(1):236–43.View ArticlePubMedGoogle Scholar
- Nicacio AC, Simõs R, De Paula-Lopes FF, De Barros FRO, Peres MA, Assumpção MEOD, et al. Effects of different cryopreservation methods on post-thaw culture conditions of in vitro produced bovine embryos. Zygote. 2012;20(2):117–22.View ArticlePubMedGoogle Scholar
- Stringfellow DA, Givens MD. A procedural guide and general information for the use of embryo transfer technology emphasizing sanitary procedures. In: Manual of the International Embryo Transfer Society, editor. International Embryo Transfer Manual. 4th ed. Savoy, IL, USA: IETS Publish; 2009. p. 151.Google Scholar
- Bó GA, Mapletoft RJ. Evaluation and classification of bovine embryos. Anim Reprod. 2013;10(3):344–8.Google Scholar
- van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, et al. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell. 2010;143(6):991–1004.View ArticlePubMed CentralPubMedGoogle Scholar
- Roepman P, de Koning E, van Leenen D, de Weger R, Kummer JA, Slootweg P, et al. Dissection of a metastatic gene expression signature into distinct components. Genome Biol. 2006;7(12):1–12.View ArticleGoogle Scholar
- Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002;30(4):e15.View ArticlePubMed CentralPubMedGoogle Scholar
- Margaritis T, Lijnzaad P, van Leenen D, Bouwmeester D, Kemmeren P, van Hooff SR, et al. Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays. Mol Syst Biol. 2009;5(1):266.PubMed CentralPubMedGoogle Scholar
- Wu H, Kerr MK, Cui X, Churchill G. MAANOVA: A Software Package for the Analysis of Spotted cDNA Microarray Experiments. In: Parmigiani G, Garrett E, Irizarry R, Zeger S, editors. The analysis of gene expression data: methods and software. New York: Springer; 2003. p. 313–41.View ArticleGoogle Scholar
- Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207–10.View ArticlePubMed CentralPubMedGoogle Scholar
- GSE63054 is the reference Series for your publication [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63054]
- Genbank [http://www.ncbi.nlm.nih.gov/nucleotide/]
- Primer-Blast [http://www.ncbi.nlm.nih.gov/tools/primer-blast/]
- SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998;95(4):1460–5.View ArticlePubMed CentralPubMedGoogle Scholar
- Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–15.View ArticlePubMed CentralPubMedGoogle Scholar
- Mfold [http://mfold.rit.albany.edu/?q=mfold/DNA-Folding-Form]
- Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: An open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676–82.View ArticlePubMedGoogle Scholar
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