Single-cell duplex RT-LATE-PCR reveals Oct4 and XistRNA gradients in 8-cell embryos
© Hartshorn et al; licensee BioMed Central Ltd. 2007
Received: 13 March 2007
Accepted: 07 December 2007
Published: 07 December 2007
The formation of two distinctive cell lineages in preimplantation mouse embryos is characterized by differential gene expression. The cells of the inner cell mass are pluripotent and express high levels of Oct4 mRNA, which is down-regulated in the surrounding trophectoderm. In contrast, the trophectoderm of female embryos contains Xist mRNA, which is absent from cells of the inner mass. Prior to blastocyst formation, all blastomeres of female embryos still express both of these RNAs. We, thus, postulated that simultaneous quantification of Oct4 and Xist transcripts in individual blastomeres at the 8-cell stage could be informative as to their subsequent fate. Testing this hypothesis, however, presented numerous technical challenges. We overcame these difficulties by combining PurAmp, a single-tube method for RNA preparation and quantification, with LATE-PCR, an advanced form of asymmetric PCR.
We constructed a duplex RT-LATE-PCR assay for real-time measurement of Oct4 and Xist templates and confirmed its specificity and quantitative accuracy with different methods. We then undertook analysis of sets of blastomeres isolated from embryos at the 8-cell stage. At this stage, all cells in the embryo are still pluripotent and morphologically equivalent. Our results demonstrate, however, that both Oct4 and Xist RNA levels vary in individual blastomeres comprising the same embryo, with some cells having particularly elevated levels of either transcript. Analysis of multiple embryos also shows that Xist and Oct4 expression levels are not correlated at the 8-cell stage, although transcription of both genes is up-regulated at this time in development. In addition, comparison of data from males and females allowed us to determine that the efficiency of the Oct4/Xist assay is unaffected by sex-related differences in gene expression.
This paper describes the first example of multiplex RT-LATE-PCR and its utility, when combined with PurAmp sample preparation, for quantitative analysis of transcript levels in single cells. With this technique, copy numbers of different RNAs can be accurately measured independently from their relative abundance in a cell, a goal that cannot be achieved using symmetric PCR. The technique illustrated in this work is relevant to a wide array of applications, such as stem cell and cancer cell analysis and preimplantation genetic diagnostics.
Accurate quantification of multiple target sequences by real-time polymerase chain reaction (PCR) has been proven difficult to achieve, particularly for measuring numbers of RNA transcripts, rather than of DNA copies . In fact, while different gene sequences are represented in the genome in similar numbers (one or two copies, depending on the chromosomal location and the possible presence of mutations), transcript levels of different genes can vary widely. Moreover, changes in gene expression are often rapid and transient in response to stimuli, stress, or cellular events such as cell division and cell differentiation. In order to detect meaningful variations in transcript numbers it is, thus, necessary to measure them in series of single cells rather than in cell cohorts where individual differences could be lost to "background noise ." From all of the above considerations it follows that a convenient and reliable experimental approach, sensitive enough to measure RNA copy numbers in individual cells, is essential for multiplex quantification of gene expression in biological systems.
We have recently developed an entirely single-tube method to measure mRNA levels in individual cells ("PurAmp") . For that and a previous study  we co-amplified and simultaneously quantified RNA and DNA copies of the Xist and the Sry genes in mouse embryos and blastomeres. These two genes were chosen because they have sexually distinct patterns of expression in the early embryo. Female cells contain two copies of the Xist gene, one on each X-chromosome, and high levels of Xist transcripts but lack the Sry-bearing Y-chromosome, while cells from early-stage male embryos have a single unexpressed copy of the Xist gene on the X-chromosome and a single unexpressed copy of Sry on the Y-chromosome. Hence, only Xist templates (cDNA+ genomic DNA) were amplified from female samples, while male embryos always generated equal numbers of Xist and Sry amplicons.
In these studies we were, therefore, never faced with the more common and problematic situation of having to simultaneously quantify unequal amounts of different target sequences, a technical challenge of great general interest. In fact, conventional symmetric PCR is not easily utilized in this situation due to the exponential nature of the reaction. With this method, abundant templates generate amplicons much more rapidly than scarcer templates and the reaction is progressively shut down by these early-accumulating double-stranded molecules that sequester the DNA polymerase, and by a number of other factors . In the case of real-time PCR the fluorescent signal of the most abundant amplicon will reach its threshold cycle (or CT value, used to quantify template copy numbers ) and plateau unaffected by the presence of any other less represented template. Amplification of the less numerous templates, on the other hand, will be greatly hindered . Thus, low copy number templates will either go undetected or their abundance will be under-estimated based on their delayed CT values.
Linear-After-The-Exponential (LATE)-PCR, invented in our laboratory, provides a much more reliable strategy for the quantification of multiplexed templates. This approach combines the efficiency of exponential amplification in the very early phases of the reaction with the advantages of linear amplification [7, 8]. The switch between the exponential and the linear phases of LATE-PCR occurs at the CT, independently for each template, so that template quantification is achieved exactly as in symmetric PCR. After the CT is reached, a single strand of each amplicon continues to accumulate linearly and, thus, at a rate much slower than in symmetric PCR. This feature and the fact that single-stranded amplicons do not engage the polymerase ensure efficient amplification of abundant as well as rare templates in a sample. Moreover, single-stranded amplicons afford great flexibility for the design of specific probes because the probe is free to bind to the amplicon without having to compete with a complementary strand. Single-stranded LATE-PCR products can also be easily and directly sequenced to confirm their identity and purity ().
As reported here, the properties of LATE-PCR have enabled us to expand our earlier studies on differential gene expression in blastomeres of preimplantation mouse embryos [4, 10, 11]. We focus in particular on the 8-cell stage embryo prior to compaction, when individual blastomeres can still be dissected and collected with a limited amount of manipulation. This developmental stage immediately precedes the formation of an embryo comprised by inner and outer cells containing distinct sets of proteins in response to their different surroundings [12–14]. It is therefore plausible to hypothesize that differences in gene expression between blastomeres of early 8-cell embryos may presage subsequent cell fate and, thus, may identify the founders of the cell lineages established during the last phase of preimplantation, the blastocyst stage [15, 16].
Xist RNA is an untranslated transcript responsible for X-chromosome silencing and dosage compensation in female cells. Its expression precedes X-chromosome inactivation and Xist RNA is present in cleavage-stage embryonic blastomeres [17, 18]. In mouse blastocysts, Xist expression is paternally-imprinted; Xist RNA is restricted to the cells of the trophectoderm (TE) surrounding the embryo and destined to generate extraembryonic tissues such as the placenta, while it is almost absent from the pluripotent inner cell mass (ICM) that gives origin to the embryo proper [19, 20]. The gene for the transcription factor Oct4 presents a reciprocal expression pattern, being highly transcribed in the ICM and down-regulated in the TE [19, 21, 22]. Initial studies on cleaving embryos have shown that the Oct4 protein is ubiquitously present in the blastomeres starting at the 4-cell stage [21, 22], but cell-to-cell differences were not assessed. More recently, the importance of quantitative data has become increasingly clear because expression of the Oct4 gene (also previously indicated as Pou5f1or Oct3/4) is necessary to maintain cell pluripotency via a stringently dose-dependent regulatory process. Variations in Oct4 levels above or below the required dosage produce cellular differentiation  and usually consist in this gene's repression concomitant to activation of lineage- or tissue-specific genes [22, 24, 25]. Hence, cells maintaining critical amounts of Oct4 RNA during early development are candidate to be ICM precursors, while lower Oct4 RNA levels and elevated Xist expression may indicate a trophectodermal fate. We and others have already reported that blastomeres of mouse 8-cell embryos contain different amounts of Xist RNA [4, 26]. Non-quantitative analyses of human cleavage-stage blastomeres have also shown a variable distribution of Oct4 RNA [27, 28], but, for ethical reasons, the cells available for these studies are limited in number and quality. To more thoroughly address the question of cell lineage onset, in the present work we simultaneously measured Xist and Oct4 RNA levels in series of blastomeres from male and female mouse embryos at the 8-cell stage. The results presented in this paper are the first report of quantification of cDNA with LATE-PCR, and demonstrate the utility of this technique for gene expression studies, particularly at the single-cell level where multiplexing targets is highly desirable.
Specificity of the Oct4 LATE-PCR assay and identification of Oct4pseudogenes
As detailed elsewhere [3, 4, 10], our approach is to co-amplify both the cDNA and genomic DNA of each gene under study by designing PCR primers within one of the gene's exons. Single cells or embryos are lysed directly into a PCR tube and both DNA and RNA molecules are released and de-proteinized in the same, single vessel where reverse transcription (RT) and PCR are also carried out. This strategy optimizes the accuracy of quantification and offers three main advantages. First, it allows the use of genomic DNA for standardization, ensuring that PCR efficiency will be exactly the same for the standard and the samples analyzed. Second, it makes it possible to count DNA copy numbers in the absence of RT or in cells or embryos that do not express the gene of interest (such as Xist in male cells, see below). The presence of the genomic sequence in the sample tells us that the cell has been successfully transferred to the assay tube, even in the absence of RNA. This feature is also useful to identify RNase contamination problems if quantitative PCR analysis demonstrates the presence of the expected gene sequence but not of its transcripts. Third, co-amplification of genomic DNA and cDNA (representative of RNA) eliminates the need for DNase digestion, a step known to affect RNA recovery.
Construction of a quantitative Oct4 DNA-specific PCR assay presented a number of technical challenges because this gene is part of a highly homologous and conserved family of transcription factors . Oct4 appears to be the most actively transcribed gene of this group during early mammalian embryogenesis, decreasing the concern for non-specific amplification of homologous RNAs, although some Oct1 and Oct6 expression has also been reported [29–33]. At the DNA level, however, the concern remains, compounded by the high frequency of retrotransposition observed for embryonic stem cell-specific genes including Oct4 . Additionally, the Oct4 sequence is highly GC-rich, which favors secondary structure and requires very stringent parameters to ensure specific but efficient amplification, particularly when a second primer pair and two probes are introduced in a duplex reaction. By running a BLAST search we identified sequences highly homologous to Oct4 mRNA on mouse chromosome 1 (GenBank Accession Number AC126050.3) and chromosome 3 (GenBank Accession Number AC107368.11). The presence of these previously unreported pseudogenes was not surprising, based on similar findings in the human and bovine genomes [34, 35]. Based on this knowledge and avoiding sequences repeated in the mouse genome, we constructed an Oct4-specific LATE-PCR assay taking advantage of the flexibility that this technique affords for primer design . A longer, high Tm primer (the limiting primer) was designed from a very GC-rich sequence in order to include several nucleotides different from the most homologous pseudogene, while a shorter, lower Tm primer (the excess primer) could be selected in an area of the gene less homologous to other DNA sequences. (See Methods for details on the LATE-PCR assay and conditions.)
Validation of the Oct4RT-LATE-PCR assay in a biological system and by sequencing
As a next step, we separately analyzed Oct4 expression in each of the two lineages present in blastocyst stage embryos. Single TE cells or small groups of TE cells protruding from the zona pellucida in blastocysts that had initiated hatching could be removed from the embryo and were tested for their Oct4 RNA + DNA content. The green line in Fig. 1 shows the amplification plot obtained from a single TE cell after RT-PCR. This signal was converted to only four template copies, at least two of which are genomic DNA, consistent with the expected down-regulation of Oct4 expression in TE cells. The additional two copies may be residual Oct4 RNA or genomic DNA, if the TE cell had completed DNA duplication. We then measured Oct4 expression in ICMs extracted from blastocysts by immunosurgery. The ICM isolated from each blastocyst was divided in two aliquots, one processed by RT-PCR (blue line in the inset of Fig. 1) and one by PCR only (pink line in the inset of Fig. 1). Immunosurgery requires the use of embryos at the very early blastocyst stage; for this reason, the Oct4 RNA levels found in these ICMs cannot be directly compared to those measured in the mature blastocysts. However, the ΔCT between the pink and the blue line is larger for the isolated ICM (six cycles, inset of Fig. 1) than for the whole blastocysts (three cycles, Fig. 1), signaling the presence of a higher Oct4 RNA copy number per cell in the ICM. ICM cells comprise only about one-third of the blastocyst's cells, thus lower levels of Oct4 transcripts per cell in whole blastocysts than in isolated ICMs are consistent with the expected active Oct4 expression in the cells of the inner mass and down-regulation in the TE. Taken together, these quantitative data provided a validation of the specificity of our LATE-PCR assay in a known biological system.
We further confirmed by sequencing the specificity of the Oct4 amplicons generated from either "+RT" or "No RT" samples prepared from 8-cell embryos. As expected, both genomic DNA and cDNA amplicons had the same sequence, identical to that of the Oct4 gene at the designated amplification site (GenBank Accession Number AH003838). Sequencing of both the "+RT" and "No RT" amplicons confirmed that the nucleotide in position 312 of this sequence (segment 1) is a C, and not a T as reported in the Oct4 mRNA sequence that we had used to design the primers and the probe (GenBank Accession Number NM_013633, residue 140). Since neither primers nor probe included this residue, PCR results are unaffected.
Construction and optimization of a duplex LATE-PCR assay for simultaneous quantification of Oct4 and Xisttemplates
Oct4 and XistRNA + DNA measurements in series of blastomeres of male and female 8-cell embryos
Correlation analysis of Oct4 and XistRNA levels in series of blastomeres of female 8-cell embryos
Discussion and Conclusion
Investigators trying to develop assays for the accurate multiplex quantification of gene expression in small samples face many technical hurdles . We report here that the combination of single-tube PurAmp sample preparation and LATE-PCR offers a new and effective strategy to overcome these problems. It is now possible to simultaneously generate multiple amplicons with optimized efficiency, even when the initial numbers of target sequences differ by several orders of magnitude.
Oct4 RNA is present in all cleavage-stage blastomeres, while Xist RNA is present in hundreds of copies in female cells but is absent from male cells. The simultaneous measurement of these two transcripts in embryos of both sexes presents, therefore, a challenging situation, because it requires that one amplicon (Oct4) is reliably generated with equal efficiency and sensitivity in the absence as well as in the presence of high amounts of a second amplicon (Xist). In our study, Oct4 amplification was not affected by Xist co-amplification, as established by careful analysis of the slopes of the real-time plots generated by different concentrations of each template, a very sensitive diagnostic parameter of LATE-PCR. Furthermore, no significant differences were observed in the Oct4 RNA contents of male and female embryos, independently from the absence or presence of Xist RNA and even though, on average, male embryos develop to the 8-cell stage faster than female embryos [36–38]. Thus, LATE-PCR offers a highly advantageous alternative to other quantitative PCR-based strategies that require prior knowledge of the relative concentration of the different templates to be amplified and, hence, are suited to multiplexing of internal standards but cannot be utilized for unknown samples .
In addition, the plots generated during real-time LATE-PCR are linear and, therefore, the fluorescence intensities reached after a given number of cycles are proportional to the number of target sequences present at the beginning of the reaction. This feature of LATE-PCR and RT-LATE-PCR opens up the possibility of end-point quantification of multiple amplicons. Preliminary experiments carried out in this laboratory have already demonstrated the validity of this approach and we envision the future application of this technique to gene expression quantification.
The present study proves that cells comprising the same embryos contain markedly dissimilar levels of both Oct4 and Xist transcripts, an indication that 8-cell blastomeres are not equivalent in their developmental properties, in agreement with the hypothesis that lineage commitment in the mammalian embryo starts very early  and possibly at the time of fertilization . Quantification of differential expression of genes involved in development contributes to this hypothesis at a deeper level than possible with traditional non-quantitative techniques, such as fluorescence in situ hybridization (FISH), agarose gel electrophoresis and immunofluorescence. For example, gel analysis suggests that the presence of Oct4 RNA in human 8-cell embryos is limited to a subset of blastomeres , while this work demonstrates that each embryo is comprised by an assortment of low-to-high expressing cells. Although we cannot exclude species-specific differences, our findings support a "gradient" model of gene activation that can be reconciled with the well-known regulative capacity of the mammalian embryo [14, 40] more easily than an "on/off" model. In addition, analysis of newly-formed blastomeres, identified through two division cycles based on their surviving connections , reveals that these paired cells contain similar numbers of Oct4 transcripts, a situation comparable to the equal OCT4 status seen in daughter cell pairs of human embryonic stem cells . These data indicate that differences in Oct4 expression among 8-cell embryonic blastomeres are established sometimes after cell division and are probably regulated by a number of unknown factors. It is possible that cells that most actively transcribe Oct4 are initially fated to be the founders of the pluripotent ICM and germ cell lineages . In the case of stress, death or removal of these cells for genetic testing, however, Oct4 expression in other blastomeres could be up-regulated to levels adequate for the formation of a new pluripotent lineage, thus preserving the integrity of the developing embryo. A similar regulation pathway can be envisioned for the correct expression of Xist in the TE lineage, although the 8-cell stage may be too early for the full establishment of complementary expression patterns of these two genes in all cells comprising an embryo. It should also be kept in mind that, in spite of its advantages for monitoring embryonic development, the use of frozen-thawed or cultured embryos rather than ex vivo specimens may lead to some alteration in gene expression patterns, even though a recent, large-scale study indicates that expression levels at the 8-cell stage are almost unaffected by culture in vitro . (These data were obtained with mouse embryos and may differ for other species.)
Beyond the details of our particular experimental model, the achievement of reliably quantitative multiplex measurements of gene expression in single cells is meaningful for a wide variety of applications. For instance, the ability to identify blastomeres with specific developmental potential at the earliest possible stage would have great relevance for embryonic stem cells preparation [44, 45]. Quantification of the activation of Oct4 and other genes involved in maintaining pluripotency is a step necessary to reach this goal, as demonstrated by an increasing number of reports [23, 41, 46]. On the other hand, the advancing knowledge that 8-cell blastomeres are not developmentally equivalent as assumed in the past also carries implications for the practice of preimplantation genetic diagnostics, which requires the random resection of at least one blastomere from human embryos . Testing expression levels of specific genes in the ablated blastomeres may, however, offset the disadvantages of the procedure by providing additional information on the embryo's health, assuming that analysis of one blastomere was reliably representative for the entire embryo. Preliminary experiments in our laboratory indicate, for example, that transcription of the stress chaperone hsp70 is up-regulated in slow-growing embryos (Anshelevich A. et al., unpublished observations). A similar increased expression of heat shock protein 70 also occurs in microsatellite-unstable colorectal cancers and is correlated with prognosis . On a larger scale, epigenetic analyses of normal and tumor cells have recently revealed a wide array of changes in genetic activity in cells that have undergone cancerous transformation . Intensive work is under way to identify which of those changes could be most valuable for use as diagnostic tools. Improvements in the methods of multiplexed quantification of gene expression thus hold great promise also for this emerging field of studies, particularly when such methods are suitable for small-sample or single-cell analysis as the one described in this work.
Embryo culture and single blastomere collection
Embryos from B6C3F1 female mice bred with B6D2F1male mice were purchased frozen at the two-cell stage from Embryotech Laboratories, Inc. (Wilmington, MA) and cultured in GEM-PS medium (Duncan Holly, Bedford, MA) to the desired developmental stage, as described elsewhere [3, 4]. For most experiments, series of single blastomeres were harvested from individual 8-cell embryos following laser-zona drilling with a noncontact 1,480-nm diode laser beam (ZILOS-tkTM zona infrared laser optical system; Hamilton Thorne Biosciences, Inc., Beverly, MA). We have previously demonstrated the safety and reliability of this method for RNA recovery [3, 4, 11].
Single trophectodermal cells or small groups of TE cells were obtained from blastocysts that had just begun spontaneous hatching (no laser was used in this case). Repeated pipetting of these embryos up-and-down produced the release of individual cells that were protruding outside the zona. Only spherical, undamaged cells were used for gene expression analyses.
ICM isolation by immunosurgery
ICMs were prepared from early blastocysts as detailed by Eckert et al. with some modifications. The zona pellucida was removed with Acid Tyrode's Solution (Sigma Chemical Company, St. Louis, MO), pH 2.3, in glass bottom dishes. Blastocysts were allowed to recover for 20 min in Modified Human Tubal Fluid (HTF) Medium, Hepes-buffered (Irvine Scientific, Santa Ana, CA) containing 1 mg/ml embryo-grade bovine serum albumin (Sigma) (HTF-BSA) at 37°C. They were then incubated for 10 min at room temperature in 200 μl of a 5% (w/v) solution of Trinitrobenzene sulphonic acid (TNBS; Sigma) diluted 1:10 with HTF containing 0.4% polyvinyl pyrrolidone (HTF-PVP), pH 7.4. After three washes in HTF-PVP, embryos were incubated for 10 min at room temperature in 25 μl droplets of goat antidinitrophenyl BSA (anti-DNP BSA; ICN Biochemicals, now MP Biochemicals, Irvine, CA) diluted in HTF-PVP (0.1 mg/ml anti-DNP BSA final concentration), under oil. Samples were again washed three times in HTF-PVP and incubated at 37°C for 10 min in 25 μl-droplets under oil containing guinea pig complement. (Guinea Pig Complement Serum reconstituted in ice-cold water and diluted 1:10 in cold HTF-BSA; Sigma.) Following a prolonged wash (at least 20 min at 37°C) in HTF-BSA, the ICMs were shelled out by repeated pipetting through a microcapillary polished with a microforge. Cell debris was removed by a final rinse HTF-BSA.
Single-tube sample collection and reverse transcription
Single embryos, single blastomeres or ICMs were delivered to dry droplets of denaturing reagents placed on PCR tube lids (LysoDots), briefly heated and dried again and stored at -20°C, as detailed in reference . A mixture of Random Hexamers (1.5 μl of a 50 ng/μl stock solution) in DEPC-treated water (4.5 μl) was then added to each lysed sample directly into the lid. (All RT reagents were from a ThermoScript™ RT-PCR System kit, Invitrogen, Life Technologies, Carlsbad, CA.) The sample was spun down and the remaining RT reagents were delivered to the same tube, according to the PurAmp procedure. As previously described [3, 10], all RT reagents were used at the suggested concentrations except for the absence of DTT, but volumes were halved so that each assay was performed in just 10 μl, which increased to 10.5 μl after RNase H digestion.
At the end of RT, real-time PCR was carried out by adding the appropriate reagents still in the same vessel, as described below.
Duplex LATE-PCR assay for Oct4/XistRNA and DNA measurements in individual embryos or blastomeres
We designed the duplex real-time LATE-PCR assay for simultaneous amplification of sequences within exons of the murine Oct4 and Xist genes (GenBank Accession Number NM_013633, Oct4 mRNA, and 202420, Xist mRNA). (Because the PCR primers used for this work are not strand-specific, transcripts of the antisense gene Tsix could also be amplified during Xist PCR . However, Tsix expression in mouse embryos starts after the 8-cell stage .) Each reaction was run in a final volume of 50 μl and contained the following reagents: 1x PCR buffer (Invitrogen) comprised by 20 mM Tris-HCl, pH 8.4, and 50 mM KCl, 3 mM MgCl2, 0.4 mM of each dNTP, 50 nM Oct4 Limiting Primer having the sequence 5' TGGCTGGACACCTGGCTTCAGACT 3', 2 μM Oct4 Excess Primer having the sequence 5' CAACTTGGGGGACTAGGC 3', 100 nM Xist Limiting Primer having the sequence 5' GGTCGTACAGGAAAAGATGGCGGCTCAA 3', 2 μM Xist Excess Primer having the sequence 5' TGAAAGAAACCACTAGAGGGCA 3', 1 μM Oct4 molecular beacon having the sequence 5' TET-CCG CCT GGG ATG GCA TAC TGT GGA AGG CGG-Dabcyl 3', 1 μM Xist molecular beacon having the sequence 5' FAM-CGT GGG TGT CTA AGA TGG CGG AAG TCC CAC G-Dabcyl 3', 0.3× PrimeSafe™ -043 (a mis-priming-preventing compound available from Smiths Detection at firstname.lastname@example.org, ), and 2 units of antibody-complexed Platinum® Taq DNA polymerase (Invitrogen, Carlsbad, CA). Molecular beacons were obtained from Integrated DNA Technologies (Coralville, IA).
(A simplified version of this assay was employed for the initial measurements of Oct4 templates only. All components were the same, except for the absence of Xist primers and probe and the fact that 0.3× PrimeSafe-045 was used in this case. The concentration of dNTPs was decreased to 0.25 mM and that of Taq DNA polymerase to 1 unit.)
PCR was carried out in an ABI Prism 7700 Sequence Detector (Applied Biosystems, CA) with a thermal profile comprised by 1 cycle at 95°C for 5 minutes; 15 cycles at 95°C for 10 sec, 63°C for 20 sec, and 72°C for 30 sec; and 40 cycles at 95°C for 15 sec, 55°C for 25 sec, 72°C for 35 sec, and 45°C for 30 sec, with fluorescence acquisition at 45°C in the TET and FAM channels. At the end of the reaction, the trendline of each fluorescent signal was plotted with Microsoft Excel software (moving average with period 4).
Amplicon identification and sequencing
Amplification products were analyzed by gel electrophoresis in a 3% agarose gel in 0.5× TBE buffer for 2 hours and stained with ethidium bromide. Both the double-stranded and the single-stranded products (more weakly stained), of the expected sizes, were visible for the two co-amplified genes, indicating efficient duplex LATE-PCR.
The identity of the amplification products obtained from Oct4 LATE-PCR and RT-LATE-PCR was also confirmed by direct dideoxysequencing after a simple dilution step. No purification was needed because the overwhelming majority of the amplicons generated by LATE-PCR is single-stranded ("Dilute'N Go" sequencing) [9, 51]. Analysis of the sequences was carried out using Chromas software (Technelysium Pty Ltd).
Male mouse genomic DNA (The Jackson Laboratory, Bar Harbor, ME) was utilized to prepare standard curves for quantification of Oct4 and Xist templates based on known genome numbers . Using these curves, the "threshold cycle" (CT) at which the fluorescent signal of an unknown sample is first detected above background can be converted into a copy number . Under optimal conditions, a two-fold difference in the number of templates amplified results in a shift of one cycle between two CT determinations. A more abundant template has a lower CT value than a less abundant template, because it accumulates sooner to a detectable level . One male mouse genome contains one copy of Xist (X-chromosome) and two copies of Oct4 (chromosomes 17).
Ken Pierce, John Rice, Aquiles Sanchez and Arthur Reis are acknowledged for their advice on LATE-PCR and direct-dilution sequencing. We thank Elaine Seliger for her editorial assistance. The laser used in this study was kindly provided by Hamilton Thorne Biosciences, Inc., Beverly, Massachusetts. This work was funded by Smiths Detection, Edgewood, MD, and Brandeis University.
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