Effects of pHE DNA addition on PCR efficiency.

a<p>A two-copy transgenic T₀ tomato plant was used;</p>b<p>The concentration was 10.20 ng µl⁻¹, containing 10,000 <i>ELIP</i> and 10,000 <i>HPT</i> molecules µl⁻¹;</p>c<p>The concentration was 0.051 pg µl⁻¹, containing 10,000 <i>ELIP</i> and 10,000 <i>HPT</i> molecules µl⁻¹.</p

Calculation of N_0ELIP when taking a C_b within I_b −10 to I_b +5.

<p>The values above/beneath the arrows indicate the coefficient of variation. Line 1-Line 6 (L1-L6) were the six transgenic T₀ tomato lines; I_b was set as the integer part for C_tb; C_b indicated cycles in the exponential amplification phase of sample B.</p

Southern blot analysis of six transgenic tomato T₀ lines.

<p>A) <i>Hind</i> III digestion; B) <i>BamH</i> I digestion. M, λDNA/<i>Hind</i> III marker; L1-L6, transgenic tomato T₀ lines, were the same as those appeared in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053489#pone-0053489-g003" target="_blank">Figure 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053489#pone-0053489-t003" target="_blank">Table 3</a>; P, positive control (plasmid); WT, negative control (wild type).</p

Effects of standard DNA addition on fluorescence intensity and C_t.

<p>Oblique lines: exponential amplification phases suggested by LinRegPCR; Sample A: with 1 µl of tomato genomic DNA (10.20 ng µl⁻¹, containing 10,000 <i>ELIP</i> molecules µl⁻¹) as PCR template; Sample B: with 1 µl tomato genomic DNA plus 1 µl of pHE (0.051 pg µl⁻¹, containing 10,000 <i>ELIP</i> molecules µl⁻¹) as PCR template; Sample C: with 1 µl tomato genomic DNA plus 3 µl of pHE as PCR template.</p

Primers used in this study.

a<p>The underlined nucleotides are the restriction site for <i>Xba</i> I; ^b The underlined nucleotides are the restriction site for <i>Hind</i> III.</p

Determination of transgene copy number of six transgenic tomato plants by standard addition qPCR (SAQPCR).

<p>A quantified amount of 10.20 ng of tomato genomic DNA, which contains around 10,000 molecules of <i>ELIP</i>, was included in each PCR reaction.</p>a<p>Refers to the copy number per diploid genome.</p

Additional file 3 of Transcriptome co-expression network analysis identifies key genes and regulators of ripening kiwifruit ester biosynthesis

Additional file 3:Table S1. Aroma biosynthesis structural genes. Table S2. Primers for real-time PCR. Table S3. Sequences (5′ to 3′) for promoter isolation. Table S4. Primers for vector construction for dual-luciferase assays

Construction of recombinant plasmid pHE.

<p>pELIP: plasmid harboring tomato <i>ELIP</i> gene; pHPT: plasmid harboring <i>Escherichia coli HPT</i> gene; pHE: plasmid harboring both tomato <i>ELIP</i> and <i>E. coli HPT</i> gene.</p

Transcript expressions of genes related to citrate degradation and transport as measured by RNA-Seq and qRT-PCR.

<p>Lines represent expression determined by RNA-Seq in RPKM value (right axis), while histograms represent transcript expression determined by qRT-PCR (left axis). The error bars represent the standard errors.</p

Throughput and quality control of RNA-Seq data from Gaocheng and Satsuma mandarin libraries.

<p>^a GCS1. GCS3 and GCS6 represent stages S1, S3 and S6 of Gaocheng, while SMS1, SMS3 and SMS6 represent S1, S3 and S6 of Satsuma mandarin.</p><p>^b The percentage of sequences with sequencing error rate lower than 1%.</p><p>^c The percentage of clean bases mapped to the reference genome.</p><p>^d The percentage of sequences aligned to two transcripts.</p><p>Throughput and quality control of RNA-Seq data from Gaocheng and Satsuma mandarin libraries.</p