Additional file 1: Table S1. of Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico

List of plants evaluated with DarTseq markers. Table S2. List of DArTseq markers and used in the analysis. Table S3. Structural SNPs contributing to the population structure in C. canephora. Table S4. Putative outlier marker loci identified by the Fst outlier method implemented in Lositan. (XLSX 457 kb

Additional file 2: Figure S1. of Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico

Genotyping error rates in technical and biological replicates. Genotyping error rates for 15 and 4 accessions with technical (a) and biological (b) replicates evaluated with SNPs. Ratios were obtained using all 4,021 markers (blue) or by selectively ignoring markers having differential missing data (red). (EPS 683 kb

Additional file 3: Figure S2. of Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico

Selection test for each of the 4021 DArTseq SNP markers in C. canephora Plotted distribution of the empirical FST values versus the expected heterozygosity. The red and blue lines indicate 99 % and 1 % confidence limits, respectively, while the gray line corresponds to the median value. (PDF 192 kb

Additional file 4: of Genome-wide analysis of LTR-retrotransposons in oil palm

Sequence coverage of LTR retrotransposon families in the E. oleifera (Eo) and in E. guineensis (Eg) genomes. (PDF 356 kb

Chromatin occupancy by TRα1 in C17.2/TRα1 cells.

*<p>Identified using NUBISCAN. Bold characters correspond to TREs with more that 2-fold enrichment after C17.2/TRα1 cells ChAP. ND: not determined, N/A: not relevant. Mean ± SD for three independent experiments.</p

Cell autonomous effect of <i>in vivo</i> expression of a dominant negative TRα1 mutation.

<p><i>TRα^AMI/S</i> data are reported from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030703#pone-0030703-g002" target="_blank">figure 2</a> for comparisons. ND: Not determined. Values are indicated as mean ± SD. Significant changes (Student T-test) are indicated in bold:</p>**<p>: p<0.01,</p>*<p>: p<0.05.</p

Q-RT-PCR confirmation of T3 mediated regulation in primary cultures of cerebellum neuronal cells.

<p>Bold characters outline fold changes superior to 2.</p

Transfection of TRα1 into C17.2 cells restores their response to T3 treatment.

<p>A. T3-induced <i>Hr</i> expression is detected earlier and stronger in transfected C17.2/TRα1 cells (black bars) than in non-transfected cells (white bars), *p<0.05, Student’s t-test difference between non-transfected cells and C17.2/TRα1 cells. B. The level of change in expression induced by T3 and measured by Q-RT-PCR in C17.2/TRα1 cells is indicated for each target gene, using non-treated cultures as reference (represented as log2 of the fold change). White bars indicate T3 treatment in proliferative medium (containing serum), black bars indicated T3 treatment in serum-deprived medium allowing for differentiation. Most genes show a response only in serum-deprived medium, *p<0.05, Student’s t-test, difference between serum containing and serum deprived cultures.</p

Additional file 1: of Genome-wide analysis of LTR-retrotransposons in oil palm

De novo consensus TE databases. Contains the E. oleifera (E08_denovoLibTEs.txt) and E. guineensis (p5_denovoLibTEs.txt) databases. (ZIP 15,038 kb

Kinetics of T3 target genes expression in wild-type and <i>TRα^AMI/S</i> mice in the cerebellum as measured by Q-RT-PCR.

<p>Expression levels were calculated for each target gene by Q-RT-PCR in wild-type and <i>TRα^AMI/S</i> littermates at P4, P8, P15 and P21 (minimum 3 animals of each genotype for each time point). Data are expressed as mean ± SD using wild-type P4 values (A), for genes with decreasing or stable expression levels over time or P21 (B), for genes with increasing expression levels, as a reference for each genotype. *p<0.05; **p<0.01 for comparisons between wild-type and <i>TRα^AMI/S</i> mice for each time point (Student’s t-test).</p