28 research outputs found
Tests for sex-differential expression in pooled organs
Cuffdiff results file; Differential expression of all pooled organ genes between 5 male and 5 female blue tit
Annotated SNPs in male-specifc transcriptome
vcf file: annotated SNPs in male-specific transcriptome; annotated using SnpEff; based on 5 male blue tit
iHS values across all informative scaffolds
based on SNPs called from the transcriptome of 5 male and 5 female blue tits
Annotated SNPs in female-specific transcriptome
vcf file: annotated SNPs in female-specific transcriptome; annotated using SnpEff; based on 5 female blue tit
Annotated SNPs in transcriptome common to both sexes
vcf file: annotated SNPs in transcriptome common to both sexes; annotated using SnpEff; based on 5 male and 5 female blue tits
Tests for sex-differential expression in gonads
Cuffdiff results files; differential expression of all gonadal genes between 5 male and 5 female blue tit
Tajima's D across all 25 kb windows of the blue tit genome
based on SNPs called from the transcriptome of 5 male and 5 female blue tits
Proliferative activity and cell size of EPHB6 wildtype and mutant cells.
<p>A) Proliferative activity of empty vector control, EPHB6 wildtype and mutant cells were analyzed using a colorimetric MTT assay after 72 hours. Data are shown as means +/â standard deviation of three independent experiments. Differences were statistically not significant (ANOVA). B) Cell size of individual cells (nâ=â20) growing on plastic dishes was analyzed by live video microscopy and recorded. EPHB6 mutant cells showed a significantly reduced cell size in comparison to EPHB6 wild type and to control cells (p<0.05, t-test).</p
Summary of non-synonymous mutations for EPHB6 (NM_004445 and NP_004436) found in tumors.
<p>Note: The table contains data from the databases of <a href="http://www.sanger.ac.uk/genetics/CGP/cosmic/" target="_blank">http://www.sanger.ac.uk/genetics/CGP/cosmic/</a>, <a href="http://strubiol.icr.ac.uk/extra/mokca" target="_blank">http://strubiol.icr.ac.uk/extra/mokca</a>, and the references were listed in the column of âPubmed Idâ. The NSCLC mutations identified in this study were marked as ânot reportedâ. Two sequence homology-based tools were used to predict the potential impact of the identified non-synonymous substitutions on protein function: Sort Intolerant from Tolerant (SIFT; <a href="http://sift.bii.a-star.edu.sg/" target="_blank">http://sift.bii.a-star.edu.sg/</a>) and Polymorphism Phenotype (PolyPhen-2; <a href="http://genetics.bwh.harvard.edu/pph2/" target="_blank">http://genetics.bwh.harvard.edu/pph2/</a>). If the SIFT prediction tolerance index score was less than 0.05, the variation was considered possibly damaging. Predictions made by PolyPhen-2 were assigned as âprobably damaging,â âpossibly damagingâ or âbenign.â Deletion mutations cannot be tested by either SIFT or PolyPhen-2.</p
Migration analysis of EPHB6 expressing NSCLC cells.
<p>A) Protein expression of stably transfected A549 cell lines expressing wild type EPHB6 or the EPHB6 deletion mutant. Cells were co-transfected using an EGFP -pcDNA3.1<sup>+</sup> vector for identification of selected clones. Multiple clones were pooled and further selected as bulk cultures. B) Transwell migration assays were performed with empty vector control cells, EPHB6 mutant and EPHB6 wildtype cells. Five different experiments in triplicates were analyzed. *: significant (p<0.05) differences by (EITHER ANOVA OR t-test) The provided p-value between the three different cell lines was statistically analyzed from all migrated cells by using the OneWay ANOVA-test. The analysis of the pair-wise t-test results in a significant p-value for the control cells vs. EPHB6-wt cells (p<0.015) and between the EPHB6-wt cells and the EPHB6-mut cells (p<0.005). C) <i>In vitro</i> wound healing scratch assay. Cells were scratched by a 10 ”l pipette tip. The scratch areas were recorded over a periode of 17 hours. Shown are means of three different experiments, calculated as percentage from one initial point for all three cell lines. The ANOVA-test (p<0.002) indicated statistically significant differences between the three cell lines. D) Representative images of the scratch assays at the beginning and the end of the experiments.</p