Additional file 3: of LimiTT: link miRNAs to targets

Data: Supplementary table, result list from LimiTT MTISEA analysis on random list of identifiers as used in use case two. Each tab contains all miRNAs identified in human and mouse respectively with the parameter “database overlap (occ)” one and two. Yellow background indicates the significant enriched (FDR < 0.05) miRNAs. (XLSX 63 kb

Boletín de Segovia: Número 89 - 1915 julio 26

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

A selected list of 50 transcripts highly up-regulated in the dorsal iris.

<p>v4: RPKM value of ventral iris 4 dpl, d4: RPKM value of dorsal iris 4 dpl, v8: RPKM value of ventral 8 dpl, d8: RPKM value of dorsal iris 8 dpl, log₂Fc4: fold expression at 4 dpl between dorsal and ventral iris, log₂Fc8: fold expression at 8 dpl between dorsal and ventral iris, log₂Fc: fold expression between dorsal and ventral iris at both the days.</p

Transcriptome Analysis of Newt Lens Regeneration Reveals Distinct Gradients in Gene Expression Patterns

<div><p>Regeneration of the lens in newts is quite a unique process. The lens is removed in its entirety and regeneration ensues from the pigment epithelial cells of the dorsal iris via transdifferentiation. The same type of cells from the ventral iris are not capable of regenerating a lens. It is, thus, expected that differences between dorsal and ventral iris during the process of regeneration might provide important clues pertaining to the mechanism of regeneration. In this paper, we employed next generation RNA-seq to determine gene expression patterns during lens regeneration in <i>Notophthalmus viridescens</i>. The expression of more than 38,000 transcripts was compared between dorsal and ventral iris. Although very few genes were found to be dorsal- or ventral-specific, certain groups of genes were up-regulated specifically in the dorsal iris. These genes are involved in cell cycle, gene regulation, cytoskeleton and immune response. In addition, the expression of six highly regulated genes, TBX5, FGF10, UNC5B, VAX2, NR2F5, and NTN1, was verified using qRT-PCR. These graded gene expression patterns provide insight into the mechanism of lens regeneration, the markers that are specific to dorsal or ventral iris, and layout a map for future studies in the field.</p> </div

List of up-regulated (>2 times) transcripts related to immune response^*.

<p>GO:0006955 immune response.</p>*<p>Transcript names are from their human homologs.</p>+<p>Potential isoforms.</p

List of up-regulated (>2 times) transcripts related to gene regulation^*.

<p>GO: 0010467 gene expression; GO:0010468 regulation of gene expression; GO:0006350 transcription; GO:0045449 regulation of transcription.</p>*<p>Transcript names are from their human homologs.</p>+<p>Potential isoforms.</p

Workflow used to select transcripts for comparison of expression between the dorsal and ventral iris.

<p>Only transcripts expressed above the cutoff (see methods, light blue) and up-regulated at least 2-fold (light green) were included. Fisher’s exact test corrected with multiple selections (FDR <0.05) was used to compare the GO of the two groups (light purple). Enriched GO terms were found (light yellow).</p

Workflow used to select transcripts for comparison of gene expression 4 and 8 days post-lentectomy.

<p>Only transcripts expressed above the cutoff (see methods) in the day of interest and up-regulated more than 2-fold in both dorsal and ventral iris (light blue) were considered. Fisher’s exact corrected for multiple selections (FDR <0.05) was used to compare the GO of the groups versus the remaining transcripts of the transcriptome. Enriched GO terms were found (light purple).</p

qRT-PCR expression validation of TBX5, FGF10, UNC5B, VAX2, NR2F5 and NTN1.

<p>Expression of the different genes at the RNA level is indicated as relative expression. Bars indicate standard deviation. Statistical test was performed with two-way ANOVA and Student’s t-test. Asterisks above the bars indicate statistical significance (*: p<0.05, ***: p<0.001) between dorsal and ventral iris samples of the same day.</p

Diagram for collecting iris pieces.

<p>A. Whole eye ball with anterior side facing up and ventral facing the screen. Iris appears in the anterior side. Red dashed line indicates the plane that anterior and posterior sides are separated. B. Anterior view of a newt’s anterior part separated previously. Arrow head indicates black pigments present in the dorsal side of the eye. Arrow indicates the v-shaped pupil in the ventral side. These marks are indicative of the dorsoventral axis of the iris. Red dash lines indicate the separation of dorsal and ventral iris pieces performed while in the anterior view of the eye. C. Posterior view of a newt’s anterior part separated previously. Red dash lines indicate the separation of ciliary body and iris performed in this view. Transparent white dash lines indicate the separation of dorsal and ventral iris sectors performed in the anterior view. di: Dorsal iris sectors that have been isolated for the experiment, vi: Ventral iris sectors that have been isolated for the experiment. m: pigmented midline, cb: ciliary body, pu: pupil. Orientation in each panel is indicated above the illustrated eye parts, a: anterior side, d: dorsal side, v: ventral side, p: posterior side.</p