MOESM1 of Gene repositioning within the cell nucleus is not random and is determined by its genomic neighborhood

Additional file 1. Supplementary information figures and tables

Cyclin A1 expression levels in FSHD and other myopathies (microarrays).

<p><i>CCNA1</i> Human Exon 1.0 ST Array signal levels in FSHD (n = 4), healthy controls (n = 7), CAV3 (n = 4), DYSF (n = 4) and FHL1 (n = 3).</p

Cross sections of muscle fibers of (A) one FSHD patient and (B) one healthy control (20×magnification, H&E-stained).

<p>Myofiber diameter size difference indicates hypertrophy in the <i>Vastus lateralis</i> muscle of the patient.</p

Distribution patterns of myofiber diameters derived from FSHD patients (n = 5) and age-matched healthy controls (n = 5).

<p>Diameters (µm) from 1000 myofibers each were measured in H&E-stained cross sections under a light microscope by using the Image J software. Cumulative data are presented (FSHD: mean 71 µm, SD 23 µm; Control: mean 59 µm, SD 17 µm), <i>p</i><0.001, Wilcoxon test.</p

Similarity clustering and STRING analysis of the regeneration-enriched genes selected by pairwise comparison between amputation and lateral wound.

<p>A. Heat map of 85 probes (representing 44 genes with a assigned human Refseq homolog) up-regulated in regenerating but not or only weakly in the lateral wound samples shows a diversity of expression kinetics. log₂ values of standard scores of normalized signal are shown. Up-regulation is indicated by reds with increasing intensities, down-regulation by blues with increasing intensities. B. STRING analysis of the gene set showing only high confidence functional connections (confidence score ≥0.7). ECM remodeling network including MMPs and elastase is shown in yellow, epithelial organization network in brown and the limb bud network including WNT5A, MSX1, LHX2 in orange color balls. Five identifiers were not recognized by STRING 9.0 interface and therefore 39 candidates were considered). See also Figure S5.</p

Selection of early regeneration-specific genes up-regulated during the blastema establishment-phase (3 and 72 hours after injury).

<p>A, B. Heat map visualization of all eleven p-value clusters that emerged from the 246 probes with up-regulation in limb amputation (top), and of four selected clusters with early up-regulation (4, 6, 10 and 11). A. Heat map of –log₁₀ LSD p-values normalized to a mean of zero and a standard deviation of one. Values are calculated between consecutive time points from 3 to 72 hours after limb amputation and lateral wound. B. Heat map of log₂ signal values normalized to a mean of zero and a standard deviation of one, shown for amputated limb and lateral wound between 3 and 528 hours after injury.</p

Hierarchical clustering of regeneration, lateral wound and limb bud samples identifies three main phases of limb regeneration.

<p>Samples were clustered using Pearson's correlation as similarity measure (sample key at bottom; numbers represent hours after injury, Prox =  mature sample from the upper arm at time 0 h, all other samples are from the lower arm). From 0–12 hours, at each time point, corresponding amputation and lateral wound samples cluster closest together. Starting at 24 hours, successive amputation samples are more similar to each other than to the corresponding lateral wound time points, indicating a divergence between regeneration and lateral wound gene programs. From 120 hours onward, the amputated samples are most similar to the developing limb bud, indicating that the limb development program has been re-established.</p

<i>In situ</i> hybridization on limb sections confirms a diversity of regeneration-specific expression patterns.

<p>A. Genes expressed in different layers of the wound epidermis. B. Genes expressed in the mesenchymal blastema or stump. C. Expression of <i>Wnt5a</i> in the basal epidermis of the amputated stump but not in the lateral injury. D. Expression of <i>DK45</i> in the limited region of the wound epidermis. E. In addition to wound epidermis, at 12 dpa, <i>Psca</i> is also expressed in the mesenchyme. Red lines depict the amputation plane. dpa =  days post amputation, dplw =  days post lateral wound. For comparison see the staining of lateral wound sections in Figure S3.</p

Detection of smooth muscle cells after differentiation of the BMP2cells

Expression of SMA in the BMP2cells detected by qRT-PCR. Microarray relative expression levels of various smooth muscle specific genes in BMP2cells. The expression levels of each gene were normalized with its maximum level set as 100%. Each result is an average of three independent experiments (Additional data file 13). Detection of smooth muscle cells 1 day after plating the BMP2cells (7 + 1 days in total; top left), 8 days after plating with puromycin (7 + 8 days in total; top right), 18 days after plating with puromycin (7 + 18 days in total; bottom left) and 18 days after plating without puromycin (7 + 18 days in total; bottom right).<p><b>Copyright information:</b></p><p>Taken from "Transcriptomic and phenotypic analysis of murine embryonic stem cell derived BMP2lineage cells: an insight into mesodermal patterning"</p><p>http://genomebiology.com/2007/8/9/R184</p><p>Genome Biology 2007;8(9):R184-R184.</p><p>Published online 4 Sep 2007</p><p>PMCID:PMC2375022.</p><p></p

Hierarchical clustering of probe sets identified as upregulated in α-MHCcells

<p><b>Copyright information:</b></p><p>Taken from "Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes"</p><p>Genome Biology 2007;8(4):R56-R56.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896009.</p><p></p> Shown is a visualization of the hierarchical clustering of probe sets identified as upregulated in the α-myosin heavy chain (MHC)cells with an expression level at least twofold higher than in 15-day-old EBs and in α-MHC embryonic stem cells. Each probe set is represented by a single row of colored boxes; each array is represented by a single column. Rectangles corresponding to intermediately expressed probe sets are colored black, upregulated probe sets are indicated with red of increasing intensity, and weakly expressed probe sets with green of increasing intensity. The dendrogram on the left of the figure represents the similarity matrix of probe sets