PDF file - 73K, Association of clinicopathological characteristics of tumours with miR-187 expression in Cohort 2 (n=470) using Pearson's chi-squared test

PDF file - 85K, qRT-PCR, standard in vitro functional assays and Western blotting description

PDF file - 414K, miR187 ectopic expression in MCF7, effects on growth, quantification of invasion

PDF - 219K, Table S1. CAS (Chemical Abstracts Service) numbers, molecular formulas, structures and references for each of the compounds used in the study.

PDF - 186K, Figure S2. Additional Retinoic Acid (RA) and cell viability. A. The effect of increased RA concentration on MYC mRNA expression in 48h doxycycline and 24h RA treated SY5Y-MYCN cells, assayed by qPCR. B. Time course of NVP-BEZ235 (dual PI3K/mTOR inhibitor) treatment on viability across the different cell lines, as measured by MTS assays. C. The effect of various inhibitors on viability across the different cell lines, as measured by MTS assays after 48h of inhibitor treatment. D. Viability results for SY5Y-MYCN cells with and without doxycycline induction (72h) of ectopic MYCN expression, treated with inhibitors for 48h as measured by MTS assays.

PDF - 98K, Table S2. Flow Cytometry full details in accordance with the MIFlowCyt Standard.

PDF file - 438K, EMT and MMP expression in miR187 expressing MCF7 cells

Articular cartilage has only very limited regenerative capacities in humans. Tissue engineering techniques for cartilage damage repair are limited in the production of hyaline cartilage. Mesenchymal stem/stromal cells (MSCs) are multipotent stem cells and can be differentiated into mature cartilage cells, chondrocytes, which could be used for repairing damaged cartilage. Chondrogenesis is a highly complex, relatively inefficient process lasting over 3 weeks in vitro. Methods: In order to better understand chondrogenic differentiation, especially the commitment phase, we have performed transcriptional profiling of MSC differentiation into chondrocytes from early timepoints starting 15 minutes after induction to 16 hours and fully differentiated chondrocytes at 21 days in triplicates.

Supplementary Data from Altered Cytoplasmic-to-Nuclear Ratio of Survivin Is a Prognostic Indicator in Breast Cancer

PDF file - 757K, Ectopic expression of miR187 in SBKR3 cells, phenotypic effects

PDF file - 65K, miRNAs associated with poor outcome in breast cancer patient cohorts

PDF file - 53K, Recurrence free survival and miR187 expression in cohort 2

PDF - 122K, Figure S1. Additional expression regulation data. A. Comparison of mRNA-seq and RT-qPCR measurements for the same differentially expressed mRNAs in IMR32 cells upon 24h GSK3 inhibitor treatments. B. Time course of azakenpaullone mediated ectopic MYCN mRNA reduction in SY5Y-MYCN, measured by RT-qPCR. C. RT-qPCR results of GSK3 inhibitor regulation of c-MYC in CRC cell lines. D. pSMAD levels in IMR32 upon GSK3 inhibitor treatment. E. MDM2 mRNA expression level in response to GSK3 inhibition, mRNA-seq data. F. Wnt Agonist 1 and BIO treatment regulated the mRNA (top) and protein (bottom) of MYC genes in a similar manner.

PDF file - 73K, Association of clinicopathological characteristics of tumours with miR-187 expression in Cohort 1 (n=117) using Pearson's chi-squared test

PDF file - 68K, Clinicopathological charactistics of tumours in Cohorts 1 and 2

PDF file - 47K, miR187 expression and patient outcome stratified according to ER status

PDF - 259K, Figure S3. Additional p53 and neuroblastoma prognostic markers overlap data. A. p53 signalling pathway schematic with LiCl differentially regulated genes overlaid, key as in image and as described in Fig. 5B. B. Overlap between IPA predicted upstream regulators from inhibitor mRNA-seq (top 110) and a 157 neuroblastoma risk stratification gene signature (all 31), image generated using Venny.

Clustal Omega is a version, completely rewritten and revised in 2011, of the widely used Clustal series of programs for multiple sequence alignment. It can deal with very large numbers (many tens of thousands) of DNA/RNA or protein sequences due to its use of the mBed algorithm for calculating guide-trees. This algorithm allows very large alignment problems to be tackled very quickly, even on personal computers. The accuracy of the program has been considerably improved over earlier Clustal programs, through the use of the HHalign method for aligning profile hidden Markov models. The program currently is used from the command-line or can be run online.

Clustal Omega is a version, completely rewritten and revised in 2011, of the widely used Clustal series of programs for multiple sequence alignment. It can deal with very large numbers (many tens of thousands) of DNA/RNA or protein sequences due to its use of the mBed algorithm for calculating guide-trees. This algorithm allows very large alignment problems to be tackled very quickly, even on personal computers. The accuracy of the program has been considerably improved over earlier Clustal programs, through the use of the HHalign method for aligning profile hidden Markov models. The program currently is used from the command-line or can be run online.

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.