Genomics

The data uploaded describes SNP data.

The present study aimed to identify the genes associated with the involvement of adjunct lymph nodes of patients with prostate cancer (PCa) and to provide valuable information for the identification of potential diagnostic biomarkers and pathological genes in PCa metastasis. The most important candidate genes were identified through several machine learning approaches including K-means clustering, neural network, Naïve Bayesian classifications and PCA with or without downsampling. In total, 21 genes positively associated with lymph nodes involvement were identified. Among them, nine genes have been identified in metastatic prostate cancer, six have been found in other metastatic cancers and four in other local cancers. The amplification of the candidate genes was evaluated in the other PCa data sets. Besides, we identified a validated set of genes involved in the PCa metastasis. The amplification of SPAG1 and PLEKHF2 genes were associated with decreased survival in patients with PCa. A TCGA dataset of Prostate Adenocarcinoma (TCGA, PanCancer Atlas) was retrieved from cBioPortal [7, 8]. RNA expression values had been standardized against the gene's expression distribution in a reference population and had been reported as log2 values. CNA data had been reported as +2 , +1, 0, -1 or -2. We initially performed the analyses on the RNA data and then used the CNA data for further validation. The samples had been assigned as either N1 or N0 groups (Figure 2). The N1 group included the samples from the patients with PCa with the involvement of lymph nodes whereas N0 group included the samples from the patients with PCa without the involvement of any lymph nodes. The NA samples were removed from the study.

Fasta format is a sequence matrix file for experiments. The JPG file is an illustration of the manuscript. The Docx file is a form of the manuscript. The Tre format file is a vector illustration of a phylogenetic tree. Pptx files are visualization files of phylogenetic trees.

RNA-Sequence data of ELOVL6 gene function in bovine adipocyte

The compressed folder contains four supplementary files linked to the current research article. Genomic coordinates and FASTA sequences of all putative lncRNAs in Tribolium castaneum are provided in supplementary file1 (Tables S2 & S3) and supplementary file2, respectively.

Table S1 Barley previously un-annotated transcrpits (Supplementary table 1)

Supplementary materials for the article

Microarray data from this article were deposited at CATdb [38] (Project Au13-11_Gravity) according to the ‘Minimum Information About a Microarray Experiment’ standards and it is available here as a Supplementary Table 6. It is also accessible from Gene Expression Omnibus database reference GSE60473 and GENELAB NASA database reference GLDS-144.

This record contains data related to article "Mechanisms of responsiveness to and resistance against trabectedin in murine models of human myxoid liposarcoma". Myxoid liposarcoma (MLPS) is a rare soft-tissue sarcoma characterised by the expression of FUS-DDIT3 chimera. Trabectedin has shown significant clinical anti-tumour activity against MLPS. To characterise the molecular mechanism of trabectedin sensitivity and of resistance against it, we integrated genomic and transcriptomic data from treated mice bearing ML017 or ML017/ET, two patient-derived MLPS xenograft models, sensitive to and resistant against trabectedin, respectively. Longitudinal RNA-Seq analysis of ML017 showed that trabectedin acts mainly as a transcriptional regulator: 15 days after the third dose trabectedin modulates the transcription of 4883 genes involved in processes that sustain adipocyte differentiation. No such differences were observed in ML017/ET. Genomic analysis showed that prolonged treatment causes losses in 4p15.2, 4p16.3 and 17q21.3 cytobands leading to acquired-resistance against the drug. The results dissect the complex mechanism of action of trabectedin and provide the basis for novel combinatorial approaches for the treatment of MLPS that could overcome drug-resistance.

We compared the patterns of global epigenomic DNA methylation during the development of HCC, focusing on the role of DNA methylation in the early occurrence and development of HCC, providing a direction for future research on its epigenetic mechanism.