Dataset Information

MELA-AU_RNA_20170516 - samples

ABSTRACT: BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases. Gene model = Ensembl version 70

PROVIDER: EGAD00001003353 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Publications

Whole-genome landscapes of major melanoma subtypes.

Hayward Nicholas K NK Wilmott James S JS Waddell Nicola N Johansson Peter A PA Field Matthew A MA Nones Katia K Patch Ann-Marie AM Kakavand Hojabr H Alexandrov Ludmil B LB Burke Hazel H Jakrot Valerie V Kazakoff Stephen S Holmes Oliver O Leonard Conrad C Sabarinathan Radhakrishnan R Mularoni Loris L Wood Scott S Xu Qinying Q Waddell Nick N Tembe Varsha V Pupo Gulietta M GM De Paoli-Iseppi Ricardo R Vilain Ricardo E RE Shang Ping P Lau Loretta M S LMS Dagg Rebecca A RA Schramm Sarah-Jane SJ Pritchard Antonia A Dutton-Regester Ken K Newell Felicity F Fitzgerald Anna A Shang Catherine A CA Grimmond Sean M SM Pickett Hilda A HA Yang Jean Y JY Stretch Jonathan R JR Behren Andreas A Kefford Richard F RF Hersey Peter P Long Georgina V GV Cebon Jonathan J Shackleton Mark M Spillane Andrew J AJ Saw Robyn P M RPM López-Bigas Núria N Pearson John V JV Thompson John F JF Scolyer Richard A RA Mann Graham J GJ

Nature 20170503 7653

Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. Here we report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. However, acral and mucosal melanomas ...[more]

PMID: 28467829

Similar Datasets

Project description:Purpose: Infection of neuroblastoma cell liner BE(2)N with a retroviral vector that overexpressed Dn-hTERT caused the conversion of these cells from adrenergic morphology to one that resembles mesenchymal cells. During prolonged passage, down-regulation of Dn-hTERT expression caused a reversal in cell morphology (i.e., from mesenchymal to adrenergic cells). The goal of this study is to characterize the transcriptomes of BE(2)N during the morphologic conversion and reversal and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes. Methods: Total RNA was isolated from parental BE2N cells and cells infected with Dn-hTERT retrovial vector at day 33, day 55, and day 82 post infection. TruSeq stranded mRNA libraries were prepared and sequenced with paired-end 50 bps on Illumina NovaSeq 6000 by the WCM Genomics Core Facility. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing. RNA reads were aligned and mapped to theGRCh37 human reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR) 56, and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM) 57, 58. The fold changes were calculated by directly comparing the FPKM values of samples and controls. Results: The gene expression changes in Dn-hTERT treated cells were identified. The list of up-regulated and down-regulated genes were found to overlap strongly with previously defined MES and ADRN signature genes, supporting the notion that Dn-hTERT triggers the transcriptional re-programming of ADRN cells into MES cells. Conclusions: This study demonstrates that the morphologic conversion mediated by inhibition of telomerase in neuroblastoma cells is accompanied by genome wide transcriptional re-programming.

Project description:Purpose: the goal of this study is to investigate the consequences of ubiquitin specific protease 15 (USP15) deletion on gene expression in mouse LSK hematopoietic progenitors. Methods: mRNA profiles of 8 weeks-old wild-type (WT) and ubiquitin specific protease 15 knockout (Usp15−/−) mice were generated by deep sequencing using Illumina Hiseq2500. The sequence reads that passed quality filters Alignments of the sequence reads that passed quality filters were performed using TopHat2.1, Genome build 38 and Ensembl gtf version 77 and genecounts have been generated using Itreecount. https://github.com/NKI-GCF/itreecount Results: We assigned about 30 million reads per sample uniquely to a gene of the mouse reference genome (mm10) We identified 21,219 genes in the LSKs of WT and Usp15−/− mice using TopHat2.1 in combination with Itreecount. https://github.com/NKI-GCF/itreecount. Distinct LSK-specific expressed genes (such as Eng, Tek, the MlI receptor and the Kit receptor) are identified. Comparison of normalized gene expression data for Usp15-/- versus WT LSK confirmed the loss of Usp15. Apart from Usp15, almost no other significantly deregurated genes were detected using a treshold of fold change ≥1.5 and p value <0.05, suggesting the maintenance of an overall stable identity of the cellular compartment in Usp15-/- mice. Conclusions: Our results represent the first detailed analyis of the consequences of USP15 deletion on gene expression in hematopoietic populations such as LSKs progenitors by genome wide expression profiling in WT and Usp15-/- mice. RNAseq of two freshly isolated biological replicas of sorted LSKs from 8 weeks old Usp15-/- animals confirmed the loss of Usp15, while showing almost no significant other up or down regulated genes among the 21,219 genes identified in Usp15-/- LSKs. We conclude that young adult hematopoietic stem and progenitor cells (LSKs) perpetuated a stable gene expression program regardless of the homozygous deletion of USP15.

Dataset Information

MELA-AU_RNA_20170516 - samples

Publications

Whole-genome landscapes of major melanoma subtypes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets