Dataset Information

Ena-DATASET-RTL-06-02-2015-14:59:15:066-180 - samples

ABSTRACT: RNA-sequencing (RNA-seq) was performed with RNA extracted from fresh-frozen human tumor tissue samples. cDNA libraries were prepared from poly-A selected RNA applying the Illumina TruSeq protocol for mRNA. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x of the annotated transcriptome.

PROVIDER: EGAD00001001244 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Publications

Comprehensive genomic profiles of small cell lung cancer.

George Julie J Lim Jing Shan JS Jang Se Jin SJ Cun Yupeng Y Ozretić Luka L Kong Gu G Leenders Frauke F Lu Xin X Fernández-Cuesta Lynnette L Bosco Graziella G Müller Christian C Dahmen Ilona I Jahchan Nadine S NS Park Kwon-Sik KS Yang Dian D Karnezis Anthony N AN Vaka Dedeepya D Torres Angela A Wang Maia Segura MS Korbel Jan O JO Menon Roopika R Chun Sung-Min SM Kim Deokhoon D Wilkerson Matt M Hayes Neil N Engelmann David D Pützer Brigitte B Bos Marc M Michels Sebastian S Vlasic Ignacija I Seidel Danila D Pinther Berit B Schaub Philipp P Becker Christian C Altmüller Janine J Yokota Jun J Kohno Takashi T Iwakawa Reika R Tsuta Koji K Noguchi Masayuki M Muley Thomas T Hoffmann Hans H Schnabel Philipp A PA Petersen Iver I Chen Yuan Y Soltermann Alex A Tischler Verena V Choi Chang-min CM Kim Yong-Hee YH Massion Pierre P PP Zou Yong Y Jovanovic Dragana D Kontic Milica M Wright Gavin M GM Russell Prudence A PA Solomon Benjamin B Koch Ina I Lindner Michael M Muscarella Lucia A LA la Torre Annamaria A Field John K JK Jakopovic Marko M Knezevic Jelena J Castaños-Vélez Esmeralda E Roz Luca L Pastorino Ugo U Brustugun Odd-Terje OT Lund-Iversen Marius M Thunnissen Erik E Köhler Jens J Schuler Martin M Botling Johan J Sandelin Martin M Sanchez-Cespedes Montserrat M Salvesen Helga B HB Achter Viktor V Lang Ulrich U Bogus Magdalena M Schneider Peter M PM Zander Thomas T Ansén Sascha S Hallek Michael M Wolf Jürgen J Vingron Martin M Yatabe Yasushi Y Travis William D WD Nürnberg Peter P Reinhardt Christian C Perner Sven S Heukamp Lukas L Büttner Reinhard R Haas Stefan A SA Brambilla Elisabeth E Peifer Martin M Sage Julien J Thomas Roman K RK

Nature 20150713 7563

We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We dis ...[more]

PMID: 26168399

Similar Datasets

Project description:To determine IL-17-induced global transcriptome changes in midbrain neurons derived from induced pluripotent stem cells (iPSC) from three sporadic Parkinson's disease (PD) patients and three age- and sex-machted controls, deep RNA sequencing (RNA-Seq) of IL-17-treated and untreated PD and control iPSC-dderived midbrain neurons was performed. Total RNA was isolated from untreated and IL-17-treated cells with the TruSeq RNA Sample Preparation Kit v2 (Illumina). RNA libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems) and cluster generation was performed on the cBot with the TruSeq SR Cluster Kit v3 (Illumina). The sequencing run was performed on a HiSeq 1000 instrument (Illumina) using the indexed, 50 cycles single read (SR) protocol and the TruSeq SBS v3 Kit (Illumina). Image analysis and base calling resulted in .bcl files that were then converted into .fastQ files by the CASAVA1.8.2 software. FastQ files were aligned to the human genome (hg19) using STAR.and annotated with gencode.v19. DESeq2 was used to determine differential expression. Criteria to determine significantly dysregulated genes were as follows: adjusted p-value below 0.05 and log2FC (fold change) of greater than one. Only genes with a mean expression value of greater than one RPKM (reads per kilobase per million mapped reads) throughout the dataset were considered. Control and PD samples were analyzed as two independent datasets. Upon IL-17 treatment only 17 genes were found to be dysregulated in controls but 125 genes were dysregulated in iPSC-derived midbrain neurons from PD patients. The 125 IL-17-dependent genes in PD iPSC-derived neurons separated the treated from untreated PD samples using an unsupervised, hierarchical clustering applying an Euclidean distance metric. More detailed study information can be found in Sommer A, Maxreiter F, Krach F, Fadler T, Grosch J, Maroni M, Graef D, Eberhardt E, Riemenschneider MJ, Yeo GW, Kohl Z, Xiang W, Gage FH, Winkler J, Prots I, Winner B. Th17 Lymphocytes Induce Neuronal Cell Death in a Human iPSC-Based Model of Parkinson's Disease. Cell Stem Cell. 2018 Jul 5;23(1):123-131.e6. doi: 10.1016/j.stem.2018.06.015. PMID: 29979986

Dataset Information

Ena-DATASET-RTL-06-02-2015-14:59:15:066-180 - samples

Publications

Comprehensive genomic profiles of small cell lung cancer.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets