11925 results for "cancer rna-seq"

in 9.89 milliseconds.

• Paired RNA-Seq data of Primary lymphomas of the central nervous system (PCNSL)

  Primary lymphomas of the central nervous system (PCNSL) are diffuse large B-cell lymphomas (DLBCLs) which are confined to the central nervous system (CNS). Paired RNA-Seq sequencing was done on Illumina HiSeq2000 machines using Illumina TruSeq RNA library preparation kit. About 36 tumor samples were sequenced.

  Dataset EGAD00001007811

• Gene Fusion Discovery through RNA Sequencing of Human Glioblastoma Stem Cell Lines

  We used massively parallel, paired-end sequencing of expressed transcripts (RNA-seq) to detect novel gene fusions in short-term cultures of glioma stem-like cells freshly isolated from nine patients carrying primary glioblastoma multiforme (GBM). The culture of primary GBM tumors under serum-free conditions selects cells that retain phenotypes and genotypes closely mirroring primary tumor profiles as compared to serum-cultured glioma cell lines that have largely lost their developmental identities.

  Study phs000505

• Expression profiling of Gorlin iPSCs in the osteoblast induction culture

  In this study, we utilized human induced pluripotent stem cell (iPSC)-based models of the two diseases, named Gorlin syndrome and McCune Albright synfrome, to understand the roles of Hh signaling in osteogenesis, especially in mineralization. To examine which signaling pathways and genetic networks were affected by Gorlin syndrome-associated PTCH1 mutation in human osteoblastogenesis, we performed RNA sequencing (RNA-seq) analysis in the osteoblast induction culture of WT and Gorlin iPSCs.

  Study JGAS000218

• RNA-seq BAM files from newborn screening dried blood spot samples

  Paired-end RNA-seq BAM files from 21 newborn screening dried blood spot (DBS) samples. These DBS samples were obtained from extremely low gestional age newborns, where 10 of them were affected by a fetal inflammatory response (FIR) before birth, and 11 were unaffected. Total RNA was sequenced using an Illumina NextSeq-500 instrument. The sample preparation protocol included the depletion of rRNA and globin mRNA using the Globin Zero Gold rRNA Removal Kit from Illumina. Libraries were prepared using the NebNext Ultra TM II Directionl RNA LIbrary Prep Kit (New England Biolabs). There is one BAM file per sample and there is an additional BAM file, corresponding to sample BS13, which was downsampled to 1/4 of its original depth (see BS13_README file for details).

  Dataset EGAD00001005009

• Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms

  In this study, we aimed to comprehensively characterize in 113 myeloproliferative neoplasms (MPN) patients the mutational landscape of the granulocyte transcriptome using RNA sequencing data. We implemented workflows for fusion and variant calling, and differential splicing analysis for patients with hotspot SF3B1 mutations. Finally, we characterized the neoantigen landscape on individualized level taking each patient's HLA genotype (derived from the same RNA-seq dataset) into account.

  Study EGAS00001003486

• RNAseq of 76 samples from Uveal Melanoma tumors

  Hotspot mutations in the spliceosome gene SF3B1 are reported in 20% of uveal melanomas. SF3B1 is involved in 3'-splice site (3'ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1 R625/K666 mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3'ss

  Study EGAS00001002932

• The paired FF/FFPE colon set, RNA-Seq

  Dataset EGAD00001000831

• RNA-seq of CML074 Tumor tissue; Timpepoint 1

  Dataset EGAD00001001259

• RNA-seq of CML074 Tumor tissue; Timpepoint 2

  Dataset EGAD00001001260

• Microbiome-Host Interactions in Oral Squamous Cell Carcinoma: a Metatranscriptomic Exploratory Study

  Oral cancer (predominantly squamous cell carcinoma; OSCC) is the 14th most prevalent malignancy worldwide, accounting for more than 300,000 new cases and 145,000 deaths annually. Despite advances in cancer treatment modalities, OSCC continues to have poor prognosis with 5-year survival rates less than 50%. Although use of tobacco and alcohol consumption constitute the major risk factors, there is emerging evidence for the role of the microbiome in OSCC. However, studies on the association between the microbiome and OSCC has so far focused on compositional analysis and has been largely limited to the bacterial component of the microbiome. The aim of this study is to characterize the transcriptional activity (function) as well as composition of the multi-kingdom microbiome associated with OSCC and correlate it with the gene expression of the host using ultra-deep metatranscriptome sequencing, which will provide new insight into the role of the microbiome in OSCC and the possible mechanisms by which the tumor’s microbial community may influence on its behavior. This project comprises RNA-Seq data from twenty OSCC tumor/normal tissue pairs and twenty tongue scraping samples from healthy controls. However, due to consent constraints, the human sequences from the control data are filtered out.

  Study phs002678