11768 results for "cancer rna-seq"

in 13.84 milliseconds.

• Non-coding RNAs Activated by the Wnt/Beta-catenin Signaling Pathway in Hepatoblastoma

  Hepatoblastoma (HB) is the most common pediatric liver tumor, affecting mostly children under 3 years of age. This rare tumor represents 1% of all pediatric cancers. Genetic studies have shown that HB is characterized by high frequency mutations of the CTNNB1 gene encoding beta-catenin (around 75%) and relative genomic stability. Here we have analyzed the transcriptional profile of 21 HBs compared to matched non-tumor livers by Cap Analysis of Gene Expression (CAGE), which provides accurate and quantitative profiling of all transcripts. CAGE analysis revealed strong upregulation of known Wnt target coding genes in most tumors analyzed, consistent with previous transcriptomic studies. To better define the Wnt-dependent transcriptional landscape of HB, we integrated CAGE data with TCF4 ChIP-seq data from a CTNNB1-mutated cancer cell line and with the FANTOM5 genomic coordinates of TCF/LEF binding motifs. Both TCF/LEF binding motifs and ChIP-seq peaks were strongly enriched in the immediate upstream region, not only for protein-coding genes, but also for non-coding transcripts. Among the selected 112 top Wnt target genes at FDR<1.0E-6 and fold change>8, we found clear over-representation (66%) of distant transcription start sites (TSSs) representing lncRNAs and enhancer RNAs, which raises the question of their role in HB pathogenesis. Analysis of the 112 promoters using CAGEd-oPOSSUM confirmed the predominant involvement of Tcf/Lef transcription factors, together with HNF4G, GATA2, Sox3 and Ets-related genes. Finally, the 112 Wnt target signature defined 3 tumor subclasses, T1, T2 and T3, characterized by progressive alteration of the non-coding part of the transcriptome and significant differences in clinical behavior.

  Study phs001433

• Pediatric Patient-Derived-Xenograft development in MAPPYACTS – international pediatric cancer precision medicine trial in relapsed and refractory tumors

  Pediatric patients with recurrent and refractory cancers are in most need for new treatments. This study developed patient-derived-xenograft (PDX) models within the European MAPPYACTS cancer precision medicine trial (NCT02613962). To date, 131 PDX models were established following heterotopical and/or orthotopical implantation in immunocompromised mice: 76 sarcomas, 25 other solid tumors, 12 central nervous system tumors, 15 acute leukemias, and 3 lymphomas. PDX establishment rate was 43%. Histology, whole exome and RNA sequencing revealed a high concordance with the primary patient’s tumor profile, human leukocyte-antigen characteristics and specific metabolic pathway signatures. A detailed patient molecular characterization, including specific mutations prioritized in the clinical molecular tumor boards are provided. Ninety models were shared with the IMI2 ITCC Paediatric Preclinical Proof-of-concept Platform (IMI2 ITCC-P4) for further exploitation. This new PDX biobank of unique recurrent childhood cancers provides an essential support for basic and translational research and new treatments development in advanced pediatric malignancies.

  Study EGAS00001007327

• SF11964 snATAC Seq Low Grade Astrocytoma IDHR132H mutant

  Single Nuclei ATAC Seq IDHR132H mutant Astrocytoma . Male, 64. Single Nuclei ATAC seq data from low grade human glioma sample. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005414

• H3K27ac ChIP-seq in Insulinomas

  H3K27ac ChIP-seq datasets in human insulinoma samples

  Dataset EGAD50000000461

• BLUEPRINT EpiVar ChIP-seq of Monocytes & Neutrophils

  BLUEPRINT EpiVar ChIP-seq of Monocytes & Neutrophils

  Study EGAS00001000870

• Mediator ChIP-Seq datasets in human islets

  6 ChIP-Seq datasets of Mediator in human pancreatic islets from 6 donors

  Dataset EGAD00001005202

• Reference epigenome Islet-derived_MSC06 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007897

• Reference epigenome Islet-derived_iPSC04 h3k4me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007892

• Reference epigenome Islet-derived_MSC08 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007907

• Reference epigenome Islet-derived_MSC08 input ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 input ChIP-Seq paired end data

  Dataset EGAD00001007908

• Reference epigenome Islet-derived_MSC06 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007898

• Reference epigenome Islet-derived_iPSC04 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007890

• Reference epigenome Islet-derived_MSC06 input ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 input ChIP-Seq paired end data

  Dataset EGAD00001007901

• Reference epigenome Islet-derived_MSC08 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007905

• Reference epigenome Islet-derived_MSC08 h3k4me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007906

• Reference epigenome Islet-derived_iPSC04 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007893

• Reference epigenome Islet-derived_MSC06 h3k27me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007896

• Reference epigenome Islet-derived_MSC08 h3k27me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007903

• Cohesin ChIP-Seq datasets in human islets

  3 ChIP-Seq datasets of Cohesin in human pancreatic islets from 3 donors

  Dataset EGAD00001005203

• Reference epigenome Islet-derived_MSC06 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007895

• Reference epigenome Islet-derived_iPSC04 h3k27me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007889

• Reference epigenome Islet-derived_MSC06 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007900

• Reference epigenome Islet-derived_MSC06 h3k4me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007899

• Reference epigenome Islet-derived_iPSC04 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007888

• Reference epigenome Islet-derived_iPSC04 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007891