3798 results for "*oma"

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• ChIPseq data for Glioblastoma (EGAS00001003953, H016)

  ChIPseq data for human glioblastoma patients, EGAS00001003953. Mix of input, H3K27ac, H3K27me1, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3 and BRD, 20 human samples, 2 cell lines (LN229, ZH487).

  Dataset EGAD00001006548

• FFPE

  The mutational status of 112 recurrently mutated genes in B-cell lymphoma was examined by targeted next-generation sequencing (NGS). Libraries were performed with 150 ng of genomic DNA (gDNA) obtained from formalin-fixed paraffin-embedded (FFPE) biopsy using molecular-barcoded library adapters (ThruPLEX Tag-seq kit; Takara) coupled with a custom hybridization capture based method (SureSelect XT Target Enrichment System Capture strategy, Agilent Technologies Inc.) and sequenced in a MiSeq instrument (Illumina, 2x150bp).

  Dataset EGAD00001006565

• cfDNA

  The mutational status of 112 recurrently mutated genes in B-cell lymphoma was examined by targeted next-generation sequencing (NGS). Libraries were performed with 15-30 ng of cfDNA obtained from plasma using molecular-barcoded library adapters (ThruPLEX Tag-seq kit; Takara) coupled with a custom hybridization capture based method (SureSelect XT Target Enrichment System Capture strategy, Agilent Technologies Inc.) and sequenced in a MiSeq instrument (Illumina, 2x150bp).

  Dataset EGAD00001006566

• A novel orthotopic patient-derived xenograft model of radiation-induced glioma following medulloblastoma

  DNA methylation arrays were performed to molecularly subtype these samples based on Capper D, Jones DTW, Sill M, et al. DNA methylation-based classification of central nervous system tumours. Nature. 2018;555(7697):469-474. doi:10.1038/nature26000

  Dataset EGAD00010002017

• CRISPR/Cas9-mediated genome editing of Schistosoma mansoni acetylcholinesterase

  Here we report successful gene knock-in (KI) in the eggs of Schistosoma mansoni by combining CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs). We targeted the acetylcholinesterase (AChE) gene of S. mansoni using two synthetic guide RNAs (gRNAs), X5 and X7, respectively. Liver eggs of S. mansoni were exposed to CRISPR-vector containing X5 or X7 by electroporation. Simultaneously, eggs were transfected with a ssODN donor encoding a stop codon in all six frames. Next generation sequencing analysis revealed that CRISPR/Cas9-mediated editing in S. mansoni eggs resulted in Homology-Directed Repair (HDR) when template DNA ssODN provided. Furthermore, soluble egg antigen (SEA) from AChE-modified eggs exhibited markedly reduced AChE activity compared with controls, indicative that programmed Cas9 cleavage mutated the AChE gene. Following injection of modified schistosome eggs into the tail veins of mice, a significant decrease in granuloma size in the lungs of these animals. Notably, an enhanced Th2 response induced by eggs in lung, and splenocytes small intestine-draining mesenteric lymph node cells was also generated in mice injected with X5-KI eggs in different methods. These findings further demonstrate the power and utility of CRISPR/Cas9-based genome editing for undertaking functional genomics studies in schistosomes.

  Dataset EGAD00001006573

• Systemic analysis of cutaneous and uveal melanoma liver metastases

  RNAseq and WES of liver metastases samples (resections and biopsies) of CM and UM patients

  Dataset EGAD00001006577

• Neuroblastoma Cell Line Circle-seq Data

  This dataset comprises Circle-seq data for 12 neuroblastoma cell lines supporting Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020).

  Dataset EGAD00001006579

• Primary Neuroblastoma Circle-seq Data

  Circle-seq data for 21 primary neuroblastoma samples supporting Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020).

  Dataset EGAD00001006580

• Small molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma (methylation dataset)

  human medulloblastoma xenograft isolated from mouse brain was frozen and genomic DNA or RNA was extracted. Bisulfite converted DNA was processed and hybridised to illumina EPIC or 450K arrays using standard protocols. RNAseq was performed on total RNA.

  Dataset EGAD00001006583

• RNA data of neuroblastoma patients

  94 sample with multi-omics analysis of ALT-positive neuroblastoma tumors, rna sequencing

  Dataset EGAD00001006587

• Transcriptomic profiling of primary tumor and paired hepatic oligometastasis of PDAC

  The dataset was generated for studying metastatic mechanism of pancreatic ductal adenocarcinoma (PDAC). It is consisted of pair-end raw RNA sequencing reads of 33 fresh froze PDAC specimens, which includes 6 tumor-adjacent normal tissues (N), 13 primary tumors (PT), and 14 hepatic metastases (HM) from 14 PDAC patients (6 N-PT-HM trios, 7 PT-HM paires, and 1 HM).

  Dataset EGAD00001006598

• Whole exome sequencing of paired primary tumor (PT) and hepatic metastasis (HM) of PDAC

  This data set contains pair-end raw whole exome sequencing data of matched primary tumors (PT) and hepatic metastases (HM) of pancreatic ductal adenocarcinoma (PDAC). Eight tumor adjacent normal tissues (N) were also evaluated. In total, there are 30 specimens generated from 11 PDAC cases, including 8 PT-HM-N trios and 3 PT-HM paires.

  Dataset EGAD00001006599

• RNAseq of NSCLC and melanoma tumor xenografts treated with ADC

  RNAseq of tumours derived from NSCLC (n=3 PDX; n=1 CDX) and melanoma (n=1 CDX) xenograft models treated with ADC or controls (64 samples; 189 FASTQ files).

  Dataset EGAD00001006620

• Alveolar Rhabdomyosarcoma sequencing data

  This dataset comprises DNA sequencing for tumor and matched normal from an Alveolar Rhabdomyosarcoma patient. It also include RNA sequencing data from the tumor sample.

  Dataset EGAD00001006622

• Sequencing data for Hepatoblastoma samples

  This dataset contains DNA sequencing data for twelve hepatoblastoma tumor samples, four of which have matched normals. Nine of the samples also have RNA sequencing data from the tumor sample. The dataset comprises six samples from patient tissues and six from cell lines; see metadata for details.

  Dataset EGAD00001006621

• scRNA data of neuroblastoma patients

  31 single-cell transcriptomes of neuroblastomas and normal human developing adrenal glands at various stages of embryonic and fetal development

  Dataset EGAD00001006624

• Chip-Seq data of neuroblastoma patients

  144 sample from individuals with ALT-positive neuroblastoma tumors, chip-seq sequencing

  Dataset EGAD00001006625

• hcWGS data of neuroblastoma patients

  238 samples from individuals with ALT-positive neuroblastoma tumors, high coverage whole genome sequencing

  Dataset EGAD00001006626

• Leiomyosarcoma RNA-Seq

  RNA was extracted from fresh frozen LMS material for 29 untreated tumors (24 primary tumors, 5 metastatic12 relapses) and 13 tumors treated with radiation(7 primaries, 6 metastatic relapses). RNA-Seq sequencing was performed using established protocols on Illumina HiSeq 2500

  Dataset EGAD00001006628

• WES inform samples

  89 samples of individuals with ALT-positive neuroblastoma tumors, exome sequencing

  Dataset EGAD00001006637

• lcWGS inform data of neuroblastoma patients

  97 samples of individuals with ALT-positive neuroblastoma tumors, low coverage whole genome sequencing

  Dataset EGAD00001006638

• hcWGS inform data of neuroblastoma patients

  63 samples of individuals with ALT-positive neuroblastoma tumors, high coverage whole genome sequencing

  Dataset EGAD00001006639

• The mutational landscape of human somatic and germline cells

  During the course of a lifetime normal human cells accumulate mutations. Here, using multiple samples from the same individuals we compared the mutational landscape in 29 anatomical structures from soma and the germline. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types but their absolute and relative contributions varied substantially. SBS18, potentially reflecting oxidative damage, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The mutation rate was lowest in spermatogonia, the stem cell from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutation processes and may be partially attributable to a low cell division rate of basal spermatogonia. The results provide important insights into how mutational processes affect the soma and germline.

  Dataset EGAD00001006641

• The mutational landscape of human somatic and germline cells

  During the course of a lifetime normal human cells accumulate mutations. Here, using multiple samples from the same individuals we compared the mutational landscape in 29 anatomical structures from soma and the germline. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types but their absolute and relative contributions varied substantially. SBS18, potentially reflecting oxidative damage, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The mutation rate was lowest in spermatogonia, the stem cell from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutation processes and may be partially attributable to a low cell division rate of basal spermatogonia. The results provide important insights into how mutational processes affect the soma and germline.

  Dataset EGAD00001006642

• The mutational landscape of human somatic and germline cells

  During the course of a lifetime normal human cells accumulate mutations. Here, using multiple samples from the same individuals we compared the mutational landscape in 29 anatomical structures from soma and the germline. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types but their absolute and relative contributions varied substantially. SBS18, potentially reflecting oxidative damage, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The mutation rate was lowest in spermatogonia, the stem cell from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutation processes and may be partially attributable to a low cell division rate of basal spermatogonia. The results provide important insights into how mutational processes affect the soma and germline.

  Dataset EGAD00001006643