4905 results for "*oma"

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• WTS and WES of Renal Cell Carcinoma Tumors From a Phase III Anti-Angiogenic Adjuvant Therapy Trial

  Archival de-identified formalin-fixed paraffin-embedded RCC tumor tissue blocks from nephrectomy or tumor biopsy were processed as per below and the same sections were used for both DNA and RNA extractions. For WES (ACE version 3; Illumina NovaSeq), samples were profiled using Personalis ACE Cancer Exome (Personalis, Inc, Menlo Park, CA) Whole-transcriptome profiles were generated by RNA-seq (Accuracy and Content Enhanced (ACE) version 3; Illumina NovaSeq) using Personalis ACE Cancer Transcriptome (Personalis, Inc, Menlo Park, CA ) Of the 615 patients in the intent-to-treat population in S-TRAC trial, 193 individual specimens were available for molecular profiling, of which 171 (27.8%) (sunitinib, n = 91; placebo, n = 80) returned results for the WES analysis, and 133 (21.6%) (sunitinib, n = 72; placebo, n = 61) returned results for the GES analysis. Of the 138 WTS samples with data, replicates for two patients were summarized by median expression, and three samples were excluded from the final analysis due to low counts.

  Dataset EGAD00001009294

• FACS sorting of ploidy populations in an undifferentiated soft tissue sarcoma for RRBS

  Groups of cells belonging to different ploidy populations (based on PI staining) were collected from an undifferentiated soft tissue sarcoma. The different ploidy populations underwent RRBS, after which copy number signatures for the ploidy-sorted populations and the bulk population were extracted.

  Dataset EGAD00001008667

• Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008925

• Sequencing data for oesophageal and related samples - Ng, Contino et al (WGS)

  Data supporting "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. WGS (BAM files) 383 oesophageal adenocarcinoma samples 383 normal samples

  Dataset EGAD00001007808

• Genome and transcriptome sequence data from an invasive ductal carcinoma of left breast patient

  Genome and transcriptome sequence data from an invasive ductal carcinoma of left breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002601

• Genome and transcriptome sequence data from a carcinoma of unknown primary patient

  Genome and transcriptome sequence data from a carcinoma of unknown primary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008927

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

  Genome and transcriptome sequence data from a lung adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008926

• Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008931

• 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

• lcWGS inform data of neuroblastoma patients

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

  Dataset EGAD00001006638

• Genome and transcriptome sequence data from a salivary gland carcinoma patient

  Genome and transcriptome sequence data from a salivary gland carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008937

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

  Genome and transcriptome sequence data from a lung adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008938

• RRBS analysis to characterize the epigenomic conservation between species in the context of Aging and Cancer.

  This dataset contains Raw Reduced Representation DNA bisulfite-sequencing data obtained from human brain samples corresponding to 3 Young and 3 Old individuals (aging context), and 3 normal and 3 Glioblastoma samples (tumor context). RRBS libraries were prepared at Diagenode SA and samples were sequenced using the Illumina Novaseq6000 sequencing platform.The accompanying samples from this study (mouse tissues) are located at the ENA database under the accession number PRJEB41460.

  Dataset EGAD00001006650

• 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

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008948

• Whole exome sequencing datasets for Low-grade Serous Ovarian Carcinoma

  This dataset includes whole exome sequencing reads from 10 normal and 14 cell lines based on Agilent SureSelect XT Human All Exon v6. They are all 2*100bp reads sequenced using Illumina HiSeq4000.

  Dataset EGAD00001006440

• DKFZ-St.Jude Medulloblastoma - 218 CEF control exomes

  218 control exomes, CEF cohort, sequenced on Illumina machines from the paper "Germline Elongator mutations in Sonic Hedgehog medulloblastoma" (Waszak et al. 2020 Nature).

  Dataset EGAD00001006659

• Blood plasma and paired genomic DNA from neuroblastoma patients

  The dataset is comprised of 3 blood plasma samples (Patient 1-3_plasma_cfDNA) paired with genomic DNA (Patient 1-3_tumor gDNA) from the corresponding primary neuroblastoma from three patients. For all these samples whole-exome sequencing (WES) data have been generated.

  Dataset EGAD00001006012

• RNA-seq from melanoma biopsies

  RNA-seq data for melanoma biopsies at baseline and after treatment

  Dataset EGAD00001009059

• Glioblastoma stem cell lines WGS data

  WGS data for 20 Glioblastoma stem cell (GSC) lines and matched blood samples. Fastq files are available. For 10 GSC samples and the 10 matched blood samples the reads are on 3 fastq files per sample

  Dataset EGAD00001006488

• Neuroblastoma patient Total RNA Seq data

  Tumor Total RNA Seq data of primary neuroblastomas. This is an update of the „Berlin Neuroblastoma Dataset” (EGAS00001004022). This data was used for the analysis of circular RNA expression and regulation in neuroblastoma.

  Dataset EGAD00001008124

• OSTEOMICS_RNA

  RNA sequencing of 79 libraries were prepared, from sample of Osteosarcoma tumors biopsied at diagnosis, with TruSeq Stranded mRNA kit following recommendations: the key steps consist of PolyA mRNA capture with oligo dT beads using 1µg total RNA, fragmentation to approximately 400pb, DNA double strand synthesis, and ligation of Illumina adaptors amplification of the library by PCR for sequencing. Libraries sequencing was performed using Illumina sequencers (NextSeq 500 or Hiseq 2000/2500/4000) in 75 bp paired-end mode.

  Dataset EGAD00001008213

• 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

• DKFZ-St.Jude Medulloblastoma - 8 MB cases, exome/WGS data

  Tumor/Control pairs for 8 medulloblastoma cases, MB cohort, mixed exome and whole genome data, sequenced on Illumina machines from the paper "Germline Elongator mutations in Sonic Hedgehog medulloblastoma" (Waszak et al. 2020 Nature).

  Dataset EGAD00001006660

• Sequencing data for oesophageal and related samples - Scott et al (WGS, RNA)

  Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files

  Dataset EGAD00001006738