5272 results for "*oma"

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• 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 EGAD00001003029

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

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

  Dataset EGAD00001003032

• Genome and transcriptome sequence data from a metastatic breast carcinoma patient

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

  Dataset EGAD00001003042

• Genome and transcriptome sequence data from a breast carcinoma patient

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

  Dataset EGAD00001003043

• BLUEPRINT September 2016, ChIPmentation Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 2 sample(s) Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002944

• RNA-sequencing of HCC of metastatic and de novo origin

  Dataset consists of tumors and matched non-tumor livers from 22 patients with multifocal hepatocellular carcinoma. Tissues were obtained from at least two distinct tumor nodules undergoing liver biopsies. Note: refer to the supplementary table of the manuscript for patient IDs and further clinical data.

  Dataset EGAD50000002957

• Whole-exome sequencing of HCC of metastatic and de novo origin

  Dataset consists of tumors and matched non-tumor livers from 22 patients with multifocal hepatocellular carcinoma. Tissues were obtained from at least two distinct tumor nodules undergoing liver biopsies. Note: refer to the supplementary table of the manuscript for patient IDs and further clinical data.

  Dataset EGAD50000002958

• RNASeq on HiSeq platform of 95 pancreatic adenocarcinoma cases

  BAM outputs from RSEM (https://deweylab.github.io/RSEM/) analysis of RNASeq sequencing on HiSeq platform of tumour samples from 95 pancreatic adenocarcinoma cases.

  Dataset EGAD00001003298

• Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

  Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

  Dataset EGAD00001003305

• Glioblastoma CRISPR Screen (2017-04-27)

  This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2017-04-27.

  Dataset EGAD00001003308

• Multiple Myeloma Diagnosis to Relapse study samples (2017-04-27)

  The study will investigate serial samples from the same patient taken at the time of MGUS or SMM diagnosis, and later at the time of evolution towards MM. Samples will be sequenced by whole genome along with a matched normal to obtain the highest possible amount of information toinvestigate genomic changes at disease evolution. This dataset contains all the data available for this study on 2017-04-27.

  Dataset EGAD00001003309

• RNA-sequencing of SYSCOL colorectal adenoma-carcinoma samples

  RNA-sequencing alignment for SYSCOL colorectal adenoma-carcinoma samples

  Dataset EGAD00001003318

• Single-cell RNA sequencing on 5063 single T cells from six hepatocellular carcinoma patients

  T cells isolated from peripheral blood, tumors and adjacent normal tissues from six hepatocellular carcinoma patients. SmartSeq2 and Tang2009 protocol were used to amplify RNA from single T cells. High depth enables simultaneously expression profiling and TCR assembling.

  Dataset EGAD00001003337

• Radiotherapy induced Sarcoma exome (2017-05-17)

  Whole exome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations This dataset contains all the data available for this study on 2017-05-17.

  Dataset EGAD00001003339

• Whole Genome Sequencing of Mutifocal HCC tisue

  The differentiation of distinct multifocal hepatocellular carcinoma (HCC): multicentric disease vs. intrahepatic metastases, in which the management and prognosis varies substantively, remains problematic. We aim to stratify multifocal HCC and identify novel diagnostic and prognostic biomarkers by performing whole genome and transcriptome sequencing, as part of a multi-omics strategy.

  Dataset EGAD00001003348

• ChIP-Seq on multiple myeloma and plasma cell leukaemia cell lines

  ChIP-seq data (H3K4Me1, H3K4Me3, H3K27Ac histone modifications) in experimental triplicates on multiple myeloma cell line KMS11 and plasma cell leukaemia cell lines L363 and JJN3. ChIP reactions were performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal Kit. ChIP libraries were generated using HTP Illumina library preparation kit, and sequenced using Illumina HiSeq 2000 with 100 bp single-ended reads. ChIP-seq files are in BED format.

  Dataset EGAD00001003349

• RNASeq on HiSeq platform of 56 samples from 46 melanoma cases

  BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases. Gene model = Ensembl version 70

  Dataset EGAD00001003353

• Identification of molecule relationship between intravenous leiomyomatosis and uterus myoma

  Up to now, there are two hypothesis about the pathogenesis of the relationship of intravenous leiomyomatosis and uterine myoma. One theory suggests that the IVL comes from the smooth muscle cell in the vessel wall.The other theory indicates that the IVL derives from the uterine myometrium. However, limited to the technology, few studies have been deeply explore the underlying relation. In this study, we employ the RNA sequencing to explore the molecule relationship between IVL and uterus myoma. In order to identify the molecule relationship between IVl and uterine myoma we conducted transcriptome sequencing and bioinformaitc analysis

  Dataset EGAD00001003356

• Whole exome sequencing on HiSeq platform of tumour-normal sample pairs from 53 melanoma cases

  Aligned, merged and deduplicated BAM files from HiSeq whole exome sequencing of 106 samples: matched tumour-normal pairs from 53 melanoma patients.

  Dataset EGAD00001003357

• DNA methylation (RRBS) data for the glioblastoma progression study (GBMatch).

  Genome-wide profiling of DNA methylation levels by RRBS in 349 samples, derived from 112 glioblastoma (IDH wildtype) patients, 13 IDH muated brain tumor patients, and 5 normal brain controls. For each patient samples from at least two and up to six tumor resections are available. For 6 patients multiple regions of each tumor were sampled.

  Dataset EGAD00001003427

• Whole-genome sequencing (WGS) data of Gastric adenocarcinoma and adjacent normal tissues

  High-coverage WGS sequencing of DNA samples from 45pairs GCs was performed on the Illumina HiSeq X Ten System.

  Dataset EGAD00001003431

• FASTQ files of total RNA-Seq data of POPS control samples

  Placental biopsies (n = 64 female placentas, n = 67 male placentas) were selected from healthy pregnancies from the POPs cohort. These patients had no evidence of hypertension at booking and during pregnancy, did not experience pre-eclampsia, Hemolysis, Elevated Liver enzymes, and Low Platelets (HELLP) syndrome, gestational diabetes, or diabetes mellitus type I or type II and other obstetric complications. They delivered live babies with a birth weight percentile in the normal range (20-80th percentile), with no evidence of slowing in fetal growth trajectory. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003457

• Spatial heterogeneity of follicular lymphoma

  Follicular lymphoma (FL) is an incurable B cell malignancy characterized by advanced stage disease and a heterogeneous clinical course. Recent genomic studies have focused on profiling “single” FL biopsies over several time-points, however, multi-site sampling in solid cancers has demonstrated profound spatial intra-tumor heterogeneity (ITH) with implications for precision medicine based initiatives. This study examined the extent of spatial heterogeneity in FL by whole exome sequencing 22 synchronously removed spatially separated biopsies from 9 patients. We observed significant differences in the extent of ITH across cases, with two distinct patterns of high and low spatial heterogeneity emerging. Site-specific alterations in genes with biological, prognostic or therapeutic relevance included, TNFRSF14, PIK3CD, TNFAIP3, PTEN, EP300 and XBP1. In depth characterization of these variants using deep-sequencing techniques confirmed their discordant nature, suggesting on-going genetic diversification driving evolution after widespread tumor dissemination. There was evidence of tumors comprising multiple competing subclones, with distinct clusters of mutations demonstrating differential expansions within spatially-separated sites. For cases where spatial tumors were examined at two time-points (FL and transformation to diffuse large B cell lymphoma (DLBCL)), the degree of heterogeneity increased with transformation. Collectively, our results demonstrate that spatial ITH is prevalent in FL. The existence of site-specific aberrations suggests that a single biopsy may not be sufficient in all patients to capture the full genomic complexity present and these spatial variations need to be considered in biomarker-led clinical studies.

  Dataset EGAD00001003553

• The genomic landscape of cutaneous squamous cell carcinoma based on 40 paired normal and tumour whole-exome sequencing samples

  40 paired normal and tumour whole-exome sequencing samples was used to investigate the genomic landscape of cutaneous squamous cell carcinoma

  Dataset EGAD00001003555

• Whole exome sequencing of SU- DIPG-XIII from different sites

  Whole exome sequencing of diffuse intrinsic pontine glioma (DIPG) cells isolated from the pons and from a sub-ventricular zone site of spread within the frontal lobe from the same individual (SU- DIPG-XIII)

  Dataset EGAD00001003563