Search Results - EGA European Genome-Phenome Archive

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

5270 results for "*oma"

in 50.40 milliseconds.

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

RNASeq on HiSeq platform of 56 samples from 46 melanoma cases

Identification of molecule relationship between intravenous leiomyomatosis and uterus myoma

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

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

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

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

Spatial heterogeneity of follicular lymphoma

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

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

Clonal evolution study of Intrahepatic cholangiocarcinoma: 69 PDPCs and 6 tissues.

Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

Genome and transcriptome sequence data from a glioblastoma multiforme patient

Genome and transcriptome sequence data from a squamous cell carcinoma of ge junction patient

Genome and transcriptome sequence data from an anaplastic ependymoma patient

Genome and transcriptome sequence data from a metastatic spindle cell sarcoma patient

Genome and transcriptome sequence data from a metastatic neuroendocrine carcinoma patient

Genome and transcriptome sequence data from an advanced adenocarcinoma of lung patient

Genome and transcriptome sequence data from a non-small cell lung carcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a adenocarcinoma of the lung patient

Genome and transcriptome sequence data from an ependymoma patient

Genome and transcriptome sequence data from a left cavernous sinus invasive skull meningioma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic rhabdomyosarcoma patient

Genome and transcriptome sequence data from a metastatic mucinous adenocarcinoma of the rectum patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the ge junction patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic adrenocortical carcinoma patient

Genome and transcriptome sequence data from a thymoma carcinoma patient

Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from an osterosarcoma patient

Genome and transcriptome sequence data from a metastatic epitheloid angiomyelolipoma patient

Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of the oropharynx patient

Genome and transcriptome sequence data from a high-grade serous fallopian tube carcinoma patient

Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient

Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

Genome and transcriptome sequence data from a pleomorphic sarcomatoid epithelioid carcinoma patient

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a metastatic meningioma patient

Genome and transcriptome sequence data from a thymic carcinoma patient

Genome and transcriptome sequence data from a metastatic myoepithelial carcinoma of parotid patient

Genome and transcriptome sequence data from a high grade serous carcinoma of the fallopian tube/ovary/peritoneum patient