4982 results for "*oma"

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• Multi-region sequencing of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region whole-exome sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Dataset EGAD00001008020

• m6A profiling in Lung Adenocarcinoma

  Applying a refined m6A RNA immunoprecipitation method, we profiled the m6A epitranscriptome on 10 non-neoplastic lung (NL) tissues and 53 lung adenocarcinoma tumors.

  Dataset EGAD00001008026

• Whole-exome sequencing laser capture micro-dissected biopsies of human renal cell carcinoma

  The dataset comprises whole exome sequences from laser capture micro-dissected biopsies of 10 patients diagnosed with clear cell renal cell carcinoma. In total over 100 regions are sampled to allow 'focally exhaustive' sequencing and explore the limits of intra-tumoural heterogeneity.

  Dataset EGAD00001008029

• Multiregional single cell RNA sequencing of human renal cell carcinoma

  The dataset comprises of 5' single cell RNA sequencing with TCR enrichment with 10x Genomics' Chromium technology of multiregional biopsies of human renal cell carcinomas. Biopsies from different tumour regions, the tumour-normal interface, normal kidney, normal adrenal, metastatic regions, peri-nephric fat, and peripheral blood were sequenced from 12 patients with kidney tumours.

  Dataset EGAD00001008030

• G-SAM: Transcriptional Evolution of Glioblastomas Treated With Standard of Care

  Collection of mostly matching primary and recurrent glioblastoma RNA-seq sample pairs, also matching with an earlier DNA sequencing study

  Dataset EGAD00001007860

• scRNAseq of neuroblastoma PDX and cell lines

  This dataset contains the 22 bam files coresponding to the scRNAseq done in PDX models and cell lines.

  Dataset EGAD00001007870

• RNA-seq data from paired tumour and germline samples from mesothelioma patients for study EGAS00001005196

  RNA-seq data from paired tumour and germline samples from mesothelioma patients for study EGAS00001005196

  Dataset EGAD00001007874

• RNA-seq on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics

  RNA-sequencing on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics. Three samples from each of the treatment condition were analysed. Next-Seq platform was used for sequencing.

  Dataset EGAD00001008035

• Myeloid cell programming in patients with non-medullary thyroid carcinoma

  This dataset contains single-cell RNA sequencing data from patients with thyroid cancer (n=7), multinodal Goiter (n=3) and healthy individuals (n=5). Mononuclear cells were taken from both the peripheral blood and the bone marrow compartments. We used a pooled single-cell design where multiple individuals were pooled in a single sample for sequencing (NextSeq 500-V2) and later demultiplexed using their genotype data. Associated metadata contains information on the phenotypes per individual, the pooling design and the linkage between the supplied files and sequenced pools. Due to limitations from EGA in uploading single-cell data, the raw fastq files were processed as follows: (i) I1/I2/R1/R2 fast files were concatenated over the different lanes. (ii) Concatenated I1 and I2 files were interleaved, as were the concatenated R1 and R2 files to generate two fastq files per pool containing all the information. To interleave the fastq files, the BBmap tool bbmap/reformat.sh was used, which can also be used to de-interleave the files.

  Dataset EGAD00001008108

• Neuroblastoma sequencing data

  This dataset contains tumor and normal whole exome DNA sequence data for a patient with neuroblastoma

  Dataset EGAD00001008120

• 46 VCF files of glioma patient 2021

  the source data in VCF format of 46 patients primary malignant glioma cohort in Chinese population

  Dataset EGAD00001008115

• Osteosarcoma sequencing data

  This dataset contains samples from 13 patients with osteosarcoma. 13 samples have whole exome tumor data. 12 samples have tumor RNAseq data. 3 samples have matched normal dna sequence data

  Dataset EGAD00001008117

• Neuroblastoma patient WGS data

  Paired tumor and normal WGS 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 EGAD00001008123

• 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

• IMCISION RNAseq

  RNA sequencing of 32 primary head and neck squamous cell carcinoma (HNSCC) samples prior to treatment with neoadjuvant anti-PD-1 (n=6) or anti-PD-1 + anti-CTLA-4 (n=26) immunotherapy, and 30 paired on-treatment HNSCC samples (i.e. after neoadjuvant immunotherapy). RNA quantity used: 10ng. Library Preparation Kit: SMART Stranded Total RNA Seq Kit (Takara). Sequencing parameters: NovaSeq 6000, 2x 100 bp. File type: fastQ

  Dataset EGAD00001008127

• Multi-region RNA-Seq data of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region RNA sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Dataset EGAD00001008133

• IMCISION DNAseq

  Whole-exome sequencing of 32 primary head and neck squamous cell carcinoma samples prior to treatment with neoadjuvant anti-PD-1 (n=6) or anti-PD-1 + anti-CTLA-4 (n=26) immunotherapy. DNA quantity used: 50ng. Library Preparation Kit: Twist Human Core Exome Plus (Twist Bioscience). Sequencing parameters: NovaSeq 6000, 2x 100 bp. File type: fastQ.

  Dataset EGAD00001008139

• EPICC: Evolutionary Predictions in Colorectal Cancer

  ATAC-seq profiling bam files from colorectal carcinoma and adenoma.

  Dataset EGAD00001008140

• RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells

  RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells. RNAseq was performed using 200 ng of total RNA by GATC Biotech. Directional libraries were performed after mRNA selection by polyA selection using UTP method. RNA-seq libraries were sequenced on HiSeq2500 Illumina machine using 100bp paired-end reads. Reads alignment was performed using the STAR aligner (version 2.4.0f1) and human genome hg19 as reference.

  Dataset EGAD00001007813

• Functional dissection of inherited non-coding variation influencing multiple myeloma risk

  This dataset contains ATAC sequencing of plasma cells from multiple myeloma (MM) patients. The data was used to investigate genotype-specific chromatin accessibility quantitative trait locus (caQTL) using caQTLseg (https://github.com/abhisheknrl/caQTLseg). This dataset contains 161 bam files.

  Dataset EGAD00001007814

• Whole genome bisulfite sequencing on 10 multiple myeloma cases

  Whole genome bisulfite sequencing on 10 multiple myeloma cases. Data quality control and adaptor-trimmed were performed with the Trimomatic tool. Paired-reads were mapped to the hg19 human reference with methylCtools aligner.

  Dataset EGAD00001007821

• Enhanced reduced representation bisulfite sequencing (eRRBS) on 45 multiple myeloma samples and 3 normal plasma cell

  Enhanced reduced representation bisulfite sequencing (eRRBS) on 45 multiple myeloma samples and 3 normal plasma cell. Enhanced reduced representation bisulfite sequencing (eRRBS) on 45 multiple myeloma samples and 3 normal plasma cell. Libraries were sequenced on a HiSeqTM4000 Illumina machine using 75bp paired-end reads

  Dataset EGAD00001007822

• Whole exome sequencing (bam files) of 55 samples of myxofibrosarcoma and 44 matched pairs

  Whole exome sequencing data (bam files) of 55 samples of myxofibrosarcoma and 44 matched pairs.

  Dataset EGAD00001007824

• Targeted-capture sequencing (bam files) of 81 samples of myxofibrosarcoma and 44 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the Targeted-capture sequencing was performed.

  Dataset EGAD00001007826

• Double/triple hit lymphoma whole exome and panel sequencing data

  Mutational landscape of high-grade B-cell lymphoma with MYC-, BCL2 and/or BCL6 rearrangements characterized by whole-exome sequencing and panel sequencing.

  Dataset EGAD00001007805

• Whole genome sequencing (bam files) of 5 samples of myxofibrosarcoma and 5 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the whole genome sequence was performed.

  Dataset EGAD00001007825

• Neuroblastoma WGS samples used for detection of seismic amplification

  Paired-end WGS data of 27 neuroblastoma patient samples (10 obtained at diagnosis, 6 at relapse and 11 matched blood samples as controls) used for detection of complex "seismic" amplification. Mean coverage is 24-55x per sample. The remaining patient samples of the dataset can be found under accession number EGAS00001001308.

  Dataset EGAD00001007807

• 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

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

  Data supporting: "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. RNAseq (BAM files) 214 oesophageal adenocarcinoma samples

  Dataset EGAD00001007809

• Paired-WGS Sequencing of Primary lymphomas of the central nervous system (PCNSL)

  Paired WGS samples, 24 tumor/control pairs of primary CNS lymphoma, sequenced on HiSeq X Ten using Illumina TruSeq Nano DNA for library preparation.

  Dataset EGAD00001007810

• RNA-seq data from 27 glioblastoma samples

  27 Fresh frozen tissue specimens were crushed by mortar and pestle, homogenized using the QIAShredder kit (Qiagen), and genomic DNA and total RNA were extracted using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer’s instructions. RNA libraries were synthesized using 200 ng of total RNA using the Ilumina TruSeq Stranded RNA LT Sample Prep Kit (Illumina), and subsequently sequenced on the NextSeq550 platform to a read depth of 80 million clusters and 160 million paired end reads (75 bp X 75 bp) using V2 chemistry.

  Dataset EGAD00001008362

• two tables containing RNASeq expression values to patients with RNA-Seq data in the study "Comprehensive genomic characterization of refractory multiple myeloma (H067)"

  two tables containing RNASeq expression values to patients with RNA-Seq data in the study "Comprehensive genomic characterization of refractory multiple myeloma (HIPO_067)". From the bam files gene expression was calculated with the annotation of Gencode.v19. Raw Counts and TPM values are given in one table, the other contains filtered TMM normalized CPM values (genes < 1CPM omitted).

  Dataset EGAD00001008363

• Aggressive genomic features in clinically indolent primary HHV8-negative effusion-based lymphoma

  Genomic profiling of effusion-based fluid samples from 8 HHV8-negative effusion-based lymphoma patients.

  Dataset EGAD00001008364

• WES Melanoma subtypes

  The dataset include sequencing data from 23 patients diagnosed with metastatic melanoma. The 23 metastatic melanoma subtypes consisted of cutaneous melanoma (CM, n=10); head and neck melanoma (HNM, n=7); uveal melanoma (UM, n=4); acral lentiginous (AM, n=1) and mucosal melanoma (MM, n=1).

  Dataset EGAD00001008336

• Mutational signatures in esophageal squamous cell carcinoma from eight countries of varying incidence – filtered vcf files

  Mutational signatures in esophageal squamous cell carcinoma from eight countries of varying incidence – filtered vcf files

  Dataset EGAD00001008339

• Whole genome sequence and RNA-seq data from paired tumour and germline samples from mesothelioma patients

  Whole genome sequencing from paired tumour and germline malignant pleural mesothelioma samples

  Dataset EGAD00001008341

• Neuroblastoma hybrid capture sequencing panel

  Patient neuroblastoma hybrid capture sequencing panel. 5 samples from 2 donors (BAM files). For each donor, we obtained neuroblastoma tumor samples and neuroblastoma ALKi resistant samples. This dataset was used to study ALKi resistance in neuroblastoma.

  Dataset EGAD00001008343

• Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens

  Enriched tumor epithelium, tumor-associated stroma, and whole tissue were collected by laser microdissection from thin sections across spatially separated levels of ten high-grade serous ovarian carcinomas (HGSOCs) and analyzed by mass spectrometry, reverse phase protein arrays, and RNA sequencing. Unsupervised analyses of protein abundance data revealed independent clustering of an enriched stroma and enriched tumor epithelium, with whole tumor tissue clustering driven by overall tumor “purity.” Comparing these data to previously defined prognostic HGSOC molecular subtypes revealed protein and transcript expression from tumor epithelium correlated with the differentiated subtype, whereas stromal proteins (and transcripts) correlated with the mesenchymal subtype. Protein and transcript abundance in the tumor epithelium and stroma exhibited decreased correlation in samples collected just hundreds of microns apart. These data reveal substantial tumor microenvironment protein heterogeneity that directly bears on prognostic signatures, biomarker discovery, and cancer pathophysiology and underscore the need to enrich cellular subpopulations for expression profiling.

  Dataset EGAD00001008344

• Multiple Myeloma ChipSeq data on six histone modifications

  The data contained in this dataset is ChipSeq BAM files aligned to reference genome hg38. The ChipSeq was based on a combination of six histone modifications as follows: H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K27Ac and H3K36me3. The samples are patient-derived xenografts generated by passaging primary patient CD138+ selected cells through the SCID-rab myeloma mouse model.

  Dataset EGAD00001008353

• Single cell atlas of neuroblastoma and the human fetal adrenal gland

  Using the chromium 3' expression assay, we generated an atlas of neuroblastoma and the human fetal adrenal gland. These data were complemented with whole genome sequencing of normal and tumour DNA from the neuroblastoma samples.

  Dataset EGAD00001008345

• Human primary melanoma project

  Mutational burden and profiles to be studied in approx. 500 human primary melanomas with matched normal samples, part of the Leeds melanoma cohort. New custom design targeted capture panel covering melanoma-specific copy number alterations, promoter mutations, gene fusions, coding genes, HLA regions and IFNg/JAK/STAT pathway genes.

  Dataset EGAD00001008360

• DNA (exome) sequencing of uveal melanoma metastases

  DNA (exome) sequencing of uveal melanoma metastases.

  Dataset EGAD00001007911

• RNA sequencing of uveal melanoma metastases.

  RNA sequencing of uveal melanoma metastases.

  Dataset EGAD00001007912

• Single-cell RNA and TCR sequencing of PBMC from patients with uveal melanoma

  Single-cell RNA and TCR sequencing of PBMC from patients with uveal melanoma.

  Dataset EGAD00001007913

• RNA-seq data from a variety of pediatric brain tumors

  RNA-seq (n=52) data from a variety of pediatric brain tumors including ependymoma (PFA, PFB, Ste, spinal), medulloblastoma (G3, G4, SHH), high grade glioma (H3K27 and H3-WT), pilocytic astrocytoma, and more. Raw data provided as FASTQ. Data generated on Illumina HiSeq2500.

  Dataset EGAD00001007915

• Hi-C sequencing from a variety of pediatric brain tumors

  Hi-C (n=72) data from a variety of pediatric brain tumors including ependymoma (PFA, PFB, Ste, spinal), medulloblastoma (G3, G4, SHH), high grade glioma (H3K27 and H3-WT), pilocytic astrocytoma, and more. Raw data provided as FASTQ. Data generated on Illumina HiSeq2500.

  Dataset EGAD00001007914

• CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  Dataset EGAD00001007938

• Embryonal Rhabdomyosarcoma sequencing data

  This dataset contains samples from 9 patients with embryonal rhabdomyosarcoma. 9 samples have whole exome tumor data (one has multiple). 7 samples have tumor RNAseq data. 1 sample has matched normal dna sequence data

  Dataset EGAD00001007939

• Cancer and germline exomes consisting of FASTQ reads from melanoma, lung and colon cancer samples

  Cancer and germline exomes consisting of FASTQ reads from 6 individuals (4 melanoma, 1 lung and 1 colon cancer). Exome sequencing was performed on illumina with a depth of 100x to 200x. 2 Melanoma datasets contain reads from 2 different tumor regions 2 Melanoma datasets contain reads from 1 tumor region and from a tumor derived cell line 1 Melanoma dataset contains reads from 2 healthy tissues Colon and lung datasets contain both 1 matched germline-tumor pair

  Dataset EGAD00001007950

• Cancer RNA-seq consisting of FASTQ paired-end reads from melanoma and lung cancer sample

  Cancer RNA-seq consisting of FASTQ paired-end reads from 6 individuals (4 melanoma, 1 lung cancer). RNASEQ was performed on illumina, Truseq capture kit, 40M-80M clusters. 2 Melanoma datasets contain reads from 1 tumor region and from a tumor derived cell line 2 Melanoma, 1 Colon and 1 lung datasets contain each reads from a single region.

  Dataset EGAD00001007951