16461 results for "sec+and+unspecified+malignant+neoplasm"

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• CosMX spatial transcriptomics

  This study consists of the spatial transcriptomics analyis data generated by : CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex); NanoString, USA for n=4 SLD-HCC and n=4 non-SLD-HCC. The goal of this data is to compare SLD-HCC vs non-SLD-HCC as well as response to immunotherapy

  Dataset EGAD50000001507

• 909 bulk mRNA sequencing samples from the UPTIDER program

  Raw sequencing data for 909 bulk mRNA samples that correspond to 749 metastases, 64 primary tumours and 96 normal tissue. These samples were sequenced using NovaSeq6000. Library was prepared with Lexogen QuantSeq 3' FWD. Raw single-end fastq samples have been deposited as gzipped files.

  Dataset EGAD50000001910

• Dataset for desmoplastic small round cell tumor - WES

  This dataset contains 45 WES sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq 2500, Illumina HiSeq 4000 and NovaSeq 6000 using Agilent SureSelect Human All Exon V5 Kit. The sequencing was always paired.

  Dataset EGAD50000000910

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer - DEDICATION co-hort

  Liquid biopsies generated for minimal residual disease monitoring of non-small cell lung cancer. Ultra deep targeted sequencing of lung cancer related genes with UMIs. This dataset contains the dedication cohort

  Dataset EGAD50000002230

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer - Biobank co-hort

  Liquid biopsies generated for minimal residual disease monitoring of advanced non-small cell lung cancer. Ultra deep targeted sequencing of lung cancer specific genes, with UMIs. This dataset consists of the biobank cohort

  Dataset EGAD50000002231

• Whole exome sequencing (bam files) of 55 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 whole exome sequence was performed.

  Study EGAS00001005442

• 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.

  Study EGAS00001005444

• 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.

  Study EGAS00001005443

• Sequencing data for oesophageal and related samples - Mourikis et al (RNA)

  Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. RNAseq (BAM files) 137 samples

  Dataset EGAD00001004776

• A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing

  We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing.

  Dataset EGAD00001002740

• Total RNA sequencing data from the Triple Negative Trial (TNT)

  BAM files from total RNA sequencing of samples from breast cancer patients in the TNT trial. Data includes 186 primary tumour samples and 13 matched recurrence samples.

  Dataset EGAD00001011141

• Pseudodiastrophic dysplasia exome sequencing dataset

  This dataset contains 7 paired end fastq files obtained with Illumina Hiseq and Nextseq sequencing of whole exomes relevant to a study of pseudodiastrophic dysplasia (PDD). It includes 3 patients from 2 unrelated families diagnosed with PDD, together with the four parents.

  Dataset EGAD00001005775

• GATCI whole genome sequence data

  Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found in the bam header

  Dataset EGAD00001005914

• Chromatin 3D interactions mediate genetic effects on gene expression (RNA-seq)

  RNA-seq data for 168 Lymphoblastoid Cell Lines (LCL) and 78 Fibroblasts (FIB) from the Gencord Cohort. This dataset was generated as part of the following study: Delaneau et al (2019). Chromatin 3D interactions mediate genetic effects on gene expression.

  Dataset EGAD00001004872

• Deep multi-region WGS of lung cancer tumours

  Deep WGS (germline and 2-5 tumour regions) was performed on 20 patients: 13 lung adenocarcinoma, 5 squamous cell carcinoma, 2 small-cell lung cancers. A total of 68 BAM files are provided, where tumours were sequenced to 60x or 150x depth.

  Dataset EGAD00001005287

• WGS of human colorectal cancer organoid exposed to genotoxic pks+ E. coli

  Organoid cultures were exposed to two different E.Coli strains and a dye control with three biological duplicates. Their original culture was harvested as a control. In total 10 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.

  Dataset EGAD00001005416

• 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

• CITE-seq for peripheral blood samples of 5 breast cancer patients

  We have 5 breast cancer patients who received VEN therapy. We collected their peripheral blood samples before and after long-term Venetoclax treatment. We apply CITE-seq protocol to these samples. This collection contains the all CITE-seq data for patients.

  Dataset EGAD00001008751

• WES data generated in multifocal ileal NETs study

  This dataset includes whole-exome sequencing data for multifocal ileal tumor samples from two patients. Exonic sequences were enriched using the Agilent V2 capture probe set and sequenced by 76-bp paired-end reads using the Illumina Genome Analyzer IIx system with a mean coverage of 80x for each base

  Dataset EGAD00001006408

• Single cell RNA-seq CD8 T cells from elder adults

  Single cell RNA-seq profiling of ~62k purified CD8+ T cell transcriptomes, from six healthy older adult donors using 10X genomics. Cells from each donor were separated based on their IL-7R protein expression (i.e. CD8+ IL7R+ and CD8+ IL7R- T cells).

  Dataset EGAD00001006000

• Single cell RNAseq of PBMC from bladder cancer patients

  This dataset contains single cell RNA sequencing data of PBMC samples from 20 bladder cancer patients. cDNAs and single cell RNA libraries were prepared following manufacturer’s user guide (10x Genomics). Each library was sequenced in HiSeq4000 (Illumina) to achieve ~300 million reads following manufacturer’s sequencing specification.

  Dataset EGAD00001006182

• smRNA-seq of human post-mortem brain data of frontal lobe (Tuebingen part)

  This dataset contains smRNA-seq data from post-mortem human brain tissue of the frontal lobe of patients with FTD and healthy controls. The smRNA-sequencing was done in two parts, this dataset depicts the data generated at the DZNE Tübingen.

  Dataset EGAD00001006846

• Single-cell RNA-seq of matched pediatric AML tumors

  Single-cell RNA-seq of pediatric AML tumours from patients enrolled in the clinical trial AAML1031. Obtained using the 10X Chromium Single Cell 3’ Reagent Kit, v3.0. A total of 75 samples were obtained from biopsies at diagnosis, remission and relapse from 28 patients.

  Dataset EGAD00001011195

• Correction of a Factor VIII genomic inversion with designer recombinases

  PromethION-based whole genome sequencing of endothelial cells differentiated from patient derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, transiently treated with a Cre recombinase, a RecF8 recombinase, and untreated cells. The dataset contains fastq files with all sequencing reads passing the standard quality filtering.

  Dataset EGAD00001007923

• Single-cell ATAC-seq of matched pediatric AML tumors

  Single-cell ATAC-seq of pediatric AML tumours from patients enrolled in the clinical trial AAML1031. Obtained using the 10X Chromium NextGEM Single Cell ATAC Reagent Kit, v1.1. A total of 64 samples were obtained from biopsies at diagnosis, remission and relapse from 25 patients.

  Dataset EGAD00001011194