16539 results for "sec+and+unspecified+malignant+neoplasm"

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• MorphoITH: A Framework for Deconvolving Intra-Tumor Heterogeneity Using Tissue Morphology

  The ccRCC-ITH study WES dataset is derived from a morphology guided multi-regional sequencing dataset used to study the relationship between morphology and genetic evolution. It contains whole exome sequencing data of 18 tumor and 2 adjacent normal samples from 2 UTSW patients, who have consented to depositing their genomic data to public repository. Tumor samples come from different tumor sites, including primary tumor, thrombus and metastases. WES was performed using 75bp paired-end fragments at an average read depth > 50x on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA). The raw data is in fastq format.

  Dataset EGAD50000001550

• CLUSTER Consortium RNAseq PBMC Dataset of pre-methotrexate UK JIA patients cohort

  This is the RNAseq PBMC dataset (paired FASTQ files, n = 82 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. Total PBMC were isolated from pre-treated blood of JIA patients and clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.

  Dataset EGAD50000001457

• Khoe-San genome Project (KSGP)

  The Khoe-San Genome Project (KSGP) includes whole genome data generated for 190 study participants from Southern Africa (Namibia and South Africa) representing people speaking a Namibian Khoe-San language (n=150, 12 groups) or regional non-Khoe-San groups (n=40), specifically defined here as Namibian Himba (n=10), South African Southern Bantu (n=12 and representing the Ubuntu Genome Project led by the University of Limpopo) or South African Coloured/European (n=18). Deep whole genome data has been generated for the purposes of cataloguing the extent of regional genetic diversity, creating population specific references and evolutionary trajectories, while creating a population-matched panel of normal (PoN) genetic diversity required for disease associated studies across the region.

  Dac EGAC50000000798

• 10X CD4 auto-antigens

  Ex vivo CD4 T-cells from 4 donors were stimulated with antigen-coupled beads to aCD3, ABD, EBNA1, ANO2 or CRYAB and the LiveCD3+CD4+CFSEdim cells were sorted by flow cytometry. Cells were labelled with barcoded antibodies to identify the original stimulus. All stimulations from each donor were pooled into four reactions, i.e. one reaction per donor. Libraries were assembled with the 10X Chromium Next GEM Single Cell 5’ Kit for TCR and transcriptome with feature barcodes. Dataset contains raw fastq reads as well as supplementary information needed to link fastq files to modality, i.e. gene-expression, protein or VDJ, and includes supplementary information to de-multiplex the reactions by stimulation condition.

  Dataset EGAD50000002201

• WES Profiles from the CheckMate-577 Clinical Trial

  The dataset contains WES profiles of 396 patients from the CheckMate-577 (CA209-577) clinical trial whose ICF allows data deposition into a public repository. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. DNA was analyzed by Whole Exome Sequencing using Swift Biosciences Accel-NGS 2S Hyb DNA Library Kit for library preparation and hybridization using Agilent SureSelect All Exon v6, followed by sequencing on the Illumina NovaSeq platform with a 100bp paired-end strategy and a target read depth of 100M per tumor sample. Fastq files are included.

  Dataset EGAD50000002395

• 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.

  Study EGAS00001004347

• The Berlin (BLN) panel of glioblastoma cell lines: RNAseq of human gliomasphere cell lines and matched parental tumors

  We generated a panel of nine glioma stem-like cell lines under serum-free cell culture conditions from human glioblastoma samples. In addition to clinical annotation, MR imaging and histological characterization of the parental tumor, as well as xenograft studies of tumorigenecity, transcriptomic profiling of tumor/cell line pairs by RNA sequencing has been performed.

  Study EGAS00001001167

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

  COG-N-519 primary neuroblastoma cells were innoculated by subcutaneous injection into NSG mice. When tumours reached a size of 100-200mm3 miRNAs conjugated to nanoparticles were injected intratumourally every 2 days for 1 week. 24 hr after the last injection, snap frozen tumour tissue was harvested for RNA extraction and RNA-seq analysis.

  Study EGAS00001005581

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: NOVA1 gain and loss of function systems

  We produced NOVA1 and EGFP over-expression RNA-seq datasets in three healthy control individuals using lentivirus-mediated gene transfer to model NOVA1 gain of function. Additionally, we produced a NOVA1 loss of function RNA-seq dataset by generating iPSC-MN with NOVA1 knock out produced by CRISPR/Cas9 in the CV-B iPSC line.

  Study EGAS00001005881

• Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

  In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

  Study EGAS00001004925