15016 results for "cancer studies using rna-seq"

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• Metagenomic data of patients with bipolar disorder or schizoprhenia spectrum disorder

  Metagenomic data of stool samples from 111 patients with either bipolar disorder or schizophrenia spectrum disorder. Data includes fq.gz files, mostly 1 forward and 1 reverse read per sample. Samples analysed in multiple lanes have 4 (paired) fastq files, which will have the same patient ID (example: 048_1 and 048_2, or 088_L1 and 088_L2. DNA was extracted from using the QIAamp Fast DNA Stool Mini Kit (Qiagen) following the manufacturer’s instructions. Shotgun metagenomic sequencing was carried out using llumina Novaseq 6000.

  Dataset EGAD50000001414

• USARC 10X Genomics Single Cell DNA Sequencing Data

  We investigated the impact of ploidy heterogeneity on copy number inference at a single cell level using fluorescence-activated cell sorted (FACS) nuclei from an undifferentiated soft tissue sarcoma. FACS revealed the presence of three aberrant subpopulations, including a haploid, a near diploid and a whole genome doubled population. Once sorted, single cell nuclei underwent whole genome sequencing using the chromium CNV single cell DNA library kit (10X Genomics). We sequenced single normal nuclei (2n) and single aberrant / tumour nuclei (1n, 2n and 2n+).

  Dataset EGAD00001008668

• SNF_OLINK_20

  Matrix of normalized values from Olink assay performed on baseline BM Plasma. The Olink Immuno-Oncology multiplex proteomic Panel included 92 proteins associated with human inflammatory conditions. Data is analyzed using real-time PCR analysis software via the Ct method and Normalized Protein Expression (NPX) manager. Data were normalized using internal controls in every single sample, inter-plate controls, negative controls and a correction factor and expressed as Log2 scale, which was proportional to the protein concentration. One NPX difference equals the doubling of the protein concentration.

  Dataset EGAD00001011147

• Identification of low frequency variants associated with ulcerative colitis using whole-genome sequencing

  2000 ulcerative colitis cases drawn from the UKIBD Genetics Consortium cohort and whole-genome sequenced at 2X depth. A case control association study using control samples whole-genome sequenced by UK10K will be undertaken to identify common, low-frequency and rare variants associated with ulcerative colitis. Data will be combined with similar data across 3000 Crohn's disease cases from the same cohort to identify inflammatory bowel disease (IBD) loci and better understand the genetic differences and similarities of the two common forms of IBD.

  Dataset EGAD00001000409

• RNASeq_EGAS00001001306

  RNASeq sequencing. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2 × 76 bp. We generated more than 20 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina Inc.) following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files.

  Dataset EGAD00001001443

• V(D)J and 5' Gene Expression data of bone marrow cells from patients with aplastic anemia

  Viably frozen blood MNCs from 9 cGVHD patients were sorted with BD Influx Cell sorter, to enrich for CD45+ cells. Gene and V(D)J transcript profiles were studied with 10x Genomics Chromium Single Cell Immune Profiling platform. The Chromium Single Cell 5’RNAseq run and library preparation were done using the Chromium Next GEM Single Cell Immune Profiling version 1.1 chemistry. The raw data was processed using Cell Ranger v3.1 pipelines.

  Dataset EGAD00001012117

• Reference exome data for Australian Aboriginal populations from Western Australia and the Northern Territory

  Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. The data is provided as 2 VCF files, one for the WA population and one for the NT population.

  Dataset EGAD00001005189

• An exome sequencing pilot study of HIV elite-long term non progressors and rapid progressors

  A pilot study examining genetic determinants associated with elite long term non progression and rapid progression using exome sequencing of individuals at the extremes of the distribution of HIV control and progression. Data can only be used for HIV related research.

  Study EGAS00001000057

• Molecular characterisation of paediatric PDX cells before and after 3D RASTRUM bioprintin

  This dataset is a part of the publication and contains source data for comparative analysis of the molecular (TSO500, RNAseq) characteristics between patient-derived xenograft (PDX) cells from high-risk paediatric neuroblastoma and sarcoma models before and after 3D bioprinting using RASTRUM Bioprinter.

  Study EGAS00001008220

• Human_Evolution_3

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Study EGAS00001000315

• Australia_and_New_Guinea_haplotype_phasing_

  Whole-genome sequencing and phasing of admixed Aboriginal Australian genomes and Papua New Guinean genomes using 10x Genomics Chromium technology. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001853

• Whole-exome sequencing of the transposition of the great arteries

  Transposition of the great arteries (TGA) is one of the most severe types of congenital heart diseases. Understanding the pathogenesis of TGA is urgently needed for patient management of this severe disease. We sought to systematically examine thegenetic etiology for isolated nonsyndromic TGA using whole-exome sequencing.

  Study EGAS00001004175

• the Yemeni-Somali 5 million SNP array dataset

  The three new samples (two from Yemen and one from Somalia) that carry a maternal lineage affiliated with the Malagasy motif were assayed for genome-wide SNP genotypes using the Illumina Human Omni5 Bead Chip (Illumina), which surveys 4,284,426 single nucleotide markers regularly spaced across the genome.

  Study EGAS00001003425

• Multi-Region WES of Metastatic Colorectal Cancer

  Study EGAS00001003573

• Evolutionary histories of breast cancer and related clones

  Study EGAS00001006282

• Chemosensitive Relapse in Small Cell Lung Cancer Patient-Derived Xenografts

  Genetic and epigenetic analysis of patient-derived xenograft models of acquired chemoresistance in small cell lung cancer.

  Study phs001249