660 results for ""option,com_discussions"+y+19"

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• RNA-Seq of human longitudinal whole blood samples from PCR-positive and PCR-negative recent household contacts of COVID-19 index cases.

  Little is known about the transcriptomic profile of individuals who are exposed to SARS-CoV-2 yet resist becoming PCR positive. To investigate this, longitudinal whole-blood samples were taken (0, 7, 14, and 28 days after enrolment) from PCR positive and PCR negative SARS-CoV-2-naïve household contacts who were recently exposed to a COVID-19 index. Samples were also taken from pre- and post-pandemic unexposed controls. Total RNA was extracted from PAXgene tubes before undergoing poly(A) selection followed by globin and rRNA depletion. DNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. All samples were then sequenced across 2 flowcells of an Illumina HiSeq 4000.

  Dataset EGAD50000000684

• Oesophageal adenocarcinoma scRNAseq from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains single-cell RNA-seq generated from the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19) and additional donors with Barrett's oesophagus using the 5' Single Cell Gene Expression assay from 10x Genomics. Samples were generated from oesophageal tumours, Barrett's oesophagus, and normal oesophagus and gastric tissues, with the aim of generating a reference atlas for cell types found in normal and disease-associated tissue states in the upper GI tract. This reference atlas was used as the basis for a deconvolution workflow to estimate the cell composition of bulk transcriptomes from these tissues, and to assess cell type-specific expression patterns of potential predictive biomarkers for immunochemotherapy regimens in this setting.

  Dataset EGAD00001009401

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the feature of age-associated helper T (ThA) cells and its contribution to autoimmune diseases, CD4+ T cell subsets from 19 rheumatoid arthritis (RA), 62 systemic lupus erythematosus (SLE), 40 idiopathic inflammatory myopathy (IIM) and 64 healthy controls (HC) were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA). RNA-seq was performed with each CD4+ T cell subset samples.

  Study JGAS000626

• Genomic profiling identified ERCC2 helicase domain mutations respond to platinum-based neoadjuvant therapy in urothelial bladder cancer

  Genomic profiling of tumours enables therapeutic decisions, and identifying drug-matched mutations will prolong survival and prognosis. Here, we generated a custom panel for detecting genetic alterations in 19 patients with urothelial bladder cancer. This panel targeted 71 genes associated with urological cancer. Targeted sequencing was performed on formalin-fixed paraffin-embedded tumour tissues. In this study, we revealed genome profiles and actionable mutations in patients with urothelial bladder cancer.

  Study JGAS000241

• Bulk RNA-seq paired fastq files from i3Ns harbouring a SNCA A53T mutation, with or without RSL3 treatment

  FASTQ files from bulk RNA sequencing of a iPSC-derived rapid neuronal model (i3Ns) harbouring the SNCA A53T mutation in a WTC11 background as a model of synucleinopathy, with or without treatment of 300nM RSL3 for 6 hours. Libraries were prepared using the Watchmaker rRNA and globin depletion kit and sequenced on a NovaSeq X with an average depth of ~27 million paired-end reads with a fragment length of 100 base pairs, per sample. 19 samples are included in this dataset, each with two paired fastq files (R1 and R2). The dataset includes control neurons (WT: dcas9 parental line and C4 CRISPR control) and A53T clones (B7, H8 and L8) across two neuronal inductions (ind1 vs ind2), with or without treatment of RSL3 (UT vs. RSL3).

  Dataset EGAD50000002209

• Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma

  Only a few studies have reported the molecular characteristics of adult cerebellar glioblastoma (C-GBM), a subtype comprising 1% of glioblastoma cases located within the infratentorial brain region due to the rarity. By identifying genomic profiles from 19 adult C-GBM samples, we revealed the genetic intertumoral heterogeneity in C-GBM as well as distinct genomic characteristics from those of supratentorial glioblastomas (S-GBMs), emphasizing the need of individualized therapies for C-GBM patients.

  Study EGAS00001002517

• Panel amplicon sequencing data of COVID-19 patients

  Amplicon sequencing data for 90 patients hospitalized for COVID-19. to general ward. Patients had a median age of 60.5 (52.0 – 69.3) years and were overweighted (Body mass index: 28.4 (24.4 – 32.6) kg/m2). 35.6% of the cohort were female. The following genes were sequenced on a NovaSeq600 instrument with an Enrichment based library preparation (IDT-xGEN) with a median coverage of 2000x: ABL1, ASXL1, ATRX, BCOR, BCORL1, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CEBPA, CSF3R, CUX1, DNMT3A, ETV6, EZH2, FBXW7, FLT3, FLT3-ITD, GATA1, GATA2, GNAS, GNB1, HRAS, IDH1, IDH2, IKZF1, JAK2, JAK3, KDM6A, KIT, KMT2A, KRAS, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PHF6, PPM1D, PTEN, PTPN11, RAD21, RUNX1, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2

  Dataset EGAD00001009416

• Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients

  We generated a dataset consisting of 79 VCF files, and respective FASTQ and CRAM files, methodically generated using the GLIMPSE1 imputation algorithm leveraging the 1000 Genomes Project Phase 3 dataset as the reference panel of haplotypes. In total this dataset is composed of approximately 325 GB of FASTQ data, 156 GB of CRAM data, and 6 GB of VCF data. Our samples were specifically derived from sequenced DNA from a highly selective cohort of patients, mostly comprised of Iberian Populations in Spain (IBS) individuals but also containing some individuals with other genetic backgrounds, who presented severe COVID-19 symptoms during the initial wave of the SARS-CoV-2 pandemic in Madrid, Spain. On average, each VCF file in this rich dataset contains 9.49 million high-confidence single nucleotide variants [95%CI: 9.37 million - 9.61 million].

  Dataset EGAD00001011363

• Sequencing data for oesophageal and related samples - Normals release 2 (RNA)

  Dataset EGAD00001003838

• Microbial infections in Multiple Sclerosis Samples

  In this study, we have examined microbial infection in brain tissue from 9 control samples from healthy patients and 10 samples from patients diagnosed with Multiple sclerosis, by Next-generation sequencing NGS using Miseq sequencing platform (Illumina).

  Dataset EGAD00001004085