12405 results for ""non-traditional+communal+storytelling+approach"+novel+segment+noted+in+critical+commentary"

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• DAC for study "Single-nucleus brain transcriptomics reveals microglia dysfunction in Multiple System Atrophy"

  Dataset containing snRNA-seq samples from MSA or PD patients, and healthy controls. We aimed at identifying molecular processes at the single cell level that could identify common and/or disease-specific differences between healthy controls and patient groups. Frozen tissue samples from healthy controls, and multiple system atrophy or Parkinson's disease patients were excised and single nuclei were isolated following the 10x Genomics Chromium workflow.

  Dac EGAC50000000809

• 10X single-cell Multiome (RNA+ATAC) of cord blood-derived HSPC

  10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries, sequenced on an Illumina NovaSeq 6000 platform. BAM files are provided. Samples from 4 donors were sequenced after sorting for primitive HSPCs in 2 libraries, each with cells from 1 male and 1 female CB.

  Dataset EGAD50000002327

• GWAS and Meta-analysis on Frontal Fibrosing Alopecia in two European Populations

  Summary statistics of a GWAS meta-analysis for frontal fibrosing alopecia (FFA). A total of 7,039,930 genotyped and imputed variants were used for 1,044 European severe FFA cases and 4,145 matched population controls.

  Study EGAS00001003460

• 10X 3' V2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This is the droplet data of this study

  Dataset EGAD00001005961

• GELATO clinical trial whole exome sequencing data (primary tumors and local recurrences)

  Paired-end whole exome sequencing of 10 lobular breast cancer primary tumors, 3 local recurrences and matched normal samples obtained from 10 unique patients from the GELATO clinical trial. The included raw sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material (tumor data) and fresh frozen material (matched normal data).

  Dataset EGAD00001009836

• Genomic analysis of pancreatic neuroendocrine tumour with MEN1, ATRX, or DAXX mutations

  This dataset includes 52 samples from 19 individuals with pancreatic neuroendocrine tumours. These samples were analyzed using RNA-sequencing, whole-exome sequencing, shallow (~0.3x) whole-genome sequencing, and a 21-gene panel targeted capture sequencing. Everything was sequenced using the Illumina HiSeq and is provided in BAM or FASTQ format.

  Dataset EGAD00001006001

• Whole exome sequencing data of Hispanic hepatocellular carcinoma

  The paired-end reads were aligned to the human reference genome (hg19) with decoy sequences (as used in the 1000 Genomes Project) using BWA (v0.7.5a) software. The duplicate reads were marked and subsequently removed using Picard (v1.140) (https://broadinstitute.github.io/picard/) and SAMtools (v0.1.19), respectively. Local realignment around insertions/deletions (indels) and base quality recalibration were performed using GATK (v3.6).

  Dataset EGAD00001011158

• Paired-WGS-two-families-with-GBA-variants-and-Parkinsons-disease

  We performed whole- genome sequencing, rare variant filtering, segregation analysis and functional validation of PD cosegregating rare genetic variation in two families (6 samples) segregating PD associated GBA variants c.115+1G>A (ClinVar ID: 93445, ) and p.L444P (ClinVar ID: 4288) respectively. The paired WGS sequencing was run on HiSeq X Ten and the library preparation kit was Illumina TruSeq DNA nano.

  Dataset EGAD00001006561

• Skeletal muscle transcriptomic comparison between long-term trained and untrained men and women

  We generated global skeletal muscle transcriptomic data from long-term endurance (9 men, 9 women) and strength (7 men) trained individuals. These data were compared with healthy age-matched untrained controls (7 men, 8 women). All 40 samples were then multiplexed in 1 lane and sequenced (2x50bp paired end) on the Illumina NovaSeq 6000.

  Dataset EGAD00001006067

• Hi-C in endometrial healthy and tumor tissues

  Hi-C libraries have been prepared by enzymatic digestion with MboI restriction enzyme and sonication. Illumina single-indexig primers have been use to amplify ligated fragments. Hi-C experiments have been performed on 10 slices (30um thick) of fresh-frozen tissues derived from 3 healthy and 3 tumor endometrial tissues of post-menopausal patients. Raw paired-end fastq.gz files are provided.

  Dataset EGAD00001010898

• Paired-end Whole Exome-seq analysis of the Hypermutation and Malignant Progression in Low-grade Glioma Patients

  113 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina WES (exome seq) paired-end technology. Dataset contains 113 BAM files aligned to hg19 using BWA v.0.5.9. After mapping duplicated reads were removed, reads were re-aligned around InDels and read base quality score was re-calibrated.

  Dataset EGAD00001005386

• Transcriptome profiling of human lung fibroblasts in COPD

  Primary lung fibroblast were isolated from well-matched control donors (no COPD, n=3) and patients with COPD (GOLD stage I-IV, n=8). Total RNA of cultured human lung fibroblast were isolated at passage 3 and rRNA was depleted. 75 bp single-end reads were generated from RNA libraries on Illumina NextSeq 500.

  Dataset EGAD00001009405

• cfMeDIP data for 22 WCDT samples

  We analyzed the cell free DNA methylomes using 22 plasma samples from patients with mCRPC prostate cancer in the WCDT project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.

  Dataset EGAD00001008713

• Salivary Gland Cancer TSO500 dataset

  DNA was extracted from archival tissue of 119 patients with various SGC subtypes and sequenced using a targeted NGS panel encompassing 523 cancer related genes (TruSight Oncology 500, TSO500). This dataset belongs to the publication entitled: 'Identification of fusion genes and targets for genetically matched therapies in a large cohort of salivary gland cancer patients'.

  Dataset EGAD00001008759

• Dataset for cancer_of_unknown_primary-RNA

  Rare cancer sequencing data of 58 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008857

• Dataset for GIST-EXON

  Rare cancer sequencing data of 64 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008875

• H3K27ac ChIP-seq of human acute leukemias and healthy donors

  H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included.

  Dataset EGAD00001011060

• Sequence-based gene expression in uterine and ovarian carcinosarcomas

  Gynecologic carcinosarcomas (CS), including more generally uterine (endometrial) and less frequently ovarian localization, are histologically defined as biphasic neoplasms composed of carcinomatous (C) epithelial and sarcomatous (S) malignant components. We report a comprehensive analysis of 20 patients of macro-dissected samples of C and S components through RNA sequencing.

  Dataset EGAD00001009099

• Epigenomic analysis of human dopaminergic neuron differentiation reveals LBX1, NHLH1 and NR2F1/2 as necessary for lineage specification

  Sample information: The 56 samples produced in this project come from the human iPSC line GM17602 (Coriell) where a tyrosine hydroxylase-T2A-mCherry reporter was inserted. A combination of epigenetic analysis (ATAC/ChIP) along transcriptomics.

  Dataset EGAD00001009288

• CRISPR iPSC methods paper

  This submission is of the sequencing data used in the CRISPR iPSC methods paper. Specifically it is 3 fastq files that each represent a replicate of an experiment to transduce the Toronto KnockOut CRISPR Library - Version 3 (TKOv3) into inferred pluripotent stem cell (iPSC) derived macrophages. The sequencing is of the guide RNAs from the TKOv3 having been extracted from the transduced iPSC derived macrophages.

  Dataset EGAD00001007020

• Exome sequencing of lung tissue conducted in SMC

  The data includes exome sequencing FASTQ files of 335 patients receiving immune checkpoint blockade therapy. The data only provides for WXS of tumor tissue.

  Dataset EGAD00001009101

• WGS Fastq files from the CPC-Gene project in support of PRAD-CA, DCC Release 26

  This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs

  Dataset EGAD00001003761

• Sequence Data for Paper: Epigenetic reprogramming during differentiation of human CD4+ T lymphocytes into memory stages

  Sequence Data of total RNA, miRNA, WGB, mRNA, NOMe, Chip (H3K27ac,H3K27me, H3K36me3, H3K4me1, H3K4me3, H3K9me3, Input) Short Desrciption: Epigenetic profiling of human CD4+ memory T cells reveals their proliferative history and argues in favor of a progressive differentiation model driven by epigenetically controlled master regulators.

  Dataset EGAD00001001865

• ESGI - Molecular diagnosis for mitochondrial disorders (2017-08-29)

  The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients. This dataset contains all the data available for this study on 2017-08-29.

  Dataset EGAD00001003596

• RNA sequencing of tumor samples from patients with BPLL

  RNA-Seq was performed on 12 samples of sorted CD19+ tumor cells. RNA-Seq libraries were prepared using the SureSelect Automated Strand Specific RNA Library Preparation Kit as per manufacturer’s instructions (Agilent technologies) and subjected to paired-end (2 x 100 bp) sequencing on HiSeq2000 (Illumina). The files are in FASTQ format.

  Dataset EGAD00001004412