12277 results for ""statistically+reactive"+taxa+in+microbial+community"

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• WES IDC samples

  PDX samples of breast cancer IDC mouse models created from patient tumor material of the NKI. Genomescan prepared the samples according to the procedure for Hybridization Capture using the Agilent SureSelectXT Human All Exon V7 kit. The prepared libraries were sequenced with Illumina sequencing technology. The samples are in fastq format and consist of the following PDX samples: IDC001, IDC125, IDC147, IDC200, IDC233, IDC244, IDC251, IDC272, IDC278, IDC281 and ILC120.

  Dataset EGAD50000001148

• CANCAP03 single-nuclear RNA sequencing

  CANCAP03 single-nuclear RNA sequencing. Tissue punch cores for six patients, 3 from each of olaparib and olaparib and degarelix cohorts, were processed for nuclear isolation and extraction, prior to single-nuclear RNA sequencing. 10x libraries were constructed. Sequencing on NovaSeq 6000. FASTQ files were processed using CellRanger pipeline. Outputs from the CellRanger pipeline were analysed using the Seurat package in R.

  Dataset EGAD50000001280

• 10x Genomics BCR Sequencing

  BCR sequencing done with 10x Genomics V(D)J kit + platform for the paper: Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma. Dataset contains paired FASTQ files for 35 samples, each was processed with the 10x Genomics V(D)J kit to obtain the sequence of the B-cell receptor sequence.

  Dataset EGAD50000001373

• Phenotype, genotype, and transcriptome data from three South Eastern Bantu groups in the SABR study

  Phenotypic data, whole genome sequencing, blood RNA-seq, imputed variant calls, cell type estimates, gene expression levels, splicing measurements, and analysis covariates from South African Blood Regulatory (SABR) resource participants, which includes South Eastern Bantu-speaking groups.

  Dataset EGAD50000001477

• Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing in Familial amyotrophic lateral sclerosis (ALS)

  To identify the genetic cause and modifiers of Familial amyotrophic lateral sclerosis (ALS), we performed Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing of Familial amyotrophic lateral sclerosis (ALS) patients.

  Study JGAS000358

• NSCLC ctDNA multigenic panel

  We analyzed cfDNA plasma samples of subjects with non-small cell lung cancer: treatment naïve (n=24) and prior-treated (n=8). Driver variants for 11 genes was available with Oncomine Lung cfDNA Assay, were assessed by Next-Generation Sequecing. Sequencing data were pre-processed in Ion S5 Torrent Server and aligned to the hg19 human reference genome. Variant calls were performed by IonReporter 5.10 software.

  Dataset EGAD50000000908

• RNA sequencing of baseline HCC PDX models

  To establish the baseline transcriptional profiles, we performed bulk RNA-seq for 36 of our HCC PDX models. 2-6 samples were collected for each model resulting in a total of 68 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000736

• NFE2 and PF4 as Translational Biomarkers for BET Inhibition-Induced Thrombocytopenia in Preclinical and Clinical Studies

  Blood samples from patients treated with BMS-986158 were investigated for association with thrombocytopenia following BET inhibition. Hypotheses of translational biomarkers for early prediction of thrombocytopenia associated with BET inhibition were explored.

  Study EGAS50000001162

• CASCADE tumour high-coverage whole genome sequencing data

  High coverage whole genome sequencing data (total: 22; median coverage: ~56X; range: 27X – 82X) from fresh frozen postmortem tissues harvested from patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.

  Dataset EGAD00001009491

• Comprehensive analyses of genetic aberrations in cholangiolocarcinoma

  The nature of CLC is still unclear and its pathological classification still remains controversial. To clarify the positioning of CLC among primary liver cancers, and to find characteristics that could distinguish CLC from other liver cancers.

  Study JGAS000597

• Single-cell CITE-seq and TCR-seq data from AIM⁺ HIV-1-specific T cells

  Single-cell sequencing data from 2 HIV-1 post-intervention controllers and 2 non-controllers reported in Fisher, Garcia, Frattari, Naasz, et al. Longitudinal samples were collected before antiretroviral therapy inititation, during suppressive therapy, and after analytical treatment interruption.

  Dataset EGAD50000002247

• Multimodal epigenetic sequencing analysis of cell-free DNA identifies biomarkers for ALS diagnosis and progression

  The role of the epigenome in age-related neurodegenerative disorders remains understudied. Here, we analyzed circulating cell-free DNA (cfDNA) from blood to detect methylation changes as a liquid-biopsy for Amyotrophic Lateral Sclerosis (ALS). Our study included 20 patients with sporadic ALS, 10 patients with C9orf72-associated ALS, 10 asymptomatic carriers of the C9orf72 repeat expansion mutation, and 21 non-disease controls.

  Dac EGAC50000000739

• 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

• Genetic screening of GPI-anchor protein synthesis

  This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. 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 (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001001928

• 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

• 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

• 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

• 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

• 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

• Paired-end Whole Exome-seq analysis of multi-centric lower grade glioma

  This dataset includes Nimblegen SeqCap EZ Exome v3 data for each lesion of three patients with multicentric glioma. For two patients, each lesion was sequenced along with whole blood. For a third patient, 3 pieces from the right lesion and 4 pieces from the left were sequenced along with whole blood. In each case BAM files that have been aligned with BWA mem alignment are available.

  Dataset EGAD00001003795

• Exome sequencing of 102 gastric cancer and matched normal from Japanese cohorts (YCU)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 102 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Dataset EGAD00001004042

• single-cell transcriptomics data from immune cells

  Smart-seq2 protocol was used to perform single cell RNA-sequencing on 465 immune cells. The immune cells analysed include 215 HLA-DQ2: gluten-(DQ2.5-glia-α1, -α2, -ω1, and -ω2) tetramer-sorted T cells, 247 transglutaminase 2 (TG2)-positive plasma cells from intestinal biopsy or peripheral blood from celiac disease patients, and 3 unassigned cells in 3 batches.

  Dataset EGAD00001004081

• 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

• 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

• 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

• Targeted DNA sequencing on bulk bone marrow and peripheral blood

  Targeted DNA sequencing was performed on 195 bone marrow samples to identify cases of clonal haematopoiesis, and on 99 paired peripheral blood samples. The SeqCap EZ HyperCap protocol was followed, and targeted capture performed against a panel of 97 genes recurrently mutated in myeloid malignancies and clonal hematopoiesis. One BAM file (mapped to the hg38 reference genome) is provided per sample.

  Dataset EGAD00001011083

• Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

  We performed whole genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and regional lymph nodes of five treatment-naive patients with locally advanced disease who underwent radical prostatectomy. Whole genome sequencing was performed as 150bp paired end reads on the Illumina NovaSeq 6000 platform.

  Dataset EGAD00001011174

• Whole genome sequencing data of tumor/normal pairs from 20 patients with hepatoblastoma

  This dataset provides whole genome sequencing data of tumor/normal pairs from 20 patients with hepatoblastoma using the illumina Novaseq sequencing system. It includes 40 samples (20 normals and 20 hepatoblastoma tumors). Our comprehensive analysis identified somatic mutations, structural variations, copy number variations and non-coding variants in hepatoblastoma.

  Dataset EGAD00001003914

• Exome sequencing of 142 gastric cancer and matched normal from Japanese cohorts (UT)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 142 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Dataset EGAD00001004041

• DNA and RNAseq of serial biopsies from 75 DLBCL patients

  This data set includes serial biopsies from 75 patients with DLBCL. Tumour tissue was preserved either in FFPE or frozen. Each biopsy was sequenced with either whole genome or exome. A custom targeted sequencing data set is available to match most whole genome samples. RNAseq data were available for a subset of biopsies.

  Dataset EGAD00001011816

• The Chinese University of Hong Kong Hereditary Spastic Paraplegia Data

  The dataset contains the whole genome sequencing data of a family with two unaffected parents and two probands that showed Hereditary spastic paraplegias symptoms. Sequencing reads were aligned to human genome (GRCh38) using BWA-MEM, followed by indel-realignment and PCR-duplicates marking. Alignment results are available for download in BAM format.

  Dataset EGAD00001002146

• Next Generation Sequencing Characterization of Tregs in Human Peripheral Blood during Autoimmunity

  Tregs were sorted as CD4+CD25+CD127- cells from peripheral blood of 14 healthy individuals, 8 patients with systemic lupus erythematosus, 9 patients with rheumatoid arthritis, and 11 patients with multiple sclerosis. RNA was extracted and polyA libraries were prepared using the Illumina Truseq sample preparation kit v.2. Single-end sequencing was performed on NextSeq500.

  Dataset EGAD00001006193

• Somatic mutations reveal embryonic genetic bottlenecks generating placental mosaicism

  The human placenta harbours chromosomal aberrations that are absent from the fetus in one to two percent of pregnancies. This confined mosaicism suggests that embryonic genetic bottlenecks exist, which phylogenetically segregate placental tissue. Here, we studied the somatic genetic landscape of human placentas by whole genome sequencing of 86 placental biopsies and of 106 microdissections.

  Dataset EGAD00001006337

• Whole Exome Sequencing of High grade T1 non-muscle invasive bladder cancer

  The dataset consists of a multisample VCF (version 4.1) and the corresponding annotated MAF file, containing the somatic point mutations found from exome sequencing across the high-grade T1 bladder cancer cohort (HGT1, n=61 samples). The VCF file is in accordance with the HTS format specifications (https://samtools.github.io/hts-specs/). The dataset comprises also a CSV file with clinical data.

  Dataset EGAD00001006346