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

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• WES Breast Patient-derived Tumor Organoid

  This dataset includes 18 Whole Exome Sequencing (WES) samples from 5 subjects. WES is performed on a matched pair of case/control samples, e.g., tumor/control or organoid/control. For each patient, the same control sample is used for the analysis of tumor and organoid samples. The sample name structure identifies the type of sample: <subjectId>_[TON][12]_[Case|Ctrl]_EX2; where T, O, and N refer to Tumor tissue, Organoid, and control sample, respectively. The number 1 or 2 refers to the specific tissue, and Case and Ctrl indicate a tumor tissue (or organoid) and a control sample, respectively. For example, ICSBCS007_T1_Case_EX2 is the first tumor tissue of subject ICSBCS007; ICSBCS007_O1_Case_EX2 is the tumor organoid derived from that tumor sample, and ICSBCS007_N1_Ctrl_EX2 is the matching control sample. More information can be found in the sample information table.

  Dataset EGAD50000000961

• Single-Nuclei RNA Sequencing and Spatial Transcriptomics of Human Heart Right Atrial Appendage and Pericardial Fluid in Cardiovascular Disease

  This dataset includes single-nuclei RNA sequencing (snRNA-seq) and spatial transcriptomics data from biopsies of the right atrial appendage and pericardial fluid, collected during open-heart surgeries. The samples represent various clinical contexts, including control, ischemic heart disease, heart failure, and myocardial infarction. For each biopsy, nuclei were isolated, and RNA sequencing libraries were prepared using the 10x Genomics Chromium v3 platform. Additionally, spatial transcriptomics was performed on the heart samples. The dataset provides raw sequencing data, which includes fastq files generated from these libraries, offering valuable insights into the cellular composition of heart tissues and associated fluids across different disease states.

  Dataset EGAD50000000927

• Whole genome sequencing of neuroendocrine tumors of the small intestine

  This dataset contains whole genome sequences for 13 patients with neuroendocrine (unique/multiple) tumor(s) of the small intestine. There are in total 25 tumor and 12 matched normal genomes. Libraries were prepared using a Illumina DNA PCR Free kit following the manufacturer’s recommendations and sequencing was performed on Illumina Novaseq6000 machine with a 2x151bp paired-end fashion. It contains data for : - 1 patient with 4 tumors and 1 matched normal - 1 patient with 3 tumors and 1 matched normal - 1 patient with 2 tumors, 1 liver metastasis and 1 matched normal - 2 patients with 1 tumor, 1 mesenteric nodule and 1 matched normal - 7 patients with 1 tumor and 1 matched normal - 1 patient with 3 tumors and 1 mesenteric nodule

  Dataset EGAD50000000907

• Whole Exome Sequencing of controls performed at the Broad Institute on a cohort from Bristol, UK

  These data were generated as part of a collaboration between University of Bristol, UK and the Stanley Center at the Broad Institute. This project sequenced and analysed the whole exomes of 2969 samples from the Avon Longitudinal Study of Parents and Children (ALSPAC). ALSPAC is a population-based pregnancy cohort with participants acting as ‘controls’ for this project. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina NovaSeq 6000 machines producing CRAM files. ALSPAC recruited pregnant women in the Avon County of south-west England between 1991 and 1992. Of the 15,447 pregnancies, 14,901 children were alive at 1 year of age.  DNA was extracted from child blood samples taken between ages 7 and 24.

  Dataset EGAD50000000716

• Targeted Sequencing of 52 Genes for Severe COVID-19

  This dataset comprises targeted sequencing data of 52 genes previously implicated in severe COVID-19 outcomes. The study includes samples from 764 individuals with severe COVID-19 and 3,939 population-based controls from the GCAT cohort (Spain). Molecular Inversion Probes (MIPs) were utilized for cost-effective and precise sequencing of the selected genes. The targeted genes include: Inflammasome/IL-1/TNF Pathway: NLRP3, CASP1, CASP8, IL1B, TNF, RIPK1, RIPK3, MYD88, TNFRSF13B SARS-CoV-2 Entry/Replication: ACE2, TMPRSS2, FURIN, SLC6A20, DDX1, DDX58, TLR4, FYCO1, CTSB, CTSL, ADAM17 Complement System: MBL2, CFH, CFI, CFB, ADAM10, CD46 Interferon Signaling: TLR3, IFIH1, IFITM3, TBK1, TLR7, IL10RB, IFNAR1, IFNAR2, SIGLEC1, MYD88, IFNGR1 Chemokine Receptor Signaling: CCR1, CCR3, CCR2, CCR9, IL8, CXCL3, CXCL10, CXCR6, XCR1, CCL2, CCL20 Immunodeficiency Genes: CASP8, CD46, CFB, CFH, CFI, IFNAR1, IFNAR2, IFNGR1, IFIH1, MYD88, NLRP3, RIPK1, TBK1, TLR3, TLR7

  Dataset EGAD50000001378

• ProstOmics - Spatial Transcriptomics

  Spatial transcriptomics data (ST) from 32 human prostate tissue samples originating from 8 prostate cancer patients (5 patients with post-surgery relapse). The ST data was acquired using the Visium Spatial Gene Expression kit which resulted in over 20 000 spatially defined spots for the 32 tissue samples. The raw transcriptomics data is RNA-seq. The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Each ST spot has metadata such as sample origin, histology class (stroma, normal epithelium, cancer of various grading etc), number of cells and estimated cell type fractions. Patient metadata include information of age at surgery, time (months) until reported relapse, total follow-up time, pre-surgery PSA, post-surgery T-stage and metastasis status.

  Dataset EGAD50000000603

• Clonal diversity analysis and inter/intra-organ heterogeneity in urothelial carcinoma under immunotherapy

  We studied a unique autopsy case of metastatic urothelial carcinoma with both sensitivity and resistance to anti-PD-1 therapy. We performed multiregional analyses of 58 paired whole exome sequencing and RNA sequencing samples of 8 different bulk tumor masses, 8 matched whole genome sequencing samples to identify structural abnormalities of each mass. Furthermore, we performed 7 whole exome sequencing from metastatic urothelial carcinoma patients who received anti-PD-1 therapy.

  Study JGAS000725

• Genomic Rearrangements in Pediatric Cancer

  Dataset EGAD00001007701

• Molecular analyses of stage IIIa NSCLC patients treated with neoadjuvant chemmoimmuntherapy

  This dataset comprises molecular and immunogenomic profiles from 60 individual NSCLC patients (30 male, 30 female), with samples collected at multiple timepoints including initial biopsies (IB), resections (RES), and peripheral blood mononuclear cells (PBMC) at different timepoints during treatment. It includes 32 FFPE tumor samples sequenced on Illumina with the FoundationOne panel, 20 FFPE samples sequenced on IonTorrent with the Oncomine Comphrehensive Assay Plus, and 41 samples assessed with IonTorrent via Oncomine Immune Response Research Assay panel for targeted gene expression. T-cell receptor (TCR) repertoire profiling was performed on 62 tumor samples (initial biopsies and resections, Oncomine TCR Beta-SR Assay), and 155 blood-derived samples were sequenced with Oncomine TCR Beta-LR Assay. Data files include processed sequencing results in bam format.

  Dataset EGAD50000001630

• Genomic Signatures of Intestinal Metaplasia in Six Countries with Varying Incidence of Stomach Cancer

  Intestinal metaplasia (IM) is a pre-cancerous condition associated with gastric cancer (GC), a deadly malignancy with varying geographic incidence. Performing a genomic analysis of over 1,500 IM samples from six countries, we identified 46 significantly mutated genes. We observed IM driver genes associated with high-risk populations and worse prognosis (ARID1A), members of the KRAS/MAPK signalling pathway (KRAS, BRAF, MAP2K1, MAP3K1, MAP2K4, NF1), and altered mucosal immunity (PIGR).

  Study EGAS50000001056