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• Pulldown DNA methylation study v2

  Pilot study to set up sequencing protocols for targeted pulldown methylation profiling

  Dataset EGAD00001001242

• Reference epigenome IPS01_N_Fibroblast_WGBS data generated from KEP study

  A IPS01_N_Fibroblast_WGBS paired end data for iPSC(Oct4)

  Dataset EGAD00001003473

• Reference epigenome IPS04_X_Fibroblast_WGBS data generated from KEP study

  A IPS04_X_Fibroblast_WGBS paired end data for iPSC(Oct4)

  Dataset EGAD00001003476

• MPB_Bonn

  1000Genomes imputed data set of 581 cases and 417 controls for male-pattern baldness

  Dataset EGAD00001001456

• RNA sequencing BRAF fusion partners

  Contains RNAseq data for 14 transduced/non-transduced organoids

  Dataset EGAD00001005380

• Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

  We profile the adult human CNS from distinct regions, sex and ages, for chromatin accessibility at the single-nuclei level. Tissue was collected from 20 different donors (10 male, 10 female) within the ages of 34 to 74 years old. Additionally we performed Single-cell nanoCUT&Tag H3K27ac and H3K27me3 profiling for 4 of the donors and multiome single cell assay (RNA-seq+ATAC-seq) for 2 of the donors. Each donor donated fresh frozen white matter from the following three tissue regions: primary motor cortex (Brodmann area 4, BA4), arbor vitae cerebelli (CB) and fasciculi cuneatus and gracilis from and cervical spinal cord (CSC). Tissue was processed semi-randomly, ensuring that each batch of experiments had a representation of both sexes and all three tissue regions. Completed libraries were again randomly multiplexed during sequencing to minimize batch effects. We also performed micro-C,2 replicates, of iPS human derived cell cultures of human oligodendrocyte precursor cells (hOPC).

  Dataset EGAD50000000410

• Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

  scGBS is a single-cell sequencing-based methodology to haplotype and copy-number profile single cells. Genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing of the restriction fragments. scGBS data serves as the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping (Zamani Esteki et al., 2015). We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells with the use of a HapMap cell line pedigree (7 single cells). A clinical validation of the methodology with a total of 14 single blastomeres and 3 trophectoderm samples biopsies from human preimplantation embryos for 6 PGT-M families were processed with scGBS and were previously haploptyped via SNP array.

  Dataset EGAD00001007794

• Genome Sequencing Reveals That RAD50 Hypomorphism Results in Enhanced Sensitivity to Checkpoint Kinase Inhibition Combined with Chemotherapy

  Outlier analyses represent a versatile method to identify predictive biomarkers of response to both targeted agents and chemotherapy. We performed whole genome sequencing (WGS) of tumor and germline blood from a patient with metastatic small cell carcinoma of the ureter who experienced a durable complete response to a combination of irinotecan plus AZD7762, a checkpoint kinase inhibitor. The patient initially had resection of the ureter followed by metastatic recurrence within the kidney and lymph nodes and underwent nephrectomy with lymph node dissection. Through WGS of tissue from the second surgery, we detected a hypomorphic L1237F mutation within RAD50, a component of the Mre11 double strand break repair complex, which resulted in heightened sensitivity to the combination of checkpoint inhibition and clastogenic chemotherapy. We validated the WGS findings using a combination of an exon capture assay and validation in model systems. The tumor samples sequenced by exon capture were derived from tissue taken from both the initial and second surgeries.

  Study phs000706

• Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

  Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer-associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1-repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.

  Study phs000443

• Identification and characterization of molecular markers in aging and neuronal disorders

  Supercentenarians, people who have reached 110 years of age, are a great model of healthy aging. Their characteristics of delayed onset of age-related diseases and compression of morbidity imply that their immune system remains functional. We performed single-cell transcriptome analysis of peripheral blood mononuclear cells (PBMCs), derived from supercentenarians and younger controls. We identified a marked increase of cytotoxic CD4 T-cells (CD4 CTLs) as a novel signature of supercentenarians. Furthermore, single-cell T-cell receptor sequencing of two supercentenarians revealed that CD4 CTLs had accumulated through massive clonal expansion. The CD4 CTLs exhibited substantial heterogeneity in their degree of cytotoxicity as well as a nearly identical transcriptome to that of CD8 CTLs. This indicates that CD4 CTLs utilize the transcriptional program of the CD8 lineage while retaining CD4 expression. Our study reveals that supercentenarians have unique characteristics in their circulating lymphocytes, which may represent an essential adaptation to achieve exceptional longevity by sustaining immune responses to infections and diseases.

  Study JGAS000230

• Detection of ctDNA in Plasma of Patients with Clinically Localised Prostate Cancer is Associated with Rapid Disease Progression

  Dac EGAC00001001718

• EGAD00010000570

  Imputation-based meta-analysis of severe malaria in Kenya.

  Dataset EGAD00010000570

• Landscape of gene mutations in Down syndrome-related myeloid disorders

  Dataset EGAD00001000628

• RHD_FJ_OMNI_Controls

  Healthy volunteers recruited in Fiji with higher density genotyping

  Dataset EGAD00010000958

• phenotype

  2619 individuals with visual contour perception phenotype scores, in the form of averaged accuracy

  Dataset EGAD00010001729

• Recurrent adeno-associated virus 2-related insertional mutagenesis in human hepatocellular carcinomas

  Dataset EGAD00001001423

• Zambian Genetic Variation DAC

  DAC to govern access to array genetic variation data from five populations in Zambia.

  Dac EGAC50000000258

• ecDNA amplification of MYC drives intratumor copy-number heterogeneity and adaptation to stress in PDAC

  Dac EGAC50000000070

• T cell receptors of pathogenic CD4 T cells isolated by using distinct phenotypic markers in celiac disease

  Study EGAS00001005582

• Increased trunk fat is associated with altered gene expression in breast tissue of normal weight women

  Study EGAS00001005138

• Molecular analysis of CRC in patients with Primary Sclerosing Cholangitis (PSC) and Inflammatory Bowel Disease (IBD)

  Study EGAS00001004497

• Secondary Resistance to Anti-EGFR Therapy by Transcriptional Reprogramming in Patient-Derived Colorectal Cancer Models (hipo_B012)

  Study EGAS00001005320

• Impaired Humoral and Cellular Immunity after SARS-CoV2 BNT162b2 (Tozinameran) Prime-Boost Vaccination in Kidney Transplant Recipients

  Study EGAS00001005280

• Identification of early disease progression in ALK-rearranged lung cancer using circulating tumor DNA analysis (hipo_K34R)

  Study EGAS00001005327

• Mutational impact in liver stem cells under precancerous alcoholic liver, NASH and PSC disease conditions

  Study EGAS00001005384

• Overexpression of the miR-17-92 cluster in colorectal adenoma organoids induces a carcinoma-like genotype

  Study EGAS00001005949

• A clinically annotated post-mortem approach to study multi-organ somatic mutational clonality in normal tissues

  Study EGAS00001006332

• Mechanism of action and resistance to Trastuzumab Deruxtecan in patients with metastatic breast cancer: the DAISY trial

  Study EGAS00001006905

• Residual ctDNA after treatment predicts early relapse in patients with early-stage non-small cell lung cancer

  Study EGAS00001005967

• Enhancer profiling to identify identifies epigenetic markers of endocrine resistance in metastatic castration resistant prostate cancer patients

  Study EGAS00001006161

• AML-MRD

  AML-MRD: Aligned sequences used in the error modeling study

  Dataset EGAD00001005270

• Chordoma Extension Study

  Extension analysis to pursue candidate genes of interest in chordoma

  Dataset EGAD00001001238

• Mitochondrial variants in CPCGene samples

  VCF files containing mitochondrial variant calls using MToolbox

  Dataset EGAD00001003361

• cqmuGWAS2

  DNA for 2482 individuals from Chongqing was extract from peripheral blood and genotyped by Illumina Omni Zhonghua-8 version 2 gene chips.

  Dataset EGAD00010001526

• Genetic and transcriptomic landscape of DLBCL

  Affymetrix SNP6.0 data for 341 DLBCL patients

  Dataset EGAD00010001980

• BelCovid_2_genotype

  Cohort: Raw genotype files for BelCovid2 cohort. Genotype Chip: Illumina Global Screening Array-24 v3.0 + Multi-Disease beadchip genomic build: b37

  Dataset EGAD00010002179

• GEN_COVID_genotype

  Cohort: Raw genotype files for GEN_COVID cohort. Genotype Chip: Illumina Global Screening Array-24 v3.0 + Multi-Disease beadchip genomic build: b37

  Dataset EGAD00010002177

• RealSeqS ovarian amplicon counts

  Dataset contains text files that describe the chromosome, position, and read count for an amplicon using the RealSeqS assay.

  Dataset EGAD50000000013

• IMvigor130 heatmap Figure 2A

  Source data for Figure.2A heatmap showing the gene expression across samples.

  Dataset EGAD50000000139

• Time course acetalax bisacodyl treatment

  RNA-Seq raw data of PDX treated with acetalaxor bisacodyl for 4h00 to 24h00.

  Dataset EGAD50000000875

• PacBio long-read scRNA-seq

  Full-length single-cell cDNA PacBio Kinnex whole-transcriptome sequencing data for adrenal sampleA and sampleB.

  Dataset EGAD50000002211

• Reference epigenome KNIH008 WGBS data generated from KEP study

  A KNIH008 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for adipocytes

  Dataset EGAD00001002756

• IPF Core Biopsy Study RNA-Seq Fastqs

  RNA-Seq fastq files for 97 Idiopathic Pulmonary Fibrosis samples.

  Dataset EGAD00001007568

• Fecal WMS UC metadata

  Metadata for fecal WMS data from NCT02749630 ulcerative colitis patients.

  Dataset EGAD00001008820

• Neuroblastoma sequencing data

  This dataset contains tumor and normal whole exome DNA sequence data for a patient with neuroblastoma

  Dataset EGAD00001008120

• Reference epigenome ADMSC04_smRNA-Seq data generated from KEP study

  A ADMSC04_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003870

• Reference epigenome CKD27_C_Mesan_WGBS data generated from KEP study

  A CKD27_C_Mesan_WGBS paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003471

• Reference epigenome CKD23_C_Mesan_WGBS data generated from KEP study

  A CKD23_C_Mesan_WGBS paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003468

• Patient 16CH

  One file of patient 16 with WGS done on Illumina HiSeq X-Ten. For research purpose and authorised user only.

  Dataset EGAD00001003440

• FFPE Normal Panel V3 Cancer Panel

  FFPE normal panel generation for use with V3 cancer panel 0618521

  Dataset EGAD00001001122