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• HGSC lines: ATACseq and RNAseq, pre- vs post-treatment with HKMTi-1-005

  Formation of a DAC to support the deposition of RNAseq and ATACseq data, from pre- vs post-treatment high-grade serous ovarian carcinoma cell lines. The lines include PEO1, PEO4, PEA2, OVCAR5, OVCAR8, and the treatment includes use of a novel epigenetic drug called HKMTi-1-005.

  Dac EGAC50000000034

• NINDS Inherited Forms of Motor Neuron Disease Study

  Sequencing data from primary fibroblasts were obtained from individuals with a family history of an inherited form of motor neuron disease (juvenile amyotrophic lateral sclerosis- ALS4).

  Study phs001322

• Human PI3Kγ Deficiency with Immunodeficiency and Tissue Immunopathology

  Whole exome sequencing of a trio (parents and offspring) reveals PIK3CG mutations that result in loss of protein in the child with immunodeficiency and immunopathology.

  Study phs001848

• BipEx_Landen_SWEBIC

  BipEx: Bipolar Exome Sequencing Broad & Karolinska Institutet. EGAS00001005860. "This research project was a collaboration between the Karolinska Institute and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of X SWEBIC Bipolar case samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x"

  Dac EGAC50000000142

• BipEx_Pedersen_Karolinska

  "BipEx: Bipolar Exome Sequencing Broad & Karolinska Institutet. EGAS00001005856. ""This research project was a collaboration between the Karolinska Institute BioBank and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 4,765 control samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x."" "

  Dac EGAC50000000141

• Exploring Genomic Mutations in Gastric Cancer among Japanese Populations

  We conducted a comprehensive analysis of whole-genome and RNA sequences obtained from biopsy samples of 65 patients with advanced gastric cancer prior to chemotherapy treatment.

  Study JGAS000754

• Metabolome analysis of persons with type 2 diabetes with or without diabetic complications

  We profiled serum metabolites of persons with T2D with or without diabetic complications using a comprehensive non-targeted metabolomics approach with mass spectrometry.

  Study JGAS000572

• Non-coding RNAs in breast cancer

  Using RNA CaptureSeq we annotated non-coding RNAs transcribed from genome intervals surrounding breast cancer risk signals in a range of mammary-derived tissue and cell lines.

  Study EGAS00001003353

• Angiosarcoma_follow_up_study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Study EGAS00001000405

• Bioinformatics analysis of chimerism in monochorionic dizygotic twins

  We conducted a bioinformatics analysis of hematopoietic chimerism of the monochorionic dizygotic twins. Whole-genome sequencing was used to understand the genomic compositions of the chimeras.

  Study EGAS00001005997

• MPN_mutation_order_followup

  To evaluate the presence of mutations in frequently mutated genes in MPN by performing targeted resequencing of a selected gene panel comprising of 111 genes across 40 samples with MPN.

  Study EGAS00001000663

• Transcriptional Reference Map of Human Natural Killler Cells

  Here we performed single-cell RNA sequencing of both bulk NK and sorted NK subsets to establish a transcriptional reference map of human natural killer cells.

  Study EGAS50000000014

• Deconvolution of bulk RNA-Seq using single cell RNA-Seq

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Study EGAS00001006723

• Angiosarcoma_follow_up_2_validation_study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Study EGAS00001000518

• Ewings_Sarcoma_RNA_seq_drug_sensitivity

  Illumina RNA-Seq will be performed on four Ewing’s sarcoma cell lines and two control cell lines. RNA was extracted from all the lines using a basic Trizol extraction protocol.

  Study EGAS00001000419

• Single-cell transcriptomic data of 9 DHG-H3G34 patient tumors.

  We applied single-cell/single-nucleus RNA-sequencing to a patient cohort of 9 fresh and frozen untreated diffuse hemispheric gliomas, H3G34-mutant (DHG-H3G34).

  Study EGAS50000000534

• Bone_Cancer___Rare_Types_Whole_Genome

  We propose to definitively characterise the somatic genetics of a selection of rare bone cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000501

• LINE_luminal_breast_cancer_Neoadjuvant_Chemotherapy_Study

  A targeted gene screen of 365 known cancer genes in luminal breast cancer samples pre-chemotherapy and at resection post-chemotherapy to evalaute clonal expansion of chemotherapy cancer cells.

  Study EGAS00001001223

• Neuroblastoma Evolution

  Here, we quantify the somatic evolution of neuroblastomas by deep (80x) whole-genome sequencing, molecular clock analysis and population-genetic modeling in a comprehensive cohort (Hipo_K09R) covering all subtypes.

  Study EGAS00001006533

• Genomics analysis of mucinous tumours of the ovary and related neoplasms

  To perform genetic and gene expression analyses on mucinous ovarian tumours to determine a progression model, cell of origin and novel therapeutic targets.

  Study EGAS00001003545

• DECONVOLUTION OF HEMATOPOIETIC STEM/PROGENITOR CELL SIGNALING IN HUMAN AML

  A comprehensive taxonomy of the predicted interactions between LEPR + stromal niches, HSPCs and adaptive/innate immune cells in the human NBM and AML

  Study EGAS00001007330

• Clonal_analysis_Bcell_activation

  We developed a B cell stimulation protocol that allowed us to expand a smaller number of naive B cells in culture (2,000 B cells at day 0). On day 6, we performed single-cell RNA-and BCR-sequencing on the entire culture, preserving both clonal diversity and size.

  Dataset EGAD50000002114

• Whole Exome Sequencing of Bipolar cases and matched a cohort from Edinburgh, Scotland, UK

  Whole Exome Sequencing of 1260 Bipolar cases and matched controls performed at the Broad Institute on a cohort from Edinburgh, Scotland, UK. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000623

• DELFI low-coverage WGS of plasma cfDNA

  The dataset "DELFI low-coverage WGS of plasma cfDNA" includes paired FASTQ files produced by WGS of 689 plasma cfDNA samples from 153 patients with colorectal cancer. WGS (100bp PE) was performed on a NovaSeq 6000 with a target depth of coverage of 8x.

  Dataset EGAD50000000630

• Clonally heritable gene expression imparts a layer of diversity within cell types

  Human datasets associated with paper 'Clonally heritable gene expression imparts a layer of diversity within cell types' published in Cell Systems

  Dataset EGAD50000000231

• Whole Exome Sequencing of a Melanoma Patient with Acquired Resistance to MEK plus CDK4/6 Inhibition

  Longitudinal biopsies from a melanoma patient who initially responded to MEK plus CDK4/6 inhibitor therapy were whole exome sequenced to identify potential resistance mutations. The biopsies included normal tissue, pre-treatment, on-treatment, and several post-resistance timepoints.

  Dataset EGAD00001003989

• BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS)

  BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS)

  Dataset EGAD00001002663

• sn-RNAseq profiling of the impact of a cytokine storm model in human cardiac organoids

  sn-RNAseq profiling of the impact of a cytokine storm model in human cardiac organoids

  Dataset EGAD00001007533

• Exome sequencing of 3 blood samples from tall man and his parents

  Exome sequencing was carried out in a tall male (height 3.5 SDS) and his parents (3 samples). The data was sequences on a Illumina Hiseq2000 and the library was prepared with Agilent SureSelect V4.

  Dataset EGAD00001007767

• IFNL4 Organoid Transcriptome Profiles

  RNAseq of liver organoids with a dG genotype (B20, nt115, U15) and with a TT genotype (nt5, U16, U19) was performed, which was used to study the impact of IFNλ4 on the cellular response to Sendai viral infection.

  Dataset EGAD00001007820

• CONTAGIOUS trial - COVID-19 16S dataset

  16S amplicon data of nasopharyngeal swabs in a COVID-19 cohort recruited at UZ Leuven. The dataset contains a single experiment, comprising 150 runs corresponding to 125 unique samples. Runs comprise paired fastq files (2*250 bases) obtained from an Illumina MiSeq instrument.

  Dataset EGAD00001006864

• Personalised therapy with MEK inhibition leads to a sustained complete response in an adolescent patient with a recurrent malignant peripheral nerve sheath tumor

  Whole genome sequencing of tumour (90X) - normal (30X) patient pair and bulk transcriptome sequencing (80M PE reads) of tumour sample.

  Dataset EGAD00001006793

• In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Dataset EGAD00001009688

• Transcriptomics sequencing 4 samples from the same KMT2A-rearranged Acute Lymphoblastic Leukemia patient

  Dataset contains four samples taken from a neonate with congenital KMT2A-rearranged Acute Lymphoblastic Leukemia patient (CHI-0391) with rare IKZF1 gene fusions. Sequencing was carried out using mRNA-seq sequencing on a Illumina NextSeq 500 machine

  Dataset EGAD00001009974

• WGS

  Purified DNA from PDX samples were subjected to WGS. Libraries were performed using the TruSeq DNA PCR-Free kit (Illumina) starting with 1μg of input DNA and performed following manufacturer's instructions. Libraries were sequenced on a NovaSeq 6000 (2x151 bp) instrument (Illumina). A mean coverage of 30.4x was obtained.

  Dataset EGAD00001010309

• NIDDM-Atherosclerosis Study (NIDDM-Athero)

  The NIDDM-Atherosclerosis Study, funded by NHLBI, was designed as a family study to examine the genetic basis of subclinical atherosclerosis and diabetes in Hispanic families. Family members of probands with T2D were recruited in the Los Angeles area. The baseline examination of the cohort included the euglycemic hyperinsulinemic clamp test from which the two key phenotypes were obtained: insulin sensitivity (M) and metabolic clearance rate of insulin (MCRI). Genome-wide genotyping was obtained under separate funding by NIDDK as a part of the GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

  Study phs001130

• Inherited Defect in ST6GalNAc1 Reveals Roles of Sialylation in Intestinal Homeostasis

  We have conducted a study of patients with unique mutations in the gene ST6GALNAC1 that encodes the protein ST6GALNAC1 (ST6). Exome sequencing was used to screen worldwide inflammatory bowel disease cohorts, which identified human loss of function mutations of ST6 in individual patients. The affected patients had very early onset (< 6 years old) inflammatory bowel disease. A comprehensive investigation of these gene mutations through in vivo and in vitro experiments revealed that decreased sialylation caused defective mucus proteins and congenital inflammatory bowel disease.

  Study phs002598

• Genetic measurement of memory B-cell recall using antibody repertoire sequencing

  We developed an improved high throughput sequencing approach to measure the quantities and sequences of the repertoire of antibody heavy chain RNA in a blood sample. Using this approach we analyzed the antibody repertoire in response to yearly vaccinations with influenza vaccines TIV and LAIV in healthy adults in two subsequent years. We determined vaccine response patterns specific to LAIV and TIV and found antibody sequences that were shared between two samples of the same individuals following influenza vaccination in subsequent years, thereby providing a genetic measurement of B-cell memory recall.

  Study phs000656

• ARID1A Mutations in Endometriosis-Associated Ovarian Carcinomas

  We have sequenced the whole transcriptomes of 18 ovarian clear-cell carcinomas and 1 ovarian clear-cell carcinoma cell line and found somatic mutations in ARID1A (the AT-rich interactive domain 1A [SWI-like] gene) in 6 of the samples. ARID1A encodes BAF250a, a key component of the SWI–SNF chromatin remodeling complex. We sequenced ARID1A in an additional 210 ovarian carcinomas and a second ovarian clear-cell carcinoma cell line and measured BAF250a expression by means of immunohistochemical analysis in an additional 455 ovarian carcinomas

  Study EGAS00000000075

• Whole genome sequencing of colon organoid cultures with artificially induced oncogenic mutations

  Using the CRISPR-Cas9 genome editing system, various oncogenic mutations were introduced in the genome of normal adult stem cells derived from the colon. The resulting clonal cultures were subjected to whole genome sequencing. In addition, the cultures were transplanted in a mouse and the resulting primary and metastatic tumors were also subjected to whole genome sequencing. The initial bulk culture, which was used to generate the mutations, was also whole genome sequenced and served as a reference sample to filter germline variants.

  Study EGAS00001001969

• DO NOT USE - Whole genome sequencing of SI-NETs from six patients

  Small intestine neuroendocrine tumor (SI-NET), the most common cancer of the small bowel, often displays a curious multifocal phenotype with several intestinal tumors centered around a regional lymph node metastasis, yet the typical path of evolution of these lesions remains unclear. Here, we determined the complete genome sequences of 24 tumor and 3 adjacent normal tissue samples with their paired normal blood samples (totally 33 whole genomes) from 6 patients with multifocal SI-NETs, allowing elucidation of phylogenetic relationships between multiple intestinal tumors and metastases in individual patients.

  Study EGAS00001005009

• Childhood B-cell acute lymphoblastic leukemia genomic and transcriptomic data

  The aim of the two studies was: 1) to genetically characterise childhood leukemia patients that lacked established cytogenetic abnormalities (termed B-other leukemia) and assess the clinical features of recurrent genetic abnormalities. 2) Assess the accuracy of whole genome sequencing as a diagnostic genetic test in childhood leukemia, relative to other traditional methods (karyotyping, FISH, MLPA) and whole transcriptome sequencing. As a result, this study includes targeted DNA-sequencing, whole genome sequencing and whole transcriptome sequencing data on childhood leukemia patients enrolled on UK clinical trials (UKALL2003 and UKALL2011).

  Study EGAS00001006863

• Leukemia sequencing study

  A custom single-cell amplicon DNA sequencing panel was designed to cover relevant somatic mutations and common single nucleotide polymorphisms (panel CO303). Frozen bone marrow mononuclear cells were thawed, stained using the antibody-derived tags panel TotalSeq™-D Human Heme Oncology Cocktail, V1.0 (Biolegend) and loaded into Tapestri single-cell DNA genotyping platform (Mission Bio) to perform microfluidic encapsulation, lysis, and barcoding according to the manufacturer’s protocol (Chemistry V2, PN_3360A). DNA and ADT libraries were prepared and underwent 2x150bp paired-end sequencing on a NextSeq 500 platform (Illumina).

  Study EGAS00001006784

• WGS files for paper titled "Preclinical Pediatric Molecular Analysis for Therapy Choice (MATCH)"

  WGS files for paper titled "Preclinical Pediatric Molecular Analysis for Therapy Choice (MATCH)"

  Dataset EGAD00001015697

• METABRIC

  The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (CNVs, SNPs) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, although the landscape was dominated by cis and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP, and MAP2K4. Unsupervised analysis of paired DNA/RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, ER-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration 0152hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the 0152CNA-devoid sub-group and a Basal-specific chromosome 5 deletion-driven mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic copy number aberrations on the transcriptome.

  Study EGAS00000000083

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Atherosclerosis Risk in Communities Study (ARIC)

  Cohort Description The Atherosclerosis Risk in Communities (ARIC) study began in the mid-1980s with the initial aims being to describe the presence of subclinical atherosclerosis, the progression of atherosclerosis to clinical cardiovascular disease (CVD), and the association of novel risk factors with CVD. ARIC recruited its cohort of men and women aged 45-64 in 1987-89 from four communities (Forsyth County, NC; Jackson, MS; suburban Minneapolis, MN; and Washington County, MD). As of 2025, ARIC counts over 4,000 participants.Data Submitted Wave 1 questionnaire data includes 356 variables for up to 5763 ARIC participants in C4R. Wave 2 questionnaire data includes 367 variables for up to 5000 ARIC participants in C4R. Wave 3 questionnaire data includes 81 variables for up to 3450 participants in C4R.Dried Blood Spot/Serosurvey data includes 8 variables for up to 2437 ARIC participants in C4R. Derived data includes 62 variables for up to 18765 observations. Phenotype data includes 163 variables for up to 5937 ARIC participants in C4R. Brain MRI data includes 13 variables for up to 2550 participants in C4R.HCU data includes 21 variable for up to 631 ARIC participants in C4R.Lung CT data includes 15 variables for 1329 ARIC participants in C4R.Neurocognitive data includes 16 variables and 49826 observations.Serosurvey data includes 20 variables for 1707 ARIC participants in C4R.

  Study phs002988

• A study of resistance to novel coronavirus infection in health care workers

  There have been cases of what appear to be nosocomial infections among healthcare workers at several hospitals. The infected healthcare workers were assumed to have contracted the disease through close contact with infected patients. However, we confirmed at each medical institution that there were many healthcare workers who had apparently had closer contact with infected patients than with infected patients, but had not contracted the disease. Thus, the purpose of this study was to clarify the internal factors that make individuals less susceptible to novel coronavirus infection and their stress tolerance, and to establish a system that contributes to the appropriate allocation of healthcare workers and the creation of a system that can more safely deal with this disease in the future.

  Study JGAS000562

• Single cell and plasma RNA sequencing

  Single cell and plasma RNA sequencing for RNA liquid biopsy for hepatocellular carcinoma

  Study EGAS00001005194

• Dataset for Manuscript: Cancer genome standards for long-read sequencing using cancer cell line mixtures

  Dataset for Manuscript: Cancer genome standards for long-read sequencing using cancer cell line mixtures

  Dataset EGAD00001015628

• FFPE WGS for optimizing mutation signature extraction from archival HGSC samples

  HGSC cases were selected for which matched fresh frozen and FFPE samples were available from the same tissue specimens. Fresh frozen, FFPE and normal blood were subject to WGS for the purpose of assessing the possibility of using FFPE WGS in place of fresh frozen for somatic mutation calling

  Study EGAS00001007521