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• Osteosarcoma_multiregion_characterisation___Methylation

  Characterisation of osteosarcoma across multiple regions of primary tumours, local recurrences and metastases using whole genome sequencing, methylation and transcriptomics. This study contains the methylation data.

  Study EGAS00001008243

• Analysis of enhancer-promoter connectivity alterations

  The study uncovers epigenomic changes associated with dexamethasone response heterogeneity in myeloma cells, revealing rewired promoter-enhancer interactions and DNA loop stabilization

  Study EGAS00001007411

• Raw BulkRNA sequencing data

  BulkRNA sequencing Human Strand Specific mRNA (WOBI) 40M reads was performed by Novogene (Netherlands) using the NovaSeq X Plus Series (PE150, Q30≥85%) sequencing platform and strategy. 24 samples were included in the study, requiring 12 G of raw data per sample.

  Dataset EGAD50000001848

• Sequence variation of rs774984872G>T

  This dataset contains the genotypes status of rs774984872G>T, a loss of function variant in ANGPTL8. 8 individuals had the reference allele (G/G), 5 were heterozygous (G/T) and 1 was a knock out (T/T).

  Dataset EGAD50000002135

• This dataset contains the cram files from the whole Exome sequencing

  Exome Sequencing of Healthy and M. Heamophilum Infected Participants

  Dataset EGAD50000001565

• Whole genome sequencing of childhood acute lymphoblastic leukaemia patients

  Whole genome sequencing of childhood acute lymphoblastic leukaemia patients. Matched diagnostic and germline samples were obtained from bone marrow aspirates and sequenced on the Illumina platform to characterise the underlying genetic features (DOI: 10.1038/s41375-022-01806-8).

  Dataset EGAD50000000975

• Whole Exome Sequencing of Bipolar cases and controls on a cohort from Umea, Sweden

  Whole Exome Sequencing of 924 Bipolar cases and matched controls performed at the Broad Institute on a cohort from Umea, Sweden. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000470

• Long-read RNA-seq of doxycycline-inducible DUX4 human myoblast cell lines

  The dataset includes the PacBio full-length isoform sequencing data of DUX4i myoblasts (Clone-5) with and without 16-hour DOX-treatment (referred to as DUX4- and DUX4+; n=1 in each condition).

  Dataset EGAD50000000718

• Homopolymer switches WES dataset

  This project used NGS (next generation sequencing) in mismatch repair deficient colorectal cancer samples. The project investigated the role of secondary MMR (mismatch repair) gene mutations in tumor evolution. This dataset includes BAM files from multi-region Whole Exome Sequencing of 49 samples from 22 patient tumors.

  Dataset EGAD50000000319

• Bulk transcriptomic analyses of monocyte-derived dendritic cells treated with CES1i

  The data published here contains bulk RNA-sequencing (RNAseq) data as obtainedfrom monocyte-derived dendritic cells in treated with/without LPS and with/without CESi (WWL113). Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000344

• Variants from germline WES data of pediatric cancer patients

  This dataset contains germline variants (in .vcf format) from six pediatric cancer patients (sample IDs D1 - D6). WES data of the children and their parents was mapped to hg38. A consensus of four variant callers was used to obtain germline variants of the children.

  Dataset EGAD00001009678

• CLL2 dataset used in FLTseq paper

  This dataset contains CLL2 data used in FLTseq paper. The dataset contains the data of CITEseq, FLTseq, RaCHseq, Exonseq and bulk RNAseq.

  Dataset EGAD00001008114

• RNA-Seq samples from the BELOB clinical trial study to find transcriptome associations with response to Bevacizumab and CCNU in glioblastoma patients

  RNA-Seq samples from the BELOB clinical trial study to find transcriptome associations with response to Bevacizumab and CCNU in glioblastoma patients

  Dataset EGAD00001006329

• WES data of one tumor of B-cell lymphoma

  paired EXOME sequencing on Illumina HiSeq 4000 using Agilent SureSelect V6 of one tumor sample of one patient with B-cell lymphoma. The bam-file was mapped to the hg19 genome.

  Dataset EGAD00001006060

• Sporadic and endemic Burkitt lymphoma have frequent FOXO1 mutations but distinct hotspots in the AKT recognition motif

  Sample set of 74 whole-exome sequencing samples from sporadic Burkitt lymphoma patients from the UK. 33 of these samples have matched constitutional data, giving a total number of 107 samples

  Dataset EGAD00001005105

• Sequencing-based counting and size profiling of plasma Epstein-Barr virus DNA enhance population screening of nasopharyngeal carcinoma.

  We used targeted sequencing to capture and measure the abundance as well as the size profiles of EBV DNA in plasma of subjects with and without NPC

  Dataset EGAD00001004204

• RNA bam files of Renal Cell Carcinoma patients

  the dataset contains RNA bam files of Renal Cell Carcinoma patients, which belongs to "An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors"

  Dataset EGAD00001003895

• Genomic alteration in Korean Young Age Diffuse Gastric Cancers

  To identify recurrent somatic alterations in this unique subset of gastric cancers, whole exome and SNP6 analyses were performed using frozen cancer tissue. The somatic mutation analyses were also performed using blood of the same patients.

  Dataset EGAD00001001984

• WGS on patients 5-7, study of metastatic prostate cancer

  Data from the study of subclonal metastatic expansion in prostate cancer. Whole genome shotgun sequencing of six samples, tumour and whole blood, from the three additional patients whose somatic variants were examined in depth.

  Dataset EGAD00001001344

• Whole-exome sequencing of breast cancer metastasis and corresponding blood samples

  Whole-exome sequencing (WES) of 216 breast cancer metastasis-normal pairs from patients who underwent a biopsy in the context of the SAFIR01, SAFIR02, SHIVA or MOSCATO prospective trials (France).

  Dataset EGAD00001002747

• Breast cancer sequential sampling study

  This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Dataset EGAD00001000387

• Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

  Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. In version 1.0 of this study, we performed RNA-based next generation sequencing (mNGS) on 41 lower respiratory samples collected from 34 children. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Potential pathogens were detected in half of samples previously negative by clinical diagnostics. In version 2.0, we included an addition 278 samples from 229 pediatric stem cell transplant patients with pulmonary disease.

  Study phs001684

• Tumour sample for patient SA1026

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1026

  Dataset EGAD00001009607

• Tumour sample for patient SA1064

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1064

  Dataset EGAD00001009606

• Tumour sample for patient SA1065

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1065

  Dataset EGAD00001009605

• Normal sample for patient SA666

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA666

  Dataset EGAD00001009604

• Normal sample for patient SA415

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA415

  Dataset EGAD00001009603

• Normal sample for patient SA299

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA299

  Dataset EGAD00001009602

• Normal sample for patient SA288

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA288

  Dataset EGAD00001009601

• Normal sample for patient SA994

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA994

  Dataset EGAD00001009599

• Normal sample for patient SA992

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA992

  Dataset EGAD00001009598

• Normal sample for patient SA610

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA610

  Dataset EGAD00001009597

• Normal sample for patient SA576

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA576

  Dataset EGAD00001009596

• Normal sample for patient SA1074

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1074

  Dataset EGAD00001009595

• Normal sample for patient SA1073

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1073

  Dataset EGAD00001009594

• Normal sample for patient SA1069

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1069

  Dataset EGAD00001009593

• Normal sample for patient SA1065

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1065

  Dataset EGAD00001009592

• Normal sample for patient SA1064

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1064

  Dataset EGAD00001009591

• Normal sample for patient SA1040

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1040

  Dataset EGAD00001009590

• Normal sample for patient SA1028

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1028

  Dataset EGAD00001009589

• Normal sample for patient SA1027

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1027

  Dataset EGAD00001009588

• Normal sample for patient SA1026

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1026

  Dataset EGAD00001009587

• Normal sample for patient SA1017

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1017

  Dataset EGAD00001009586

• Tumour sample for patient SA720

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA720

  Dataset EGAD00001009585

• Tumour sample for patient SA718

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA718

  Dataset EGAD00001009584

• Normal sample for patient SA720

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA720

  Dataset EGAD00001009583

• Normal sample for patient SA718

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA718

  Dataset EGAD00001009582

• Tumour sample for patient SA415

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA415

  Dataset EGAD00001009581

• Tumour sample for patient SA095

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA095

  Dataset EGAD00001009580

• Tumour sample for patient SA299

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA299

  Dataset EGAD00001009579