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• germline variants in children with hematological cancer

  Trio parent-child whole exome sequencing has been used to identify cancer predisposing syndrome (CPS) in our pediatric patients with hematological cancer, and it was identified in 3.8% of the total number of patients(131).

  Study EGAS00001006907

• RNAseq of ribosomal footprints

  Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens.NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit

  Dataset EGAD00001001930

• Exome sequencing of two siblings with a neurodegenerative disorder identifies causative compound heterozygous variants in SLC5A6

  Exome sequencing data of two siblings of with a neurodegenerative phenotype due to SMVT deficiency. Exonic sequences were enriched using the SeqCap EZ Human Exome Library v3.0 kit (Roche NimbleGen) and libraries sequenced as 100bp paired-end reads on the HiSeq 2000 platform (Illumina).

  Dataset EGAD00001005364

• RRBS DNA methylation analysis of in vitro differentiation from induced pluripotent stem cells to hepatocyte-like cells

  Fastq files of Reduced Representation Bisulfite Sequencing data (HaeIII, covering about 7 million CpGs per sample) of induced pluripotent stem cells (iPSC), definitive endoderm (DE) and hepatocyte-like cells (HLC). The dataset comprises data generated by the in vitro differentiation protocol Cellartis (Takara Bio, "CEL", n = 4).

  Dataset EGAD00001005933

• Single-cell TCR sequencing of gluten-specific T cells from 20 celiac disease patients uploaded on 2021_Data access committee

  In order to characterize the T cell receptor (TCR) repertoire of gluten specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.5:DQ2.5-gluten tetramer binding CD4+ T cells isolated from blood, biopsies and T cell line from celiac disease patients.

  Dataset EGAD00001006977

• Bioinformatics analysis of chimerism in monochorionic dizygotic twins

  We conducted whole-genome sequencing on blood and buccal specimen from a family with chimerism identified in the two monochorionic dizygotic twins. Blood DNA was obtained from all family members. In addition, we obtained buccal specimen from the chimeric twins. Whole-genome sequencing was conducted on Illumina NovaSeq.

  Dataset EGAD00001009508

• GELATO clinical trial whole exome sequencing data (metastatic lesions)

  Paired-end whole exome sequencing of 19 lobular breast cancer metastatic tumors and matched normal samples obtained from 19 unique patients from the GELATO clinical trial. The included raw sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009837

• RNASeq data from one small cell prostate cancer patient (4 samples from 3 time points)

  RNASeq data from one small cell prostate cancer patient - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points. mRNA was selected using the Magnetic mRNA Isolation Module (NEB) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

  Dataset EGAD00001011154

• Ultra-fast deep-learned pediatric CNS tumor classification.

  In this study nanopore sequencing was applied to obtain sparse DNA methylation profiles from pediatric CNS tumor samples. A neural network was used to classify the tumor based on the obtained methylation profile.

  Dataset EGAD00001011303

• The Institute of Cancer Research - Endocrinology Team

  Dac EGAC00001000532