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• 10X snMultiome (ATAC+GEX) for the study of "SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities"

  10X snMultiome (ATAC+GEX) sequencing of 1 human reactive tonsil sample and 1 DLBCL sample for the study of "SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities"

  Dataset EGAD50000002277

• 10x Genomics BCR Sequencing

  BCR sequencing done with 10x Genomics V(D)J kit + platform for the paper: Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma. Dataset contains paired FASTQ files for 35 samples, each was processed with the 10x Genomics V(D)J kit to obtain the sequence of the B-cell receptor sequence.

  Dataset EGAD50000001373

• SCIMAP PILOT D21

  This dataset includes the RNA-seq and ATAC-seq fastq files, as well as the Cellranger ARC count table, for the first experiment with multimodal sequencing in the SCI-MAP project (1 sample). Here, human induced pluripotent stem cells underwent differentiation to chondrocytes for 21 days following an established protocol. Nuclei were isolated and sequenced in two modalities simultaneously; RNA and ATAC.

  Dataset EGAD50000001516

• HighIGHG1 CRISPR-Cas9 edited alleles in IGHUND COH-DHL1 HGBCL2-DH-BCL2 cells

  High-throughput sequencing of IGHG1 alleles amplified from genomic DNA and the IGG1 (IGVH-CG1) functional transcript, flanking the gRNA-targeted region, from IGHUND HGBCL-DH-BCL2 COH-DHL1 cell line. IGHG1 targeting gRNAs were cloned into lentiCRISPRv2-Puro lentiviral vector (Addgene #98290). COH-DHL1 transduced cells were selected in Puromycin for 7 days, and expanded for further 17 days in the absence of any antibiotic selection.

  Dataset EGAD50000001525

• RNA fastq files and mutation annotation files

  This dataset contains the results of both RNA sequencing and DNA sequencing. For RNA sequencing, it includes data from 12 samples derived from 9 patients, provided as raw sequencing files in FASTQ format. For DNA sequencing, it contains mutation information obtained from targeted panel DNA sequencing, including data from 35 individuals in the mutation annotation file (MAF) format.

  Dataset EGAD50000001768

• Emirati Phased Diploid Trio-Assemblies (27 Individuals, 54 Assemblies)

  This dataset comprises 27 phased diploid genome assemblies (i.e., 54 haplotypes) from Emirati family trios, provided in FASTA format. Sequencing used PacBio HiFi reads generated on the Revio platform at ≥25× coverage for each parent and offspring. Assemblies were produced with hifiasm (trio mode), then scaffolded with NTLink and reference-guided merging via RagTag against CHM13v2. The collection offers haplotype-resolved references suitable for downstream variant discovery and pangenome analyses.

  Dataset EGAD50000001755

• scRNA-seq of Patient-derived tumor fragments (PDTFs)

  scRNA-seq of Patient-derived tumor fragments (PDTFs) which were treated with either Isotype (DP47), Isotype-IL2v (DP47-IL2v), anti-PD1 (PembroPGLALA) or PD1-IL2v (PembroPGLALA-IL2v) for 48 hours. Dataset content: 10 samples from 3 donors File type: paired-end fastq files Protocol: Chromium Single Cell 3' Reagent Kits User Guide (Dual Index) with Feature Barcoding technology for Cell Surface Protein (CG000317) Technology: Illumina sequencing Experimentation: scRNA-seq using the 10X technology

  Dataset EGAD50000000584

• scRNAseq and scTCRseq of three tumor lesions derived from one patient receiving adoptive TIL therapy

  scRNA sequencing and scTCR sequencing on three tumor lesions derived from one patient receiving adoptive tumor-infiltrating lymphocyte (TIL) therapy. Expanded metastasis was used for TIL expansion and yielded the TIL product which also was used for scTCR sequencing. 10 weeks after transfer of the TIL product the regressing metastasis was resected. After the patient progressed the progressing metastasis was removed (61 weeks).

  Dataset EGAD50000000406

• Parallel Detections of Somatic Gene Mutations in Surgically Resected Tumor tissues and Matched Plasma Specimens in Early-Stages of Primary Breast Cancer

  We developed two panel successively, contain 68 and 136 genes respectively. Combination with ultrasound or mammography, it could be used for breast cancer early detection and avoided unnecessary surgery or other invasive detection.

  Study EGAS00001003075

• Single cell RNA sequencing of lung adenocarcinoma.

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes.

  Study EGAS00001003681

• Mutational_burden_in_skin_following_UV_treatment_Nanoseq

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007681

• Mutational_burden_in_skin_following_UV_treatment_WGS

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007682

• Mutational_burden_in_oesophagus__nanoseq_

  We wish to accurately assess mutational burden and signature from patients of different ages using clonal oesophageal epithelium and duplex-seq. We will also attempt to look for differences between smokers and non-smokers and individuals with different levels of alcohol consumption.

  Study EGAS00001007695

• Molecular profiling of DLBCL patients treated in the PETAL trial

  Using whole-exome sequencing and shallow whole genome sequencing for simultaneous screening of mutations, copy number alterations, and translocations, 5 biology-based risk profiles could be reproduced in an independent cohort of DLBCL patients, from the PETAL trial.

  Study EGAS00001005828

• Chromatin accessibility analysis of TFEB overexpression in LT-HSC

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentivirus overexpressing GP91 (CTRL) or TFEB. Six days later, BFP+ transduced cells were sorted for DNA extraction, library preparation and sequencing

  Study EGAS00001004971

• Molecular and clinical effects of selective TYK2 inhibition with deucravacitinib in psoriasis

  Investigate changes in IL-23/Th17- and type I interferon-pathway biomarkers and gene responses, and measures of selectivity for TYK2 over Janus kinases (JAKs) 1–3, in patients with moderate to severe psoriasis receiving deucravacitinib.

  Study EGAS00001005875

• Transcriptomic analysis of MYC overexpression in LT-HSC.

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors (empty E CTRL or MYC). Six days after transduction, BFP+ transduced cells were sorted for RNA extraction and sequencing

  Study EGAS00001004970

• Single Cell Genome Sequence for DLP+ library A96228A

  Single Cell Genome Sequence for Immortalized lymphoblastoid cell line GM18507 cell line SA928,Triple negative breast cancer patient-derived xenograft SA609 passage 2 patient-derived xenograft SA609 passage 2 on DLP+ library A96228A

  Dataset EGAD00001009645

• iPSC and iNeuron RNAseq, chip-seq and single cell CRISPR activation

  Dataset includes 1) RNAseq for Bob_Ngn2 cell differentiation from iPSC to iNeuron stage (time point 0, 24, 48 and 96 hours). 2) Bob_Ngn2 cell line chip-seq (H3K4me3, H3K4me1, H3K27me3, H3K9me3, H3K27ac, H3K36me3) for both iPSC and iNeuron stage with 3 replicates at each time point. 3) Single cell CRISPR activation experiment with 96 endogenous genes.

  Dataset EGAD00001010050

• Genomic Data for Integrative Profiling of T790M Negative EGFR Mutated NSCLC

  Contains WES and RNA-seq for the 59 patients with first- and second-generation EGFR TKI-resistant metastatic EGFR-mutated NSCLC.

  Dataset EGAD00001010272

• Sequencing data for oesophageal / related samples - Kazachenka et al (DNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" WGS for 452 samples

  Dataset EGAD00001011095

• WXS dataset of Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  WXS dataset of Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  Dataset EGAD00001015638

• RNA-seq dataset of Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  RNA-seq dataset of Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  Dataset EGAD00001015639

• Fetal body map

  From 2nd trimester human foetuses we derived liver and intestinal stem cells. These were clonally expanded until enough material was available for whole genome sequencing. For each foetus, reference tissue (skin or bulk liver) was also sequenced to determine all germline variants. These were subtracted from the clones to determine all somatic mutations that had been acquired during embryonic and fetal development.

  Dataset EGAD00001003997

• Sequencing data for oesophageal and related samples - Alex Frankell et al (RNA)

  Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. RNAseq (BAM files) 116 tumours

  Dataset EGAD00001004423