22928 results for "ega"

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• CLL_cancer_Sample_Sequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from CLL cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000011

• Whole_Genome_Sequencing_of_hiPS_cells

  Human induced pluripotent stem (hiPS) cells hold great promise for regenerative medicine. Safety issues of use of hiPS cells however remain to be addressed. One of such issues is mutations derived from somatic donor cells and introduced during genome manipulation. We sequence whole genomes of hiPS cells and analyzed mutations. Our study brings hiPS cell technology one step closer to application to regenerative medicine.

  Study EGAS00001000008

• To reveal the spectrum of gene mutations in grade II/III gliomas, whole exome sequencing of 52 samples including 4 multi-regional and 10 multi-time points sampling cases and 293 SNP-array were performed.

  To reveal the spectrum of gene mutations in grade II/III gliomas, whole exome sequencing of 52 samples including 4 multi-regional and 10 multi-time points sampling cases and 293 SNP-array were performed. Our analysis revealed high degrees of temporal/spatial heterogeneity generated during tumor expansion and relapse.

  Study EGAS00001001045

• We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  Study EGAS00001002718

• CentralAfricanCMC_Pemberton

  The CentralAfricanCMC_Pemberton dataset encompasses 153,798 SNPs from the Illumina Cardio-MetaboChip (Voight et al. 2012) genotyped in 406 individuals from 19 Central African Populations from Gabon, Cameroon, Centralafrican Republic and Uganda). Individual phenotypic and cultural information at the individual level for this data set encompass gender, lifestyle (hunter-gatherer or farmer), and, when available, stature phenotype (standing height in cm, sitting-height in cm, and weight in kg). Other cultural, linguistic, and geographical location information about the sampled populations can be found in Pemberton et al. , Human Genetics, 2018 (https://doi.org/10.1007/s00439-018-1902-3).This dataset can only be accessed and used for non-commercial research purposes with a finality complying with the informed consent provided by Central African donors for the study of human evolutionary history only.

  Dataset EGAD00010001584

• The mutational landscape and its longitudinal dynamics in relapsed and refractory Hodgkin lymphoma

  In classical Hodgkin-lymphoma (cHL), only a few cases recur, and only a limited fraction of patients is primary-refractory to standard-polychemotherapy. Underlying genomic features of unfavorable clinical courses remain sparsely characterized. Here, we investigated the genomic characteristics of primary-refractory/relapsed cHL in contrast with long-term-responders (LTR). In total, data from 84 samples were submitted.

  Study EGAS50000000149

• Sample Multiplexing Oligo Comparison

  In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, in patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust to ex vivo manipulation but suffered from signal-to-noise issues in more delicate sample types. We also compared the performance of fixed scRNA-Seq kits and CRISPR-based destruction of non-informative genes.

  Study EGAS50000000153

• WES data from tumors and matching controls collected from 11 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates the progression of translocation renal cell carcinoma (tRCC) based on Whole Exome Sequencing (WES) data from 11 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. Tumor samples and their matched normal DNA were sequenced on the Illumina platform.

  Study EGAS50000000126

• scATAC-seq of CD4+ T cells from blood and tumor of NSCLC patients

  This study explore the CD4+ T cells diversity in paired blood and tumor of 2 different NSCLC patients. After FACS-sorted of Tregs (DAPI- CD45+ CD4+ CD25hi CD127lo) and Tconvs (DAPI- CD45+ CD4+CD25lo CD127lo/hi), cells were mixed in equal proportion (fifty/fifty ratio) and procesed with 10X Chromium (10X Genomics) scATAC kit and sequenced using Illumina platforms.

  Study EGAS50000000294

• 10x Genomics raw data of intestinal plasma cells

  The dataset contains raw fastq files (fastq.gz) for Chromium Single Cell 5’ gene expression (GEX), human B cell VDJ and feature barcode (CSP) sequencing from transglutaminase 2-specific and other small intestinal plasma cells isolated from four untreated celiac disease patients. Single cell 5’ gene expression, V(D)J-enriched and cell surface protein libraries were generated using Chromium single cell kits, and barcoded cDNA from a total of 5,000-10,000 cells per sample was generated using the 10x Genomics Chromium Controller. The libraries were pooled prior to sequencing on a NovaSeq 6000 instrument (Illumina) using the following configuration: read 1: 26 cycles, read 2: 89 cycles, index read 1: 8 cycles.

  Dataset EGAD50000000342

• Separation, characterization, and identification of individuals from multi-person blood mixtures with single cell ATAC-seq

  We report a deconvolution and identification strategy of scATAC-seq datasets using mixed PMBCs data. After sequencing the data were processed with the de-goulash pipeline and analyzed with aim to identify and acquire biogeogrpahical ancestry of the involved individuals. The study includes samples of biological mixtures and in silico mixtures in different mixed ration and cell volumes.

  Study EGAS00001007380

• HiDEF-seq single-molecule sequencing of single-strand mismatches and damage

  Our study sought to resolve, with single-molecule fidelity, the mismatches and damage events that precede DNA mutations. Using a novel single-molecule, long-read sequencing method (HiDEF-seq) we detect base substitutions when present in either one or both DNA strands. We also detect cytosine deamination, a common type of DNA damage, with single-molecule fidelity. This study profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes. These samples revealed single-strand mismatch and damage signatures. Since double-strand DNA mutations are only the endpoint of the mutation process, our approach enables new studies of how mutations arise in a variety of contexts, especially in cancer and aging.

  Dataset EGAD50000000460

• BRCA1 secondary splice-site mutations

  BRCA1 splice isoforms d11 and d11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out mutation-containing exons, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers of BRCA1 exon skipping remain undetermined. We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with BRCA1 exon 11 frameshift mutations for splice isoform expression and therapy response.

  Study EGAS50000000022

• Integration of T Cell Repertoire, CyTOF, genotyping and symptomatology data reveals subphenotypic variability in COVID-19 Patients

  A total of 61 patients (33 mild and 28 severe) with a median age of 51 years who recovered from COVID-19 were included in this study (Table 1). All collected samples were confirmed in diagnosis of COVID-19 by RT-PCR and positive IgG serolog. For the 61 patients, TCR-seq, CyTOF, and genotyping data were generated and analyzed in separate studies, as part of larger cohorts. In total, there are 143 variables, with 129 being quantitative (TCRseq and CyTOF metrics) and 13 being qualitative (symptomatology and genotyping). For more information about cohort characteristics, data adquisition an pre-processing, please visit PMID: 39227859, 36969980 and 37287057.

  Dataset EGAD50000000840

• RNA-Seq analysis of cocaine use disorder in Brodmann Area 9

  We aimed to identify cocaine use disorder associated changes in gene expression in the Brodmann Area 9 subregion of the human prefrontal cortex. RNA-sequencing was performed in N=13 individuals with and N=12 individuals without CUD. The individuals are originating from a cohort of N=42 individuals where DNA methylation (DNAm) levels were previously analyzed using the EPIC array.

  Study EGAS50000000150

• RNA-Seq of human longitudinal whole blood samples from PCR-positive and PCR-negative adults following controlled inoculation with Influenza A H3N2 virus.

  Understanding of the transcriptomic profile of individuals in early influenza infection is limited. To investigate this, longitudinal whole-blood samples (n=178) were taken from adult participants following controlled inoculation with Influenza A H3N2 virus (sampling at baseline (0) and days 1, 2, 3, 7, 10 and 14 post-challenge). Most participants became influenza PCR-positive; a minority remained PCR-negative. Total RNA was extracted from PAXgene tubes before undergoing globin and rRNA depletion. DNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. All samples were then sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000000956

• Luminal progenitor cell line iHBEC(CD117)

  Basal-like breast cancer originates in luminal progenitors, frequently with an altered PI3K pathway, and focally in close association with genetically altered myoepithelial cells at the site of tumor initiation. The exact trajectory behind this bi-lineage phenomenon remains poorly understood. Here we used a breast cancer relevant transduction protocol including hTERT, shp16, shp53, and PIK3CA(H1047R) to immortalize FACS isolated luminal cells, and we identified a candidate multipotent progenitor. We found that the apparent luminal phenotype of these oncogene transduced progenitors was metastable giving rise to basal-like cells dependent on culture conditions. After culturing the cells for more than 60 passages, cells were subjected to scRNA-seq as well as bulk RNA sequencing of two subpopulations (CD271+ and CD271-).

  Dataset EGAD50000000723

• Targeted long-read snIso-Seq of the human brain in neurodegenerative diseases

  Nuclei were extracted from postmortem human brain, and cDNA libraries were generated using the 10X Genomics 3' v3.1 kit. Prior to fragmentation, 75% of the library was reserved for long-read sequencing. This unfragmented library was used for target enrichment with a custom 50 gene probe panel from Twist Biosciences. The resulting amplified cDNA libraries were sequenced on a Sequel II. The files provided have undergone CCS generation, and we recommend following the guidelines in https://isoseq.how/ for further analysis starting with removal of primers using lima. The primer sequences that should be supplied are the Read 1 and TSO primers from the 10X Genomics kit.

  Dataset EGAD50000000179

• Whole genome sequencing to detect spontaneous acquired mutations in mismatch repair-deficient human colon organoids

  Individual outgrowing organoids surviving the medium-based selection were manually picked and propagated as clonal lines for a couple of passages to avoid unexpected mutation accumulation before being harvested for WGS/WES. 1 µg of DNA was used for WGS/WES by Agilent SureSelect V7 kit, with 8Gb per sample (50X average mapped) data throughput, sequencing on NovaSeq 150PE

  Study EGAS50000000114

• A Phase Ib/II Study of Regorafenib and Paclitaxel in Beyond First-line Advanced Esophagogastric Carcinoma (REPEAT)

  Regorafenib showed promising results in gastric cancer. We aimed to assess the tolerability of regorafenib and paclitaxel in advanced esophagogastric cancer (EGC) patients refractory to first-line treatment and explore potential biomarkers.. We performed enzyme-linked immunosorbent assay measurements of galectin-1, RNA sequencing, and shallow wholegenome sequencing of metastatic tumor biopsies for biomarker analyses.

  Study EGAS00001006054