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• GM18507 direct library preparation (DLP) single-cell genomes

  Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized lymphoblastoid cell line GM18507.

  Dataset EGAD00001003148

• Sequencing data for the manuscript "Early on-treatment changes in circulating tumor DNA fraction and response to enzalutamide or abiraterone in metastatic castration-resistant prostate cancer"

  This submission contains gzipped fastq files from paired-end targeted sequencing.

  Dataset EGAD00001010105

• Human serum small non-coding RNA sequencing

  Human small non-coding RNA sequencing of serum from sons of PCOS mothers (n=9) and sons of control mothers (n=9), see publication for details.

  Dataset EGAD00001010165

• Single-cell RNA-Seq (Chromium Next GEM Single Cell 3' Reagent Kits v3.1 from 10X Genomics )

  Human data for transcriptome (scRNA-Seq) in CD34+ B cell precursors.

  Dataset EGAD00001010907

• scRNA-seq

  This dataset gather scRNAseq data performed for MM.1S cell line in control and dex conditions at 4h and 24h

  Dataset EGAD00001011139

• RNA-seq dataset of CD34+ HSPCs from LRMDS patients

  To profile transcriptional alterations of HSPCs in LR-MDS patients, 7AAD−CD45+Lin-CD235a−CD34+ cells were isolated from healthy donors and LR-MDS patients for RNA sequencing.

  Dataset EGAD00001015771

• SNV vcf files for CPCG Subclonal Heterogeneity

  SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study

  Dataset EGAD00001004400

• BRIDGE Bleeding and Platelet Disorders

  Whole exome sequencing BAM files for samples from the BRIDGE Consortium with pathogenic or likely pathogenic variants on genes linked to bleeding or platelet disorders.

  Dataset EGAD00001001333

• Long-read amplicon sequencing data per risk gene

  Each gene contains individual nanopore long-read amplicon sequencing FASTQ files for: individual (IND) 01-05 and brain regions: Brodmann Area (BA): 10, 24, 9, 46, caudate (CAUD), cerebellum (CBM) and temporal cortex (TCX).

  Dataset EGAD00001015350

• BLUEPRINT Gene expression profiles of human hematopoietic progenitors

  Gene expression was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).

  Dataset EGAD00001002733

• Chromatin 3D interactions mediate genetic effects on gene expression (genotypes)

  This dataset contains the imputed genotypes for the gencord samples. Genotyping was done using Illumina OMNI2.5M. Imputation was done using SHAPEIT2/IMPUTE2 with 1000 genomes project phase 3 reference panel.

  Dataset EGAD00001004790

• Wilms Tumour organoid sequencing WGS (2019-09-05)

  This study investigates the genomic and transcriptomic characteristics of Wilm's tumour organoids . This dataset contains all the data available for this study on 2019-09-05.

  Dataset EGAD00001005312

• UCSF brain tumor data

  Single Nuclei ATAC seq data from GBM tumor samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005314

• Target capture sequence for Primary-recurrent HCC study

  This dataset contains target capture sequence data from 255 samples, including 154 tumors and 101 normal samples. All the experiments were performed on Illumina HiSeq 2000 platform with raw reads stored in fastq format.

  Dataset EGAD00001005450

• Targeted sequencing of in vitro colonies - bulks (2020-05-05)

  In this study we will perform targeted sequencing on the bulk samples of in vitro colonies. This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006118

• WES raw data for study "Molecular and functional profiling of plasmablastic lymphoma"

  1 cell line and 123 patient samples including 38 normal (22 paired normal and 16 unpaired), 85 tumor-initial, FASTQ file types, Agilent SureSelect Human All Exon V6 Kit

  Dataset EGAD00001006400

• RNA Expression in Diverse Donor Derived Dermal Fibroblasts Correlates with Reprogramming to Pluripotency

  The cohort used in this study includes 36 African American (17 female, 19 male) and 36 White American (19 female, 17 male) individuals. The total cohort has a median age of 32 years, with a range of 20-64 years. The African American cohort has a median age of 34, with a range of 21-52 years. The White American cohort has a median age of 31, with a range of 20-64 years. Primary dermal fibroblast lines were derived from skin biopsies obtained from adult individuals at the NIEHS under institutional review board approved protocol human subjects 10-E-0063, "Sample Collection Registry for Quality Control of Biological and Environmental Specimens and Assay Development and Testing protocol" (ClinicalTrials.gov #NCT01087307). All participants gave written informed consent for tissue donation. Donor sex, age, and ancestry were voluntarily self-reported. Fibroblast cells were reprogrammed via lentiviral transduction using six transcription factors contained in three plasmids (ADDGENE/PSIN4-EF2-N2L, ADDGENE/PSIN4-EF2-O2S and ADDGENE/PSIN4-CMV-K2M). Reprogramming efficiency was determined by alkaline phosphatase staining of triplicate 10cm reprogrammed dishes containing colonies, which were then scanned. The saved images were analyzed with ImageJ 1.51h (Wayne Rasband, National Institutes of Health, USA) to count colonies, using color threshold adjusted and binary converted images of each dish. Triplicate plates were averaged and reported as colony counts or percent reprogramming efficiency ((# of colonies/250,000) x100). The African American cohort had reprogramming efficiencies ranging from 0.06-1.37%, with a median of 0.655%. The White American cohort had reprogramming efficiencies ranging from 0.02-1.13%, with a median of 0.455%. Our goal was to define transcriptomic heterogeneity that could be contributing to differences in reprogramming efficiency between individuals and between groups. Total RNA was obtained from dermal fibroblasts and matched iPSCs. For each sample, 500 ng total RNA was used as input for preparation of whole transcriptome rRNA depleted libraries. An adapter-ligated library was prepared with the KAPA HyperPrep Kit (KAPA Biosystems, Wilmington, MA) using Bioo Scientific NEXTflex™ DNA Barcoded Adapters (Bioo Scientific, Austin, TX, USA) according to KAPA-provided protocol. Sequencing was performed using an Illumina HiSeq 2500 following Illumina-provided protocols for 2x150 bp paired-end sequencing. Each transcriptome was sequenced to a target depth of 125 million reads. The following mean raw reads were obtained: African American dermal fibroblasts= 129,571,450; White American dermal fibroblasts= 131,939,505; African American iPSCs= 132,501,335; White American iPSCs= 134,394,164. Raw reads were aligned to hg19 using the STAR alignment tool (https://github.com/alexdobin/STAR). The following mean aligned reads were obtained: African American dermal fibroblasts= 123,315,343; White American dermal fibroblasts= 125,178,035; African American iPSCs= 123,148,312; White American iPSCs= 123,886,992. Reprinted from L. C. Mackey et al., Epigenetic Enzymes, Age, and Ancestry Regulate the Efficiency of Human iPSC Reprogramming. Stem Cells 36, 1697-1708 (2018), with permission from Wiley. Reprinted from L. S. Bisogno et al., Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes. Science Advances 6 (47) (2020) (PMID: 33219026), with permission from AAAS.

  Study phs002341

• NanoString raw data

  NanoString raw data for a noeadjuvant combination PD-L1 plus CTLA-4 blockade trial on patients with cisplatin-ineligible operable urothelial carcinoma. All samples were FFPE tumor samples. Raw probe count data (.RCC files) were generated from nCounter Digital Analyzer (4.0.0.3).

  Dataset EGAD00010001852

• Genotype data of human CD4 Treg cell

  Genotype data obtained using the coreExome Illumina SNP chip array for all the individuals included in the study of gene expression regulation in human primary regulatory CD4+ T cells (Tregs)

  Dataset EGAD00010001848

• SNPArray_Viet

  The compressed file contains plink format file for the Affymetrix Human Origins SNP array data of 260 individuals generated and analyzed in Liu et al 2020 study of 22 ethnolinguistic groups in Vietnam.

  Dataset EGAD00010002287

• AmsterdamUMC Data Access Committee for the MAPS study

  The current data access committee reviews and assesses data requests of researchers that seek to gain access to data acquired from the MAping the Peritoneal immune System (MAPS) project as performed at the AmsterdamUMC, Amsterdam, Netherlands.

  Dac EGAC50000000096

• Dataset for WGS head and neck cancer samples

  This dataset contain WGS sequencing data of head and neck cancer samples as well as blood plasma controls. Sequencing was performed on Illumina Novaseq 6000 using KAPA HyperPrep Kit. The sequencing was always paired.

  Dataset EGAD50000000233

• CHIC_TPO3_2023

  Human engineered CRC organoids (APC KO; KRAS G12D; TP53 KO) were grown in glucose, lactate or with DCA. Samples were collected 7 hours after the treatments and processed for bulk CHIC-seq.

  Dataset EGAD50000000090

• RNA-seq FASTQ files studied in A first-in-human clinical study of an allogenic iPSC-derived corneal endothelial cell substitute transplantation for bullous keratopathy

  This data set contains 18 paired fastq files (RNA-seq).

  Dataset EGAD50000000948

• The taxonomic composition of the human microbiome of healthy donors

  Single homogenized human stool samples from five healthy donors and mix were analyzed by shotgun sequencing to generate a baseline for the establishment of humanized microbiome to be transferred into mice.

  Dataset EGAD50000001119

• NICHE - DNA-seq of MMR proficient early stage colon cancers

  The dataset includes 152 FASTQ files from paired-end WXS sequencing on Illumina HiSeq2500 or Novaseq 6000 for 31 pMMR patients. This includes 31 tumor DNA and 31 blood germline samples.

  Dataset EGAD50000001247

• cell-free methylated DNA immunoprecipitation and high-throughput sequencing data for samples from liver transplant recpients with graft pathologies

  Bam and indexed bam files after removal of duplicates and trimming of the unique molecular identifiers. Sequencing was performed on NovaSeq 6000 platform.

  Dataset EGAD50000001727

• Clinical Utility of BRCA Research by Inocras, CMC and SMC (CUBRICS)

  This dataset consists of whole-genome sequences from 1,364 Korean breast cancers, with transcriptome data available for most cases

  Dataset EGAD50000001546

• Genetics and Networks of Congenital Heart Defects

  Exome sequencing of families with Congenital Heart Defects of diverse sub-phenotypes. Comprises both parent-offspring trios for sporadic cases and multiplex families. Collaboration with David Brook, University of Nottingham. Funded by the British Heart Foundation.

  Dataset EGAD00001002251

• Sci Trans Med - Mouliere et al, 2018. Non-ovarian cancer samples - STM4

  fastq files for shallow whole genome sequencing data as described in Mouliere et al, 2018. Files are those not included in STM2 i.e. these are largely non-ovarian cancer samples

  Dataset EGAD00001006132

• Response labels from NABUCCO cohort 1 (NCT03387761)

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes the Response labels used for the analysis of the data. Details about the clinical definitions of Response can be found on the paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006853

• Cell-free DNA TAPS provides multimodal information for early cancer detection

  TAPS data from 21 patients with HCC, 23 patients with PDAC, 30 non-cancer controls, 4 patients with cirrhosis, and 7 patients with pancreatitis.

  Dataset EGAD00001006871

• Reference DNA standards for GCLP pipeline

  The use of reference DNA standards generated from cancer cell lines sequenced in the Cancer Genome Project to establish the sensitivity, specificity, accuracy and reproducibility of the WTSI GCLP sequencing pipeline

  Dataset EGAD00001002015

• sWGS of RCC patients

  Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of renal cell carcinoma (RCC) patients (MonRec Cohort)

  Dataset EGAD00001005804

• Whole genome sequencing generated from metastatic gliosarcoma patient samples

  This dataset contains whole genome sequencing data aligned to the b37 reference genome for 4 spatially and temporally distinct tumors from one patient with a matched normal blood sample.

  Dataset EGAD00001005745

• single cell RNAseq data of lung adenocarcinoma

  Single-cell RNA sequencing was performed for cells from five early-stage LUADs and fourteen multi-region normal lung tissues of defined spatial proximities from the tumors.

  Dataset EGAD00001006936

• Whole exome sequencing datasets for Low-grade Serous Ovarian Carcinoma

  This dataset includes whole exome sequencing reads from 10 normal and 14 cell lines based on Agilent SureSelect XT Human All Exon v6. They are all 2*100bp reads sequenced using Illumina HiSeq4000.

  Dataset EGAD00001006440

• HV31 - PacBio continuous long read (CLR) sequencing

  PacBio continuous long read (CLR) sequencing data for individual HV31 generated on PacBio Sequel II instrument, using DNA from CD14+ monocytes, to a sequencing depth of ~35×. Sequencing was performed at the Wellcome Sanger Institute.

  Dataset EGAD00001007047

• Target pilot trial

  In vitro and in vivo drug screens of tumor cells identify novel therapies for high-risk child cancer

  Dataset EGAD00001008358

• RNA-seq colorectal carcinomas NKI-AvL TGO series Gut2009

  The dataset "RNA-seq colorectal carcinomas NKI-AvL TGO series Gut2009 " includes 2 x 29 fastq files from paired-end mRNA sequencing on Illumina HiSeq2500 for 29 snap-frozen colorectal carcinomas.

  Dataset EGAD00001004059

• WXS dataset of Ewing and Ewing-like-sarcoma tumoroid biobank reveals distinct drug sensitivities: translocation makes the difference

  Creation of living organoid biobank for ewing and ewing-like sarcomas

  Dataset EGAD00001015417

• mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel and secondary fusion transcripts in formalin-fixed paraffin-embedded tissue: a sarcoma showcase

  mRNA capture sequencing data (FASTQ files) of 28 FFPE sarcoma tumors

  Dataset EGAD00001007696

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas

  This dataset contains BAM files for RNA-sequencing of stage I lung adenocarcinomas from Asian patients. In total, there are 107 patients and 107 tumor samples.

  Dataset EGAD00001006187

• Genome-wide prediction of human embryos

  This dataset includes whole genome sequence information for three individuals (Mother, Father and Newborn) used in this study. Genomes were sequenced using Illumina HiSeq technology. Files included are fastq files in paired read format.

  Dataset EGAD00001002257

• Dataset for cancer_of_unknown_primary-WHOLE_GENOME

  Rare cancer sequencing data of 46 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008869

• Small variant calling for 110 Egyptian individuals

  This data set comprises WGS small variants and structural variants called in a cohort of 110 Egyptian individuals (10 individuals have been sequenced as part of this study and 100 are from EGAD00001001372/EGAD00001001380).

  Dataset EGAD00001006039

• RNAseq - Colorectal organoids and tumoroids (2015-08-05)

  Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer. This dataset contains all the data available for this study on 2015-08-05.

  Dataset EGAD00001001459

• Low input LC (WGS) (2019-04-01)

  R&D project to develop low input library construction methods. . This dataset contains all the data available for this study on 2019-04-01.

  Dataset EGAD00001004878

• CBD-RAW-RNASEQ-MINI: Mini-bulk RNAseq data

  SmartSeq2 RNAseq data from 16 samples. For further information regarding this dataset, please contact Julian Knight and Alexander Mentzer at contact@combat.ox.ac.uk.

  Dataset EGAD00001007932

• Dataset for MCPlus_WES

  WES/WGS sequencing data of 75 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009276