15167 results for "cancer studies using rna-seq"

in 20.17 milliseconds.

• Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

  This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

  Dataset EGAD50000002408

• RNAseq and ATACseq data

  RNAseq and ATACseq data for the FMF patients and healthy control. The RNAseq data was sequenced on a BGI MGI G400 machine, with PE100 reads. ATAC-seq libraries were prepared with Illumina Nextera primers and sequenced on NovaSeq 6000 platform with 50bp paired-end sequencing, where each sample was sequenced to approximate 60 million reads.

  Dataset EGAD00001010304

• Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls

  We created three technical replicates of cell-free DNA from AML patient plasma to assess batch effects and utility of spike-in controls for the cfMeDIP-seq method. Each set of samples were given to three different technicians with slightly different protocols. Details can be found in Wilson et al. "Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls".

  Dataset EGAD00001006986

• WGS of cell line MMML-seq / MALY-DE tumor_4167452

  This dataset contains the aligned whole genome sequencing data of cell line 380. This cell was established from the peripheral blood of a 15-year-old boy with acute lymphoblastic leukemia at relapse, showing an immature phenotype and carrying an IGH-MYC (t(8;14)) as well as an IGH-BCL2 (t(14;18)) chromosomal translocation. The sequencing was performed on an Illumina X-ten sequencer.

  Dataset EGAD00001004090

• Indonesian Methylation dataset

  Illumina Infinium MethylationEPIC BeadChip kit (Illumina, Inc., San Diego, CA). Standard Illumina procedures using Illumina iScan scanner.

  Dataset EGAD00010001711

• Whole exome sequencing of two BPDCN patients for tracing clonal evolution

  Whole exome sequencing data was mapped to GRCh38 using bwa-mem2 as implemented in the nfcore sarek workflow.

  Dataset EGAD50000000309

• H3Africa ACEGID Omni 2.5M and 5M Genotype

  SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina Omni 2.5M and 5M

  Dataset EGAD00010002509

• H3Africa EPIGEN EWAS

  Data from 59 whole blood samples from pregnant mothers, unexposed and exposed to the Rwandan genocide, was generated using Infinium MethylationEPIC BeadChip Kit.

  Dataset EGAD00010002383

• Tissue Site

  Tissue site for RNAsequencing data. Tissue site is associated with the clinical biomarker data and be linked to the biomarker data using the SAMPLE and PAT identifiers.

  Dataset EGAD50000000931

• H3Africa ACEGID Array Phenotype

  Phenotype data for Lassa Fever cases and population controls from Nigeria and Sierra Leone associated with genotype data generated using Illumina H3Africa array version 1.

  Dataset EGAD00001010923

• Dataset of Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  This dataset contains genomic profiles of 7 PPM1D-mutated patients across the spectrum of myeloid disorders using single-cell analyses (Tapestri technology) on diagnostic and longitudinal samples.

  Dataset EGAD50000001229

• Tumor Whole-exome sequencing

  20 tumor tissue WES data with paired cfDNA sWGS data. This data is used for concordance analysis between cfDNA-based and tissue-based CNA. The WES libraries were sequenced across 3 independent runs using multiple lanes.

  Dataset EGAD50000001864

• Repertoire sequencies from three different protocols

  This dataset contains sequencing data from Bulk RNAseq, PCR-based RepSeq and SMRT sequencing to compare immunoglobulin repertoire profiling strategies using matched human B-cell samples

  Dataset EGAD50000002217

• HV31 - MGI single-tube long fragment read (stLFR) linked-read sequencing

  MGI single-tube long fragment read (stLFR) linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~51×.

  Dataset EGAD00001007045

• Whole Genome Sequencing of Normal Singaporean Volunteers

  Whole-genome sequencing (WGS) data for 546 Singaporean volunteers used to estimate WGS-LTL in the study. Samples were sequenced using Illumina Hiseq X to a mean coverage of 30X.

  Dataset EGAD00001005480

• Trio Sequencing results for the AnkyrinG MIPS screening study

  Approximately 1000 trio's with varying degrees of cognitive disorders. All samples have been sequenced for the AnkyrinG interactome using MIPS technology. Data is presented as BAM and unfiltered VCF files.

  Dataset EGAD00001006823

• Nanopore medulloblastoma data

  Nanopore data from 3 medulloblastoma samples of which 2 are tumor-normal pairs sequenced with the MinIon and one is tumor only data sequenced on the PromethIon. The data consists of BAM files aligned using minimap2

  Dataset EGAD00001010851

• 10xscRNA sequencing of 2 samples RRMM (multiple myeloma)

  Paired scRNA sequencing using 10xgenomics library preparation and Illumina HiSeq4000 for sequencing of 2 samples RRMM (relapsed refractory multiple myeloma)

  Dataset EGAD00001009681

• Targeted sequencing of healthy bone marrow without antibodies

  Targeted sequencing using BD Rhapsody with 462 mRNA of healthy young adult bone marrow mononuclear cells from iliac crest aspirations (BM3/Young3).

  Dataset EGAD00001008184

• ARIC

  Bam files are from matched normal + "very early" plasma (diagnostic) samples, sequenced on Illumina NovaSeq 6000 instrument. After bwa alignment, duplicates were removed by picard markduplicate, and base quality scores recalibrated using gatk baserecalibrator + apply bqsr.

  Dataset EGAD00001015603

• Whole-genome sequencing (Illumina HiSeq X-Ten) of tumor-stage mycosis fungoides

  This dataset contains whole-genome sequencing data of tumors from 9 patients with mycosis fungoides. The data was generated using the Illumina HiSeq X-Ten platform.

  Dataset EGAD00001003982

• METABRIC miRNA landscape

  MicroRNAs (miRNAs) are key players in cancer pathogenesis1. They display differential expression across breast cancer subtypes, and play oncogenic and tumor-suppressive roles2-6. A systematic study of the global miRNA landscape in breast cancer and the factors shaping it has not been undertaken. Here we report the results of profiling miRNA expression in 1,302 breast tumors with detailed clinical annotation and long-term follow-up, and for which matching genomic and mRNA expression data were available7. This provides a comprehensive view of the quantity, distribution and variation of the miRNA population and dissects how much genomic, transcriptional and post-transcriptional events contribute to miRNA expression architecture. The key clinical parameters and cellular pathways related to the miRNA landscape are identified, exemplified by context-dependent interaction with cell adhesion and Wnt signaling. Strikingly, in breast cancer miRNAs appear to act as modulators of mRNA-mRNA interactions rather than molecular switches. We demonstrate an important modulatory role for miRNAs in the biology of breast tumors devoid of somatic copy number aberrations, a common subtype where immune response is prominent. Remarkably, prognostic miRNA signatures derived in this subtype are consistently prognostic across several other subtypes and validate in external cohorts. These findings represent a new framework to study the biology of miRNA in human cancer.

  Study EGAS00000000122

• Copy number profiling of putative cancer stem from pleural effusion aspirates from breast cancer patients

  A common symptom during late stage breast cancer disease is pleural effusion, which is related to poor prognosis. In pleural effusions malignant cells can be detected, which indicates a metastatic spread from the primary tumor site. Beside the usefulness for investigation of the metastatic process, it has been a source to isolate cells with putative cancer stem cell (CSC) properties. For this study, pleural effusion aspirate from 25 metastatic breast cancer patients were processed to establish in vitro culture. Patient-derived aspirates were cultured under sphere forming conditions and isolated primary cultures were sorted for cancer stem cell populations ALDH1+ and CD44+CD24-/low and sphere forming efficiency of CSC and non-CSC subpopulation was determined. Unsorted cells had a higher potential to form spheres compared to CSC subpopulations. Subsequently, DNA was isolated from pleural effusions before and after cell sorting, to compare their copy number profiles generated by low-coverage whole genome sequencing to DNA from FFPE primary tumors or bone metastasis. Unbalanced profiles could be detected in four pleural samples before sorting, in two ALDH1+ sorted samples, in one CD44+CD24-/low and in all control samples. Additionally, spheroid culture from one pleural sample could be passaged on and was characterized. Therefore, pleural effusions are an appropriate media for enrichment of putative CSC. However, low-coverage sequencing is difficult due to low quantities of abnormal cells compared to normal cells.

  Study EGAS00001002343

• Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

  Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

  Dataset EGAD00001000284

• Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

  Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

  Dataset EGAD00001000290