3659 results for "RNA AND sequencing OR transcriptome"

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• Integrated Exome and RNA Sequencing of Dedifferentiated Liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000177

• Multi-omics profiling of PSCCE

  We performed whole-exome sequencing, RNA sequencing and immunohistochemistry profiling of primary small cell carcinomas of the esophagus.

  Study EGAS00001004889

• FBSeq: RNA sequencing of human fetal brain.

  RNA sequencing of 120 human fetal brains (aged 12-19 post-conception weeks) was performed as part of a Medical Research Council (U.K.) funded project (MR/L010674/2) to investigate genetic effects on gene expression in the developing human brain and their role in neuropsychiatric disorders. Human fetal brain tissue from elective terminations of pregnancy was provided by the Human Developmental Biology Resource (HDBR) (http://www.hdbr.org), with ethical approval (#08/H0712/34), and with consent for use of fetal material for medical research provided by female donors. Total RNA was extracted from half of the available brain tissue from each fetus using Tri-Reagent and treated with TURBO DNase. RNA-Seq libraries were prepared using 1µg of purified total RNA and the Illumina TruSeq Stranded Total RNA Library Prep kit, following ribosomal RNA depletion. Libraries were sequenced on the Illumina HiSeq 2500 or HiSeq 4000 systems, generating at least 50 million read pairs per sample.

  Study EGAS00001003214

• raw RNA-seq data from patients infected with COVID-19 or influenza

  Dataset consists of fastq files from bulk RNA-seq done on peripheral blood acquired from two well characterised hospitalised cohorts, a cohort of patients infected with influenza and a cohort of patients infected with SARS-CoV-2 during the first wave of the pandemic and prior to availability of COVID-19 treatments and vaccines.

  Dataset EGAD00001008505

• Long-read and short-read isoform sequencing in breast cancer

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Study EGAS00001004819

• Kidney_tumour_RNA

  This is a bulk DNA and RNA sequencing study of human renal tumours

  Study EGAS00001002487

• Genomic Analysis of Diffuse Large B Cell Lymphoma

  Tumors from 383 newly diagnosed diffuse large B cell lymphoma were included in this study. Tumor DNA was extracted from formalin-fixed, paraffin embedded (FFPE) tissue sections, germline DNA was extracted from blood, and whole exome sequencing (WES) of all samples (n=340 tumor normal pairs) was performed using the Agilent SureSelect XT AllExon v5 + UTR kit and sequencing was carried out on an Illumina NovaSeq, 100 x 2 paired end reads. Tumor RNA (n=321) was extracted from formalin-fixed, paraffin embedded (FFPE) tissue sections and RNA sequencing was performed using the Illumina TruSeq RNA Exome Kit (Illumina) for library preparation, sequencing platform HiSeq 4000, 100 x 2 paired end reads.

  Study phs003634

• RNA sequencing of high hyperdiploid and ETV6/RUNX1-positive pediatric acute lymphoblastic leukemia

  We performed RNA-sequencing of high hyperdiploid and ETV6/RUNX1-positive ALL cases by using the Human Ribo-Zero rRNA Removal Kit to investigate the gene expression in high hyperdiploid ALL.

  Study EGAS00001003079

• Immune Determinants of Resistance to PD-1 Blockade in Renal Cell Carcinoma

  We performed an integrated bulk and single-cell transcriptomic analysis of tumors from 102 advanced renal cell carcinoma patients enrolled in a phase II clinical trial of frontline nivolumab (NCT03117309) to investigate determinants of response to anti-PD1 monotherapy. The present study includes 112 archival or pre-treatment tumors of clear cell and non-clear cell histologies from 90 patients that underwent bulk RNA sequencing (RNA-seq). For 76 patients, 74 of whom had matched RNA-seq, whole exome sequencing (WES) was also performed on tumor samples as well as matched peripheral blood. Additionally, 19 fresh tumor samples from 17 patients, including pre and post-treatment samples and mixed histologies, were locally cryopreserved and centrally processed for single cell RNA (scRNA-seq) and TCR (scTCR-seq) sequencing. 7 patients had matched scRNA/scTCRseq, RNAseq, and WES.

  Study phs003618

• Control samples, breast cancer clinical samples and matched patient-derived tumour xenografts (PDTXs) to develop and test a computational approach to discriminate human and mouse sequences in PDTXs

  Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. In this study we generated Whole Exome Sequencing (WES) and RNA sequencing (RNA-seq) data from samples with known mixtures of mouse and human DNA or RNA.

  Study EGAS00001002445