15167 results for "cancer studies using rna-seq"

in 13.63 milliseconds.

• Identification of mutations and structural rearrangements in plasma DNA form metastatic prostate cancer patients

  In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit.

  Study EGAS00001000453

• RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

  Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect.

  Study EGAS50000000667

• BAM files ChIP-Seq

  Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015

  Dataset EGAD00001001669

• Prostate cancer datasets WGS

  Low pass WGS: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (Next Seq )

  Dataset EGAD00001004466

• Characterizing Advanced Breast Cancer Heterogeneity and Treatment Resistance through Serial Biopsies and Comprehensive Analytics

  This dataset accompanies the manuscript "Characterizing Advanced Breast Cancer Heterogeneity and Treatment Resistance Through Serial Biopsies and Comprehensive Analytics". In this study we discuss the clinical implications and consequences of molecular heterogeneity in a metastatic breast cancer patient identified through serial biopsies, multi-omic analysis, and longitudinal patient monitoring, performed through the precision oncology program, Serial Measurements of Molecular and Architectural Responses to Therapy (SMMART). This case study describes a metastatic breast cancer patient with a highly heterogenous tumor that began as ER positive/HER2 negative on diagnosis, then was found to be ER negative/HER2 positive in a metastatic liver lesion (Study biopsy #1), and finally triple negative (TNBC) in another metastatic liver biopsy (Study biopsy #2). Multi-omic assays included clinical genomic panel sequencing, clinical immunohistochemistry, a clinical protein profiling assay (Intracellular Signaling Protein Profiling), RNA sequencing, and RPPA. Here we provide the expression data from RNAseq and RPPA data on Study biopsy #2 for the patient discussed in this case report. Note: The first liver biopsy did not yield sufficient material for RNAseq or RPPA.Raw RNA FASTQ files from Study biopsy #2 of the liver Gene expression (RNAseq) files from Study biopsy #2Protein expression (RPPA) files (level 2, 3, 4) for Study biopsy #2

  Study phs002321

• Single cell RNA sequencing data of advanced melanoma patients treated with checkpoint inhibitor immunotherapy

  Single cell RNA libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3’ v2 reagents. The samples were barcoded and each library were pooled with two samples at equimolar concentrations. The pooled libraries (n=4) were sequenced on the NextSeq 500 machine (Illumina) with paired-end sequencing and dual indexing as recommended in the manufacturer’s protocol; 26 and 98 cycles for the respective Read 1 and 2, and 8 cycles for i7 index.

  Dataset EGAD50000000493

• WES profiles from the CheckMate-142 clinical trial.

  The dataset contains WES profiles of 59 patients from the CheckMate-142 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. Baseline tumor tissue and matched whole -blood samples were processed using the Agilent SureSelect Human All Exon V5 in-solution hybrid capture panel and underwent subsequent next-generation sequencing (NGS) on the Illumina NovaSeq platform. Fastq files are included.

  Dataset EGAD50000000610

• RNA-sequencing from ALL patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study.

  Dataset contains RNA-sequencing data (fastq files) from 45 patients treated on the the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study, an MRD-stratified Paediatric Protocol. Patient samples (bone marrow or peripheral blood) were taken at diagnosis. mRNA was extracted from blast cells and underwent paired-end sequencing (75bp) using the illumina NextSeq platform. Genomic data was used for identification of genomic drivers of acute lymphoblastic leukaemia (ALL).

  Dataset EGAD50000001111

• cryopreserved PBMC

  This dataset consists of 12 RNA samples derived from peripheral blood mononuclear cells (PBMCs) collected from three healthy donors. The samples cover four experimental conditions: fresh PBMCs (ID: 517210–517212), PBMCs subjected to a single freeze–thaw cycle (ID: 517213–517215), PBMCs refrozen in freezing mix (ID: 517216–517218), and PBMCs refrozen in TRIzol (ID: 517219–517221). Each sample is provided as a FASTQ file, and RNA sequencing was performed using the Illumina platform. This dataset enables the assessment of cryopreservation effects on PBMC transcriptomic profiles.

  Dataset EGAD50000001703

• RNAseq in pleural mesothelioma primary cell lines

  Pleural mesothelioma (PM) requires new treatments. Drug repurposing offers a potential approach to finding effective therapies. This study aimed to explore new therapeutic options for PM using RNA sequencing. RNA sequencing was performed on 58 patient-derived PM cell lines. Drug screening of over 1300 compounds was conducted on 11 lines, with further testing of selected drugs on 48 lines. Top candidates were validated in 3D culture and mouse models.

  Dataset EGAD00001015408