15169 results for "cancer studies using rna-seq"

in 21.64 milliseconds.

• Targeted DNA sequencing of TTFields-treated glioblastoma, IDH wildtype

  This dataset contains raw paired-end FASTQ files from targeted DNA sequencing using the TruSight Oncology 500 panel in patients with glioblastoma, IDH wildtype, treated with surgery, standard chemoradiotherapy and Tumor Treating Fields at Charité – Universitätsmedizin Berlin. Tumour samples were collected at first surgery and are linked to pseudonymised clinical and molecular annotations described in the associated EGA study.

  Dataset EGAD50000002117

• Single-cell whole-genome sequencing dataset of sorted CD3+, CD33+, and CD34+ cells from aplastic anemia

  This dataset contains raw single-cell whole-genome sequencing data generated from a single patient with aplastic anemia using the BioSkryb platform. Single cells were isolated based on surface marker expression (CD3+, CD33+, and CD34+) and subjected to whole-genome amplification followed by sequencing on an Illumina platform.

  Dataset EGAD50000002195

• Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing

  This dataset includes raw nanopore, base-called, and 6mA frequency data for EcoGII-treated NA12878 and MCF7 chromatin samples. It also includes raw nanopore data for the HG002 EcoGII-treated DNA.

  Study EGAS00001007852

• 666PG Whole genome alignment

  Aligned whole genome sequences in this dataset are from CPCG-GENE Normal/Tumor pairs used in the 666PG study. Raw sequences data was aligned against the human reference (GRCh37 + decoy) using bwa-mem and GATK for indel-realignment and recalibration

  Dataset EGAD00001004957

• Targeted sequencing of Burkitt lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  Targeted sequencing was applied to an unselected population-based Burkitt lymphoma cohort (n=39) diagnosed in the UK's Haematological Malignancy Research Network catchment population of ~4 million (14 centres). DNA extracted from tumour samples was sequenced with a 293-gene panel using the Illumina HiSeq 2500. All data are provided in the CRAM format.

  Dataset EGAD00001007658

• WES of oral-mucosa-derived organoids

  Tumor and matching normal tissues were collected from 8 patients and organoids were derived from each tissue. Whole exome libraries were prepared for tumor tissue, normal tissue, tumor organoids and normal organoids, and paired-end sequencing was performed using Illumina Novaseq 6000 system. Only tumor and matching normal tissues were sequenced for the patients without available organoids.

  Dataset EGAD00001005063

• FFPE WGS for optimizing mutation signature extraction from archival HGSC samples

  HGSC cases were selected for which matched fresh frozen and FFPE samples were available from the same tissue specimens. Fresh frozen, FFPE and normal blood were subject to WGS for the purpose of assessing the possibility of using FFPE WGS in place of fresh frozen for somatic mutation calling.

  Dataset EGAD00001011331

• Whole-exome/genome sequencing of childhood acute leukemia in Iraq

  This dataset contains 26 whole-genome sequencing (13 paired tumor and normal), 106 whole-exome sequencing (53 paired tumor and normal), and 43 targeted sequencing data. Sequencing was performed using an Illumina platform. The data are BAM files aligned to the hg19 reference genome.

  Dataset EGAD00001007873

• Single-nucleus Isoforms of Down Syndrome Brains (long-read)

  16 DS and Control brains samples were prepared using the 10X Genomics Single Cell 3' v3 kit. Pre-fragmented cDNA libraries were loaded onto a Pacific Biosciences Sequel II to sequence single-nucleus isoforms.

  Dataset EGAD00001008286

• HiC (chromosomal conformation capture) data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains chromosomal conformation capture data from fourteen samples (eleven tumor samples and three tumor derived cell lines). Libraries were prepared using the Illumina TruSeq LT sequencing adaptors. Sequencing was performed on the HiSeq X or NovaSeq platforms resulting in 28 FASTQ files.

  Dataset EGAD00001008801

• scATAC sequencing of FACS sorted CD4+ T and CD25+ T from isolated tissues

  T cells were isolated from human blood and tissues: skin and fat. Subsequently, CD4+ T cells and CD25+ T cells were FACS sorted. scATAC libraries were prepared using the 10x Genomics Kit (CG000168_ChromiumSingleCell_ATAC_ReagentKits_UserGuide_RevD.pdf) and sequenced on an Illumina NextSeq550. In total 15 samples were prepared

  Dataset EGAD00001006779

• Single-cell whole-genome sequencing of matched primary GBM tumours and patient-derived organoids

  Single-cell whole-genome sequencing of primary GBM tumours and matched patient-derived organoids. Obtained using the 10X Genomics single-cell CNV solution. Samples from two spatially distinct regions of five tumours from three patients (three primary, two recurrent).

  Dataset EGAD00001007937

• Neoplastic pancreatic cysts and associated cancers

  Data from a study of 148 samples from IPMNs, MCNs, and small associated invasive carcinomas from 18 patients using whole exome or targeted sequencing. Sequencing data from 77 samples out of the 148 samples in the complete study are available in this dataset, based on the permissions given by the participating patients and the informed consents.

  Dataset EGAD00001006229

• ICR Exome Optimization series

  Exome sequencing of 142 samples with corresponding Sanger sequencing results for 416 variants and 288 negative sites. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.

  Dataset EGAD00001001462

• Validation of AML Mutational Screening

  We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose.

  Dataset EGAD00001000445

• RNAseq profiling of pediatric osteosarcoma

  Primary pediatric osteosarcoma samples were collected and profiled using RNAseq. When possible, germline and tumor samples were collected. For some patients, multiple tumor tissues were collected and sequenced. Some of the samples were used to derive PDTX models, which were also profiled with RNAseq. Paired end sequencing was performed on Illumina HiSeq instruments and FASTQ files reported.

  Dataset EGAD00001004538

• ICR1000 UK exome series

  Exome sequencing of 1000 samples from the UK 1958 Birth Cohort. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.

  Dataset EGAD00001001021

• SPATC1L variants associated with age-related and hereditary hearing loss.

  The dataset contains three BAM files that include SPATC1L variants identified in Italian patients affected by hearing loss (both hereditary and age-related hearing loss). Data have been produced by whole exome sequencing and targeted re-sequencing, using Ion Proton and Ion Torrent PGM platforms respectively.

  Dataset EGAD00001004147

• WES of probands in KLB project

  These are the vcf files of exome sequencing of the two probands who were found to harbor mutations in KLB. Sample: EGAN00001564799 is the proband 1; Sample: EGAN00001564800 is the proband 11 in the KLB paper. Exome capture was performed using the SureSelect All Exon capture (Agilent Technologies, Santa Clara, CA USA) and sequenced on the HiSeq2500 (Illumina, San Diego CA USA).

  Dataset EGAD00001003463

• DNA Dataset

  The DNA dataset includes 5 samples sequenced using the Oncomine Comprehensive Assay (OCA) panel. Libraries were prepared following the manufacturer’s protocol and sequenced on the Ion Torrent S5 System. The dataset contains FASTQ files and includes information on single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variations (CNVs). (non so se hanno sequenziato su ION Torrent)

  Dataset EGAD50000002501

• A National Translational Science Network of Precision-Based Immunotherapy for Primary Liver Cancer (PLC)

  The primary objective of the NCI-CLARITY study is to establish a biospecimen repository for genomic, genetic and epigenetic analysis to study the biology of primary liver cancer (PLC) development and progression. Secondary objectives include predicting overall and progression-free survival following immunotherapy. In the retrospective phase, anonymous archival tissue from PLC patients was obtained from five participating sites. Whole exome and transcriptome sequencing was generated and used to predict overall survival in response to immunotherapy.

  Study phs003074

• EOSC4Cancer Longitudinal Synthetic Colorectal Cancer Genomic data developed at BSC

  The synthetic genomes have been created trying to mimic real cancer data of 4 patients (Named 185,186,187 and 188). Mutations are based on real CRC patients from the PCAWG dataset. For each patient, two tumor samples at different time points and one healthy sample have been simulated. The cancer intra-tumor heterogeneity and evolution in the patients is depicted by simulating reads from tumor subclones separately and then mixing them according to their clonal proportions in each sample. For rapid use and transfer only selected chromosomes have been generated for each patient. Chromosomes per patient: -185: chr4, chr5, chr7, chr17 -186: chr1, chr7, chr12, chr17 -187: chr1, chr2, chr5, chr12, chr17 -188: chr2, chr5, chr12, chr13, chr17 Worflows used to create BAM/BAI, VCF and MAF files from FASTQ (Alignment with GRCh38): - https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e - https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e

  Dataset EGAD50000000276

• Genetic differences between primary colorectal cancer and its paired synchronous and metachronous metastases

  In this study we present for the first time the genetic differences associated with different chronicity of colorectal cancer liver metastases identified by whole-exome sequencing of 210 CRC samples. We focus on differences in primary tumors as we hypothesize that these are the cause of the differences in the time course of the disease. The results suggest that distinct tumor progression pathways account for different chronicity outcomes with ultimate impact on patient’s prognosis

  Study EGAS50000000996

• WES sequencing of metastatic colorectal cancer patient-derived xenografts with known response to irinotecan.

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we expand a pre-existing collection (https://doi.org/10.1158/2159-8290.CD-24-0556) of molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. We complemented previous mutational profiles with whole exome sequencing for 46 xenografts with known response to irinotecan.

  Study EGAS50000001484

• Spatial Profiling of Patient-Matched HER2 Positive Gastric Cancer Reveals Resistance Mechanisms to Trastuzumab and Trastuzumab Deruxtecan Sequencing

  HER2-positive gastric cancer (HER2+ GC) exhibits significant intra-tumoral heterogeneity and frequent development of resistance to HER2-targeted therapies. This study aimed to characterize the spatial tumor microenvironment (TME) and identify mechanisms of resistance to HER2 blockade including trastuzumab and trastuzumab deruxtecan (T-DXd) in HER2+ GC, with the goal of informing novel therapeutic strategies. We performed spatial transcriptomics on pre- and post-treatment samples from patients with HER2+ metastatic GC who received trastuzumab-based therapy.

  Study EGAS50000000636