14977 results for "cancer studies using rna-seq"

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• Genomics-based characterization and personalized treatment in pleural and peritoneal mesothelioma

  Study EGAS00001007294

• Low_Coverage_Sequencing_of_rare_human_histiocytic_tumour

  Sequencing of rare human histiocytic tumour

  Study EGAS00001000768

• Sequencing_of_rare_human_histiocytic_tumour

  Sequencing of rare human histiocytic tumour

  Study EGAS00001000591

• Primary_angiosarcoma_Whole_Genome_Sequencing

  Whole genome sequencing of primary angiosarcoma

  Study EGAS00001000851

• Genome-wide DNA Copy Number Analysis of high hyperdiploid acute lymphoblastic leukemia

  Study EGAS00001007049

• Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer

  Study EGAS00001005061

• Epigenomic timecourse of brain organoid development

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. At each time point used scCut&Tag to profile histone modifications (H3K27me3, H3K27ac, H3K4me3) as well as multiome-seq (10X) to jointly profile transcriptome and chromatin accessibility from the same cell suspension. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000222

• Bulk 3' mRNA-Seq of dome and suspension tubuloids

  Bulk 3' mRNA-sequencing of human kidney tubuloids grown in dome and suspension culture for the identification of transcriptional differences associated with culture method, passage, and donor. Tubuloids were generated from 4 separate donors and collected for sequencing at day 7 of passage 3, 4, and 5 in dome and suspension culture.

  Study EGAS50000001629

• bulk TCR-seq data IMCISION

  We performed bulk TCR sequencing (Adaptive Biotechnologies, Seattle, WA) on peripheral blood monocytic cells (PBMCs) from 9 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021) that responded to anti-PD-1 and anti-CTLA4 combination immunotherapy. DNA was extracted from PBMCs that were isolated from pre-treatment and on-treatment blood.

  Study EGAS00001007367

• LCM-ATACseq on human lung macrophages

  In this study we employed Laser Capture Microdissection (LCM) for the multimodal profiling of lung macrophages cell populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (~100 cells) were collected from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation), and processed for ATAC-seq.

  Dataset EGAD00001008693

• DNA methylation-based classification of sinonasal tumors [Proteomics data]

  This dataset includes raw label-free mass spectrometry proteomics data of different sinonasal tumor entities as well as normal sinonasal tissue. 72 samples were processed on a Q Exactive HF-X instrument coupled to an easy nanoLC 1200 system using one microgram of peptides and an 110 minutes gradient.

  Dataset EGAD00010002381

• Korean WGS

  We sequenced the genomes of 141 Korean never-smoker lung adenocarcinoma patients, excluding EGFR and ALK alterations. We utilized the TruSeq DNA Library Prep Kit and performed by the Illumina NovaSeq 6000 instrument, yielding sequencing paired reads of approximately 150 bp in size. Afterward, we processed the FASTQ files using the GATK Best Practice pipeline.

  Dataset EGAD50000000346

• Exome sequencing data, phenotypic information, and somatic mutation analysis results for 44 diagnosis-relapse DLBCL pairs

  This dataset contains exome sequencing data, phenotypic information, and somatic mutation analysis results for 44 diagnosis-relapse DLBCL pairs. Exon sequencing data were captured using the Agilent HaloPlex exon kit. bam files were obtained from illumina sequencing followed by BWA alignment.

  Dataset EGAD50000000049

• Moroccan Genome Project: Sequencing Data from 109 Whole Genomes of Moroccan Individuals

  This study is the first phase of the Moroccan Genome Project, which included the complete sequencing of 109 genomes from the Kingdom of Morocco. The sequencing was performing using the Illumina NovaSeq6000 platform, with a mean coverage of 30X.

  Dataset EGAD50000000750

• Cas9-targeted-based long-read sequencing for genetic screening of RPE65 locus

  The dataset includes sequencing data from five inherited retinal dystrophies (IRD) patients using three diferent platforms: Clinical Exome (CES), Long-read sequencing of RPE65 locus, and 3) whole genome sequencing.

  Dataset EGAD50000000847

• APS-1 TCR Sequencing

  Single cell TCR sequencing of expanded regulatory T cells (Tregs) in 9 APS-1 patients and 9 ange and gender matched controls. T-cell receptor (TCR) libraries were generated using the Single Cell Human TCR Amplification Kit and the Library Construction Kit from 10x genomics.

  Dataset EGAD50000000261

• HIV-phyloTSI: PANGEA (veSEQ-HIV)

  This dataset includes sample numbers TSI_0001 to TSI_0202 and TSI_0316 to TSI_0425 for the PANGEA (veSEQ-HIV) cohort of the study. Samples were sequenced using the Illumina NovaSeq system and the veSEQ-HIV method (see Bonsall, Golubchik et al 2020, DOI: 10.1128/JCM.00382-20). Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001309

• HIV-phyloTSI: PANGEA (PCR amplicon)

  This dataset includes sample numbers TSI_0426 to TSI_0527 for the PANGEA (PCR amplicon) cohort of the study. Samples were generated by pooling four overlapping PCR amplicons (see Gall et al 2012, DOI: 10.1128/JCM.01516-12). The sequencing was conducted using the Illumina NovaSeq system. Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001308

• Dataset for single cell transcriptome sequencing

  This datasets contains single cell transcriptome sequencing of 10 control samples. Sequencing has been performed on Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single Cell 5 Reagent Kits. Sequencing was always paired. This dataset additionally contains a .QS file from Seurat Analysis performed in R, generated as described in the related publication.

  Dataset EGAD50000001549

• Paired FastQ files from deep targeted DNA sequencing

  This dataset comprises paired-end and time-matched FastQ files from 356 cell-free DNA samples and 356 white blood cell DNA samples, derived from 299 patients with metastatic renal cell carcinoma or urothelial carcinoma. A baseline sample was available for all patients. Sequencing was performed using Illumina technology.

  Dataset EGAD50000001267

• Variant calling dataset from the whole-exome study of sepsis and acute distress respiratory syndrome in Spain

  Whole-exome sequence reads were obtained from a set of 934 unrelated individuals from the study of sepsis and acute distress respiratory syndrome in Spain (GEN-SEP study), using Illumina paired-end reads.

  Dataset EGAD50000001613

• PacBio Revio WGS on 10 carriers of ring and marker chromosomes

  Bam files containing PacBio HiFi reads from carriers of ring and marker chromosomes. The reads where genereated using the PacBio Revio platform. Each individual was sequenced to roughly 30X coverage on one flow cell per individual. The chromosome of interest is indicated in the file name.

  Dataset EGAD50000002111

• WGS of thymic epithelial tumors and paired normal

  Among the 20 newly sequenced cases, we conducted additional whole-genome sequencing (WGS) on five out of eight CN-type thymomas, excluding three with low tumor cell fractions (< 0.1). Libraries for WGS were prepared using the TrueSeq DNA PCR-free Prep Kit following standard Illumina protocols.

  Dataset EGAD50000001160

• Whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients

  This dataset contains whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients. Whole exome sequencing with a minimum coverage of 100x was performed using the Illumina Novaseq6000 platform and the Agilent SureSelect Human All Exon V7 kit.

  Dataset EGAD50000002264

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• Whole genome sequencing of GM09237 cells with and without folate depletion

  Two DNA samples extracted from GM09237 cell line cultured with either normal medium or medium with no folic acid for 5 days were sequenced using the BGISEQ500 platform (BGI whole genome 100 bp paired-end sequencing 60x) as well as PacBio Sequel long read sequencing.

  Dataset EGAD00001007732

• Exome sequencing of control DNA samples from patients with BPLL

  DNA extracted from sorted CD3+ cells (16 patients) was used for exome capture with the SureSelect V5 Mb All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments.The files are in FASTQ format.

  Dataset EGAD00001004411

• Pleomorphic invasive lobular carcinoma targeted exome sequencing

  Fifteen pleomorphic invasive lobular carcionoma samples and their matched normal controls were subjected to targeted exome sequencing using the Beijing Genomics Institute TumorCare gene panel. Genomic DNA samples were randomly fragmented and captured libraries of each exome were sequenced on an Illumina Hiseq2000 system. CRAM files are provided for each tumor and normal pair.

  Dataset EGAD00001003995

• Exome sequencing of tumor DNA samples from patients with BPLL

  DNA extracted from sorted CD19+ tumor cells (16 patients) was used for exome capture with the SureSelect V5 All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments. The files are in FASTQ format.

  Dataset EGAD00001004410

• WGS profiling of pediatric osteosarcoma

  Primary pediatric osteosarcoma samples were collected and profiled using WGS. 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 WGS. Paired end sequencing was performed on Illumina HiSeq instruments and FASTQ files reported.

  Dataset EGAD00001004537