15075 results for "cancer studies using rna-seq"

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• Premalignant SOX2 in ovarian cancer patients

  Whole Genome Sequencing data set for the study "Premalignant SOX2 in ovarian cancer patients"

  Dataset EGAD00001002734

• SNV and indel calls from 8921 individuals in the British Autozygosity Populations BioResource dataset

  This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies: 1. 5236 British Pakistani/British Bangladeshi adults from East London Genes and Health (ELGH) 2. 2624 British South Asian mothers from Born in Bradford (mostly Pakistani) (BiB) 3. 1061 British South Asian adults from Birmingham (mostly Pakistani) (Birm) All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866. In the sample list file, the columns of interest to most people will be: vcf.id - sample ID from the vcf cohort - which cohort they're in sex.assigned - sex inferred from coverage on the X and Y chromosomes. Individuals for whom this did not match their reported sex have been discarded total, chrX and chrY - coverage within bait regions across all chromosomes, chrX and chrY respectively Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true: SNPs: "QD < 2.0 || FS > 30 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" Indels: "QD < 2.0 || FS > 30 || ReadPosRankSum < -20.0"

  Dataset EGAD00001005469

• CALGB 80303:Genome-Wide Association Study of Advanced Pancreatic Cancer Patients - A Randomized Phase III trial of Gemcitabine Plus Bevacizumab versus Gemcitabine Plus Placebo in Patients with Advanced Pancreatic Cancer

  CALGB 80303 was a randomized, phase III study in advanced pancreatic cancer patients treated with Gemcitabine plus either Bevacizumab or placebo. No difference in overall survival (OS) was observed between the two arms. We prospectively collected germline DNA and conducted a genome-wide association study (GWAS).

  Study phs000250

• CAGEKID: Cancer Genomics of the Kidney

  The aim of CAGEKID is to carry out comprehensive detection of DNA markers for conventional (clear cell) renal carcinoma. The project includes complete analysis of somatic and constitutional DNA variation, methylation patterns and expression in a large number of constitutional/tumor pairs. CAGEKID is a part of the International Cancer Genome Consortium, ICGC.

  Study EGAS00001000083

• Identification of drug resistance genes in cancer cell lines by insertional mutagenesis

  Our aim is to identify genes involved in resistance to anti-cancer therapies. In order to do this we have taken advantage of a lentiviral vector (LV)-based insertional mutagen to mutagenize cancer cell lines. LV-transduced cell lines were then treated with anti-cancer therapies and the emergence of resistant clones scored. DNA from pools of resistant clones was collected, subjected to custom capture by baits designed against the LV sequence, and then sequenced to identify the LV-genomic junction. We hope that the identification of recurrently targeted genes in resistant cell population will allow us to identify genes that mediate drug resistance.

  Dataset EGAD00001002207

• AVENIO Expanded ctDNA panel sequence alignments (BAMs) from plasma DNA of BC, CRC and NSCLC patients

  The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.

  Dataset EGAD00001006301

• Transcriptome atlas of brain organoid developent

  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. We used scRNA-seq to profile transcriptome. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000223

• BIOMIROX

  This dataset regroups RNAseq of paired primary colorectal cancers and liver metastases extracted from 113 patients In Paris and Besançon University Hospitals. 216 FASTQ files from single-end 3' PolyA (QuantSeq 3′mRNA-Seq Kit FWD for Illumina (Lexogen)) RNAseq samples were generated On NOVASEQ 6000 (ILLUMINA).

  Dataset EGAD50000000443

• MissionBio single cell DNA and protein seq for 2 samples

  This dataset contains MissionBio Targeted single-cell DNA and Protein sequencing data from a primary sample and a patient-derived xenograft (PDX) model, which is used to investigate the clonal evolution in the FOXF1/FENDRR ALL subtype. All the 2 samples are in bam file type.

  Dataset EGAD50000001793

• Sequencing data

  WES: (7 samples, BAM files), scRNA-Seq (4 samples, BAM files), TruSight (56 samples, BAM or FASTQ files)

  Dataset EGAD00001007749

• KCL PRECSION Mutations targeted-seq

  105 Normal, DCIS and recurrences samples target-sequenced

  Dataset EGAD00001008376

• Mixture of 4

  Mixture of 4 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008724

• Mixture of 3

  Mixture of 3 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008729

• EGAD00010000634

  WTCCC2 People of the British Isles (POBI) samples using Affymetrix 6.0 array

  Dataset EGAD00010000634

• Oncotrack_450K_tumor

  Oncotrack primary tumor samples using 450K. The dataset includes shared AF analysis files oncotrackDNAmAnalysis.R and oncotrackDNAmBetaScores.txt which were applied for both Oncotrack_450K_tumor (EGAD00010001162) and Oncotrack_450K_metastatic (EGAD00010001161) datasets.

  Dataset EGAD00010001162

• Whole Genome Sequencing of tissues

  Whole genome sequencing profiling of 4 primary PDAC tissue samples - WGS unmapped reads, sequenced using NovaSeq 6000, 15x coverage 160 million reads per sample.

  Dataset EGAD50000000279

• AVENIO mutation analysis

  Mutation analysis in cfDNA from plasma and urine (stored under different storage conditions) from CRC patients using the AVENIO Expanded Kit

  Dataset EGAD50000001588

• 10K Project Metagenomic

  This dataset includes metagenomic sequencing of faecal samples from 7,190 Israeli individuals. Single-end sequencing was performed using a NovaSeq sequencing platform (Illumina).

  Dataset EGAD00001010925

• Somatic SNVs and Indels for INSPIRE Tumor WES

  Somatic SNVs and Indels for INSPIRE Tumor WES called using Mutect, Mutect2, Varscan2, Vardict, and Strelka2

  Dataset EGAD00001006569

• HLA Genotypes

  Imputed HLA alleles and variation. Imputation was carried out using the Multi-Ethnic HLA reference panel (version 1.0 2021) available on the Michigan imputation server

  Dataset EGAD00001009965

• Hi-C datasets of primary glioblastoma cultures

  High-resolution (Sub-5 kbp resolution) Hi-C datasets generated using glioblastoma primary cultures from 3 different adult patients.

  Dataset EGAD00001004968

• Amplicon sequencing

  Fastq files from amplicon sequencing in 106 Multiple Sclerosis patients and 105 healthy volunteers in CD4 T cells, CD8 T cells and genomic DNA using PE300 Illumina MiSeq.

  Dataset EGAD00001005774

• An aggregated vcf file

  Germline variants calls were defined using the sequenced reads derived from 230 patients with hepatocellular carcinoma. This dataset is comprised of one aggregated vcf file.

  Dataset EGAD00001009410

• Targeted sequencing of head and neck squamous cell carcinomas

  This dataset includes 112 head and neck tumour samples with matched normal (blood) samples sequenced using a custom hybrid capture panel.

  Dataset EGAD00001004269

• Spatially resolved single-nucleus RNA sequencing of Choroid Plexus Tumours reveals clinically relevant hypoxia- and stress-driven dedifferentiation programs that sculpt an immunosuppressive and pro-angiogenic microenvironment

  Our study leverages single-nucleus RNA sequencing (~124,500 nuclei) and spatial transcriptomics (~40,650 spots) to dissect the molecular architecture of CPTs. We generated a comprehensive transcriptomic atlas of 45 CPT samples spanning all three methylation groups and a reference cohort of 16 non-neoplastic choroid plexus (ChP) samples, spanning foetal, paediatric and adult specimens. Key discoveries from this investigation include that paediatric B tumorus exhibit a dedifferentiated state and enrichment of stress-related metaprograms, including hypoxia, TGFß signaling, Interferon I signaling and early stress response, that correlate with poor clinical outcome and antagonise multiciliogenesis. On a spatial level, these stress-linked programs co-localise with immunosuppressive, pro-angiogenic microenvironment, suggesting a link between developmental arrest, microenvironmental remodelling and aggressive behaviour.

  Study EGAS50000001617

• "Single nucleotide variant detection in multiple foci of three prostate cancer tumors"

  "Single nucleotide variant detection in multiple foci of three prostate cancer tumors"

  Dataset EGAD00001000035

• "Copy number variant detection in multiple foci of three prostate cancer tumors"

  "Copy number variant detection in multiple foci of three prostate cancer tumors"

  Dataset EGAD00001000036

• Whole_genome_sequencing_of_rhabdomyosarcoma_tumouroids

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008270

• Whole_Genome_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008274

• WGS data of serially passaged TIC-enriched spheres of colorectal cancer

  WGS data of serially passaged TIC-enriched spheres of colorectal cancer

  Dataset EGAD00001006265

• Single cell sequencing of ovarian cancer

  Single cell sequencing of 12 ovarian cancer biopsies from 7 patients.

  Dataset EGAD00001006898

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established three kinds of esophageal tumoroids derived from esophageal cancer patient. We performed whole exome sequencing to analyze genetic background of the tumoroids.

  Study JGAS000749