7825 results for "canc*"

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• Genetic and immune landscape evolution defines subtypes of MMR deficient colorectal cancer

  Genomic data from a cohort of 19 MMR deficient colorectal cancers and 1 MMR proficient colorectal cancer. All cases were target gene DNA sequenced using multiple primary and where available metastatic tumour regions from surgical resection samples.

  Dataset EGAD00001008334

• Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens

  Enriched tumor epithelium, tumor-associated stroma, and whole tissue were collected by laser microdissection from thin sections across spatially separated levels of ten high-grade serous ovarian carcinomas (HGSOCs) and analyzed by mass spectrometry, reverse phase protein arrays, and RNA sequencing. Unsupervised analyses of protein abundance data revealed independent clustering of an enriched stroma and enriched tumor epithelium, with whole tumor tissue clustering driven by overall tumor “purity.” Comparing these data to previously defined prognostic HGSOC molecular subtypes revealed protein and transcript expression from tumor epithelium correlated with the differentiated subtype, whereas stromal proteins (and transcripts) correlated with the mesenchymal subtype. Protein and transcript abundance in the tumor epithelium and stroma exhibited decreased correlation in samples collected just hundreds of microns apart. These data reveal substantial tumor microenvironment protein heterogeneity that directly bears on prognostic signatures, biomarker discovery, and cancer pathophysiology and underscore the need to enrich cellular subpopulations for expression profiling.

  Dataset EGAD00001008344

• Target pilot trial

  In vitro and in vivo drug screens of tumor cells identify novel therapies for high-risk child cancer

  Dataset EGAD00001008358

• Spatial transcriptome sequence data from prostate cancer needle biopsies

  Spatial transcriptome sequencing data from prostate cancer needle biopsies. Dataset contains biopsies from before and after androgen deprivation therapy of 3 patients with 8 biopsies per patient in total. 2 sections (replicates) are taken from each biopsy.

  Dataset EGAD00001008636

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-5)

  Whole Genome sequencing of colorectal cancer patients (SG-BULK-5)

  Dataset EGAD00001008637

• EPICC: Evolutionary Predictions in Colorectal Cancer WGS-3

  WGS profiling bam files from colorectal carcinoma and adenoma.

  Dataset EGAD00001008642

• Spatial transcriptome sequence data from cross section of cancer containing prostates

  Spatial transcriptome sequence data from two tumour containing prostates. Entire cross section of organ divided into cubes to fit spatial transcriptomics arrays. The dataset contains paired-end sequences from 21 sections of 1k array sections and 9 sections of 10x Visium sections for patient 1 as well as 28 sections of 10x Visium sections for patient 2.

  Dataset EGAD00001008644

• sWGS of dried blood spots (cfDNA/ctDNA)

  This dataset contains paired-end fastq sequencing files (n=212) from shallow WGS of 106 dried blood spot (DBS) samples, containing 91 DBS collected from OV04 ovarian cancer PDX mice, 10 DBS collected from healthy non-tumour bearing NSG mice, and 5 DBS generated from whole blood samples from 4 OV04 ovarian cancer patients.

  Dataset EGAD00001008651

• Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor infiltrating T cells.

  Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying functional and dysfunctional states of human tumor infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify tissue-specific and general gene-regulatory landscapes in the wide breadth of CD8+ TIL functional states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor entity-matching samples and prioritize key elements by super enhancer analysis. Our analysis reveals a human core chromatin trajectory to TIL dysfunction and identifies key enhancers, transcriptional regulators, and deregulated target genes involved in this process. Finally, we validate enhancer regulation at loci encoding PD1, TCF1, and TIM3 by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study advances the understanding of molecular regulation of TIL (dys-)function and provides a framework for modulating immunotherapeutic relevant TIL genes via their enhancers.

  Dataset EGAD00001008662

• Lung cancer and non-cancerous plasma cfDNA samples

  The dataset contains 90 lung cancer and 5 non-cancerous lung lesion plasma cfDNA samples collected in EDTA blood collection tubes. Shallow WGS was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD00001008666