7793 results for "canc*"

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• ERa ChIP-seq in breast healthy, primary cancer and metastatic tissues

  ChIP-seq has been perfomed on fresh-frozen tissue derived from healthy breast (HB), primary breast cancer (PB), BCa-derived liver metastasis (LM). Immunoprecipitation has been performed for ERa (sc-542, SantaCruz). Raw paired-end fastq.gz files are provided for both immunoprecipitated DNA and input samples.

  Dataset EGAD50000000642

• Hi-C in breast healthy, primary cancer and metastatic tissues

  Hi-C libraries have been prepared by enzymatic digestion with MboI restriction enzyme and sonication (Covaris). Illumina single-indexig primers have been use to amplify ligated fragments. Hi-C experiments have been performed on 10 slices (50um thick) of fresh-frozen tissues or 10x10e6 Pleural Effusion cells. Raw paired-end fastq.gz files are provided.

  Dataset EGAD50000000643

• WES of precancerous lesions from 10 lynch patients and 3 sporadics

  Raw sequencing data of WES that were obtained from precancerous samples as adenoma and MMR-deficient crypts and paired healthy tissue from MSI CRC patients of which 10 are diagnosed with lynch syndrome and 3 had sporadic cancer. These data were analyzed in order to evaluate microsatellite instability though tumorigenesis and associated to splicing deregulation in MSI tumors RNA.

  Dataset EGAD50000000644

• DIAMOND PCR : plasma DNA LINE-1 targeted bisulfite sequencing, a new non-invasive multi-cancer detection marker

  The detection of circulating tumor DNA, which allows non-invasive tumor molecular profiling and disease follow-up, promises optimal and individualized management of patients with cancer. However, detecting small fractions of tumor DNA released when the tumor burden is reduced remains a challenge. We developed a PCR-based targeted bisulfite method coupled to deep sequencing to detect methylation patterns of L1PA elements,which we named DIAMOND (for Detection of Long Interspersed Nuclear Element Altered Methylation ON plasma DNA). We used sodium bisulfite chemical conversion to achieve base-pair resolution analysis and designed a multiplexed PCR based on 8 amplicons covering L1PAs .

  Dataset EGAD50000000646

• Breast Cancer bulk RNA-Seq Dataset

  Bulk RNA-Sequencing of 18 primary breast cancers from Wu et al. (2021) study.

  Dataset EGAD50000000649

• Healthy control cfMeDIP-seq

  This dataset comprises 46 raw fastq files derived from 23 plasma cfDNA samples from 23 healthy (CTL) cancer-free donors. For each sample, 10ng of cfDNA was used for library preparation utilizing the cfMeDIP-seq technology based on the 5mC antibody-immunoprecipitation strategy. Libraries were validated via Bioanalyzer trace analysis and sequenced on the Illumina NovaSeq 6000 platform with paired-end 150-bp model for ~100 million reads per sample.

  Dataset EGAD50000000652

• Clinical panel sequencing of cancer of unknown primary using Comprehensive cancer panel (CCP)

  This database includes comprehensive cancer panel (CCP) on paired tumour and germline DNA from cancer of unknown primary samples, all of which are matched to WGS data under this study. This data was used to compare biomarker yield against what was achieved with WGS. This dataset contains n=34 tumour-germline paired samples. All samples are in BAM format aligned with GRCh38 reference genome.

  Dataset EGAD50000000655

• Whole genome and transcriptome sequencing of cancer of unknown primary tumours

  Whole genome and transcriptome sequencing of cancer of unknown primary tumours was used to determine yield of clinical biomarkers for a molecular guided trial or for resolving cancer type of origin. This study includes profiling of germline DNA and tumour DNA and RNA by whole genome and transcriptome sequencing. All samples are in BAM format aligned with GRCh38 reference genome. This dataset includes: 1. Whole genome sequencing (WGS) of 78 cancer of unknown primary tumour samples and 73 matched germline DNA. 2. Whole transcriptome sequencing (WTS) of 69 cancer of unknown primary tumour samples (matched to WGS cases) 3. Whole genome sequencing of 22 cell-free DNA samples from cancer of unknown primary patients and matched Germaine DNA(8 samples matched to tumour WGS)

  Dataset EGAD50000000656

• Clinical panel sequencing of cancer of unknown primary using TruSight Oncology 500 (TSO500)

  TruSight Oncology 500 (TSO500) cancer panel sequencing data on paired tumour and germline DNA from cancer of unknown primary samples. All of the samples in this dataset are matched to WGS data. This data was used to compare biomarker yield against what was achieved with WGS and contains n=51 tumour-only samples. All samples are in BAM format aligned with GRCh38 reference genome.

  Dataset EGAD50000000657

• Comprehensive molecular phenotyping of ARID1A-deficient gastric cancer reveals pervasive epigenomic reprogramming and therapeutic opportunities

  This dataset includes paired tumor-blood whole exome sequencing data for 209 gastric cancer (GC) patients, along with whole transcriptome sequencing data for 125 GC samples. Whole exome sequencing was conducted using Agilent SureSelect Human All Exon V6 kits. For RNA sequencing, total RNA was isolated using the RNeasy Mini Kit, and libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina). Aligned BAM files for both exome and RNAseq data are included in this dataset.

  Dataset EGAD50000000660