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• BAM files ChIP-Seq

  Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015

  Dataset EGAD00001001669

• Epigenomics of Prostate Cancer from Cell Free Plasma

  We sought to perform epigenomic characterization of prostate cancers by profiling circulating nucleosomes isolated from patient plasma using cell free chromatin immunoprecipitation followed by sequencing (cfChIP-seq). Our major findings include identification of prostate-cancer specific regulatory elements using a novel statistical method accounting for variable tumor DNA fraction in plasma, inferring transcription factor activity based on binding motif enrichment within regulatory elements, and epigenetically phenotyping patients based on clinical and genomic features. Data available in dbGaP will include cfChIP-seq and targeted sequencing from approximately 50 patients with a known diagnosis of cancer and healthy patient controls.

  Study phs003482

• scRNA-seq of patient-derived PDAC organoids and matched CAFs

  We established direct three-dimensional (3D) co-cultures of primary PDAC organoids and patient-matched CAFs. Single-cell RNA sequencing was performed for three organoid/CAF pairs in mono- and co-culture to uncover transcriptional changes induced by tumor-stroma interaction. Single-cell RNA sequencing data evidenced induction of a pro-inflammatory phenotype in CAFs in co-cultures. Organoids showed increased expression of genes associated with epithelial-to-mesenchymal transition (EMT) in co-cultures and several potential receptor-ligand interactions related to EMT were identified, supporting a key role of CAF-driven induction of EMT in PDAC chemoresistance.

  Study EGAS00001006661

• Normal sample for patient SA234

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA234

  Dataset EGAD00001009557

• Normal sample for patient SA233

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA233

  Dataset EGAD00001009556

• Normal sample for patient SA232

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA232

  Dataset EGAD00001009555

• Normal sample for patient SA231

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA231

  Dataset EGAD00001009554

• Normal sample for patient SA230

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA230

  Dataset EGAD00001009553

• Normal sample for patient SA229

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA229

  Dataset EGAD00001009552

• Normal sample for patient SA228

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA228

  Dataset EGAD00001009551

• Normal sample for patient SA226

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA226

  Dataset EGAD00001009550

• Normal sample for patient SA225

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA225

  Dataset EGAD00001009549

• Normal sample for patient SA224

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA224

  Dataset EGAD00001009548

• Normal sample for patient SA214

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA214

  Dataset EGAD00001009547

• Normal sample for patient SA212

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA212

  Dataset EGAD00001009546

• Normal sample for patient SA211

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA211

  Dataset EGAD00001009545

• Normal sample for patient SA101

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA101

  Dataset EGAD00001009544

• Tumour sample for patient SA285

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA285

  Dataset EGAD00001009543

• Tumour sample for patient SA294

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA294

  Dataset EGAD00001009542

• Tumour sample for patient SA399

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA399

  Dataset EGAD00001009541

• Tumour sample for patient SA284

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA284

  Dataset EGAD00001009540

• Tumour sample for patient SA277

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA277

  Dataset EGAD00001009539

• Tumour sample for patient SA271

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA271

  Dataset EGAD00001009538

• Tumour sample for patient SA237

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA237

  Dataset EGAD00001009537

• Tumour sample for patient SA233

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA233

  Dataset EGAD00001009536