ABSTRACT: This dataset includes Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data, in FASTQ format, from 70 metastatic castration-resistant prostate cancer tumor samples from the SU2C/PCF West Coast Dream Team (WCDT) project. The sequencing data is paired-end, 150 bp sequencing data from an Illumina NovaSeq 6000 machine. ATAC-seq libraries were prepared following the protocol described in Buenrostro et al. Nature Methods. 2013 (PMID: 24097267) and Corces et al. Nature Methods. 2017 (PMID: 28846090).
Project description:DNaseI hypersensitivity using DNase-array method on Affy platform overall design Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197 Keywords: genomic
Project description:224 pairs of FASTQ files from metastatic Castration-Resistant Prostate Cancer (mCRPC) sequenced on HiSeq 4000 instruments. Patients were enrolled in the West Coast Dream Team study. Biopsies include various tissue sites including bone, soft tissue, and lymph node.
Project description:DNaseI hypersensitivity using DNase-array method on Affy platform overall design Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197 This study is part of an ongoing screening process designed to obtain high quality cell-lines/tissues for further high throughput sequencing analysis. Bed files based on hg17 genome build Keywords: genomic
Project description:DNA strands have a complex and highly structured three-dimensional shape within the nucleus that has profound but poorly characterized impacts on transcriptional activity. Herein, we performed the first integrated deep Hi-C sequencing on 80 metastatic castration-resistant prostate cancer biopsy samples from the West Coast Dream Team consortium.
Project description:DNA strands have a complex and highly structured three-dimensional shape within the nucleus that has profound but poorly characterized impacts on transcriptional activity. Herein, we performed the first integrated deep Hi-C sequencing on 80 metastatic castration-resistant prostate cancer biopsy samples from the West Coast Dream Team consortium.
| EGAS00001006604 | EGA
Project description:Chevrette et al 2019 Nature Communications
Project description:Primary human foreskin fibroblasts (HFF) were exposed to either salt stress (80mM KCl) or heat stress (44ºC). ATAC-seq libraries were prepared starting with 50,000 cells per condition following the protocol described by Buenrostro et al., Nature Methods 2013
Project description:The human iPSC line H19101 was differentiated in vitro into cardiomyocytes using a 20-day differentiation protocol (Burridge et al. 2014 PMID 24930130 and Montefiori et al 2018 PMID 29988018 ). 50,000 cardiomyocytes were used in each ATAC-seq experiment. 8 replicates were pooled to obtain the final peak file.
Project description:164 pairs of FASTQ files from metastatic Castration-Resistant Prostate Cancer (mCRPC) sequenced on HiSeq 4000 instruments. Patients were enrolled in the West Coast Dream Team study. Biopsies include various tissue sites including bone, soft tissue, and lymph node. 42 pairs prior to enzalutamide treatment and at progression from 21 patients are included.
Project description:Comparison of miRNA expression profiles in malignant germ cell tumors compared to non-malignant control group. Use of bioinformatic algorithm Sylamer to interrogate mRNA expression profiles from malignant germ cell tumors for enrichment or depletion of binding sites for differentially expressed miRNAs. Use of Gene Ontology (GO) analysis to demonstrate functional significance of differentially expressed miRNAs in malignant germ cell tumors. mRNA profiling: Analyzed global mRNA expresion profiles from 21 pediatric samples (17 malignant germ cell tumors, 1 benign germ cell tumor and 3 gonadal controls) using Sylamer (van Dongen et al, Nature Methods 2008, PMID 18978784) to study functional significance of differentially expressed miRNAs in malignant germ cell tumors. 16 of these files previously published - Palmer et al, Cancer Research 2008, PMID 18519683; GEO Accession Number GSE10615. Similarly, re-analyzed published global mRNA expresion profiles from 25 adult samples (20 malignant germ cell tumors and 5 testis controls) using Sylamer (van Dongen et al, Nature Methods 2008, PMID 18978784) to study functional significance of differentially expressed miRNAs in malignant germ cell tumors. These files previously published - Korkola at al, Cancer Research 2006, PMID 16424014; GEO Accession Number GSE3218. miRNA profiling: Analyzed global miRNA expression files from 48 samples including 32 pediatric gonadal and extragonadal germ cell tumors, 2 adult testicular seminomas, 8 gonadal and developmental control samples and 6 germ cell tumor cell lines. Re-analyzed published data (TaqMan MicroRNA Assays) from study of miRNA expression in adult gonadal germ cell tumors (Gillis et al, J Pathol 2007, PMID 17893849) and compared with pediatric findings. Re-analyzed data linked below as supplementary file.