DAC for patient-derived cell line samples

Dac ID Contact Person Email Access Information
EGAC00001000594 Christian Conrad christian [dot] conrad [at] bihealth [dot] de No additional information is available

This DAC controls 6 datasets:

Dataset ID Description Technology Samples
EGAD00001003146 We performed whole genome sequencing of nine OC patient-derived cell lines and one normal cell line (HOSEpiC) to analyze if the cell lines harbor OC-typical genomic aberrations absent in normal cells and to relate genomic features to drug sensitivities. 10
EGAD00001004131 Pheno-seq is a new approach that integrates high-throughput imaging and transcriptomic profiling of clonal spheroids/organoids to dissect functional tumor cell heterogeneity in 3D cell culture systems. The method is based on the iCELL8 technology (TakaraBio) that uses barcoded nanowells and a micro-solenoid valve dispenser. The CRC_spheroid dataset contains demultiplexed RNA-sequencing profiles (FASTQ file format, NextSeq 500) of 95 clonal tumor spheroids derived from a patient with colorectal cancer. NextSeq 500 1
EGAD00001005315 NA NextSeq 500 9
EGAD00001005524 Colorectal cancer (CRC) is characterized by functional intratumor heterogeneity that shares many similarites with the hierarchical organization of the normal intestinal epithelium. In order to relate transcriptional subtypes to functional tumor cell heterogeneity we applied scRNA-seq to 12 patient-derived CRC spheroid cultures. We identified shared expression programs that relate to intestinal lineages and revealed metabolic signatures that are linked to cancer cell differentiation. In addition, we validated and complemented sequencing results by quantitative microscopy using live-dyes and multiplexed RNA fluorescence in situ hybridization, thereby revealing metabolic compartmentalization and potential cell-cell interactions. Finally, we demonstrate functional differences between metabolically distinct lineage subtypes that might have strong implications for future treatment strategies of CRC. NextSeq 500 8714
EGAD00001006185 ALI culture bronchial cells and alveolar lung surgical resection scRNA-Seq Illumina HiSeq 4000 16
EGAD00001006448 NA NextSeq 500 25