Data from: Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction
type: Dataset
distribution: Landing page for the dataset
description: Dataset Description This record is a collection of Whole-genome sequencing (WGS), RNA sequencing (RNA-seq), NanoString's nCounter® Breast Cancer 360 (BC360) Panel and cell viability assay data, generated as part of the study “Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction" by Chen et al., 2022. The WGS dataset contains raw sequencing data (BAM files) from tumor scraping cells (TSCs) at the time of surgical resection, derived whole-tumor cell (WTC) cultures from each patient's specimen, and normal skin biopsy for germline control, from five (5) breast cancer (BC) patients. Genomic DNA samples were isolated by using the QIAamp DNA mini kit (QIAGEN). The library was prepared by using Illumina TruSeq PCR-free (350 bp) according to the manufacturer’s protocol. The bulk DNA samples were then sequenced by Illumina Hiseq X and processed via the Science for Life Laboratory CAW workflow version 1.2.362 (Stockholm, Sweden; https://github.com/SciLifeLab/Sarek). The RNA-seq dataset contains raw sequencing data (fastq files) from the TSC pellets at the time of surgical resection, and the pellets of derived WTC cultures with or without tamoxifen metabolites treatment (1 nM 4OHT and 25 nM Z-Endoxifen), from 16 BC patients. 2000 ng RNA was extracted using the RNeasy mini kit (QIAGEN) from each sample, and 1 μg of total RNA was used for rRNA depletion using RiboZero (Illumina). Stranded RNA-seq libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit (Illumina), and paired-end sequencing was performed on HiSeq 2500 with a 2 x 126 setup using the Science for Life Laboratory platform (Stockholm, Sweden). The NanoString's nCounter® BC360 Panel dataset contains normalized data from FFPE tissue samples of 43 BC patients. RNA was extracted from the macrodissected sections using the High Pure FFPET RNA Isolation Kit (Roche) following the manufacturer's protocols. Then, 200 ng of RNA per sample we…
modified: 2023-05-30T00:00:00Z
issued: 2022-12-01T00:00:00Z
publisher: Karolinska Institutet
theme: HEAL
access rights: NON PUBLIC
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Xinsong Chen
    type: Agent
    account: https://orcid.org/0000-0002-3214-9075
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Emmanouil Sifakis
    type: Agent
    account: https://orcid.org/0000-0001-9919-4471
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Johan Hartman
    type: Agent
    account: https://orcid.org/0000-0002-6500-8527
    type: PrivateIndividual(s)
keyword: Oncology and carcinogenesis not elsewhere classified
keyword: Genomics and transcriptomics

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: Data from: Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction
availability: stable

Karolinska Institutet
type: Agent
type: Academia-ScientificOrganisation
source: https://ror.org/056d84691