Gene Expression Nebulas
A data portal of transcriptomic profiles across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA471582: Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain AA]

Source: NCBI / GSE114461
Submission Date: May 15 2018
Release Date: Aug 01 2018
Update Date: Mar 27 2019

Summary: 10X Genomics single cell RNAseq of MCF7 cells treated with bortezomib.Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the

Overall Design: MCF7 cells (strain AA) were treated with bortezomib (500nM) and harvested before treatment, after 12 hours of exposure (t12), after 24 hours of exposure (t48), or after 72 hours of exposure followed by drug wash and 24 hours of recovery (t72+24)

GEN Datasets:
GEND000090
Strategy:
Species:
Healthy Condition:
Cell Type:
Cell Line:
Protocol
Growth Protocol: MCF7 cells were cultured in RPMI-1640 (Life Technologies), with 10% Fetal Bovine Serum (Sigma-Aldrich) and 1% Penicillin-Streptomycin-Glutamine (Life Technologies).
Treatment Protocol: MCF7-AA cells were exposed to 500nM of bortezomib (Selleckchem S1013 ) and harvested before treatment, after 12 hours of exposure (t12), after 24 hours of exposure (t48), or after 72 hours of exposure followed by drug wash and 24 hours of recovery (t72+24).
Extract Protocol: DissociateCells were washed, trypsinized, passed through a 40μM cell strainer, centrifuged at 400g, and resuspended at a concentration of 1,000 cells/μL in PBS + 0.5% BSA.Single cells were processed through the Chromium Single Cell 3′ Solution platform using the Chromium Single Cell 3’ Gel Bead, Chip and Library Kits (10X Genomics), as per the manufacturer’s protocol.
Library Construction Protocol: -
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Specific
Publications
Genetic and transcriptional evolution alters cancer cell line drug response.
Nature . 2018-08-08 [PMID: 30089904]
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate