|
| Status |
Public on Feb 08, 2021 |
| Title |
t7 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: epithelial, adenocarinoma
time point: 7 weeks
cell line: MDA-MB-231
agent: doxorubicin
|
| Treatment protocol |
Cells were passaged into the center 60 wells of 96 well plates at a density of about 2000 cells per well. Two days later, cells were treated with a 24 hour pulse-treatment of doxorubicin at concentrations ranging from 0-1000 nM, with 6 replicates of each dose. Dosed media was applied to cells and treatment response was monitored using the Incucyte. After 24 hours, the dosed media was replaced with normal media and monitoring continued. Cells were fed fresh media every 2-3 days for the duration of the monitoring period (up to 5 weeks).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cryopreserved samples from drug-naïve and two samples of doxorubicin-treated cells frozen at 7 and 10 weeks post-treatment were harvested, sorted by FACS to collect the BFP+ population.
Cells were loaded into wells of a Chromium A Chip, and libraries were prepared using the 10XGenomics 3’ Single Cell Gene Expression (v2) protocol. Paired end (PE) sequencing of the libraries was conducted using a NovaSeq 6000 with an S1 chip (100 cycles) according to the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
7 weeks after doxorubicin treatment
|
| Data processing |
The GTF file included with cellranger’s GRCh38 3.0.0 reference was modified to create a “pre-mRNA” GTF file so that pre-mRNAs would be included as counts in the later analysis.
Cellranger’s (v3.0.2) mkref command was then used to create a pre-mRNA reference from the GTF file and a genome FASTA file from the GRCh38 3.0.0 reference.
FASTQ files of the scRNA-seq libraries were then aligned to the new pre-mRNA reference using the cellranger count command, producing gene expression matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered cell barcodes and gene expression counts produced by cellranger
|
| |
|
| Submission date |
Jul 22, 2020 |
| Last update date |
Feb 09, 2021 |
| Contact name |
Amy Brock |
| E-mail(s) |
amy.brock@utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Street address |
107 West Dean Keeton St.
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE154932 |
Integrating multimodal data sets into a mathematical framework to describe and predict therapeutic resistance in cancer |
|
| Relations |
| BioSample |
SAMN15608811 |
| SRA |
SRX8801421 |
