|
| Status |
Public on Sep 01, 2020 |
| Title |
DU145_Res_7 |
| Sample type |
SRA |
| |
|
| Source name |
DU145_Res
|
| Organism |
Homo sapiens |
| Characteristics |
docetaxel: Resistant
disease state: Prostate cancer
cell line: DU145
|
| Treatment protocol |
Docetaxel resistance was maintained with the addition of 10 nM docetaxel in DMSO in growth media while sensitive cells were maintained with the addition of a final concentration of 0.1% DMSO.
|
| Growth protocol |
Cells were cultered in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were trypsinized in 0.05% Trypsin EDTA for 5-10 mins at 37°C and washed with media. The cell suspension was loaded into the Fluidigm C1TM machine and processed into single cell cDNA libraries according to the manufacturer protocol.
Full length mtotal RNA-seq libraries were generated from single cells captured using the Fluidigm C1TM Single Cell mtotal RNA Seq IFC, 10-17 um and Fluidigm C1TM Single-Cell Reagent Kit for mtotal RNA Seq. Full length cDNA was converted into sequence ready libraries using SMART-seq v4 Ultra Low Input total RNA kit for Fluidigm C1TM System and SeqAmpTM DNA Polymerase. Library preparation was completed using Nextera XT DNA library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Samples were sequenced on Illumina HiSeq 2500 for DU145 cell line and Illumina HiSeq 4000 with single end option for PC3 cell line.
Samples were aligned to Human genome hg38 using bowtie alignment tool.
Poor quality cells were removed as determined using the Fluidigm Singular package.
Genome_build: Human genome hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts
|
| |
|
| Submission date |
Nov 15, 2019 |
| Last update date |
Sep 01, 2020 |
| Contact name |
Evan T Keller |
| E-mail(s) |
etkeller@med.umich.edu
|
| Organization name |
University of Michigan
|
| Street address |
2800 Plymouth Rd
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE140440 |
Single Cell Analysis Reveals NUPR1 Promotes Docetaxel Resistance in Prostate Cancer |
|
| Relations |
| BioSample |
SAMN13291059 |
| SRA |
SRX7156177 |
