|
| Status |
Public on Jul 07, 2022 |
| Title |
P1C2_day6_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
The breast cancer CTC line BRx68
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BRx68
treatment: P1C2
days_in_culture: 6
batch: A
|
| Treatment protocol |
Single cells were treated with either 1μM of P1C2, P4D8, or P1G7, or 0.3mM of NAC or a combination of 1μM of P1C2 and 0.3 mM of NAC. Cells cultured in media containing DMSO served as a control. Cells were cultured under treatment for either 6 days or 13 days.
|
| Growth protocol |
Single cells were cultured in the presence of EGF, bFGF containing RPMI media for either 6 days or 13 days at 37°C, 5% CO2 and 4% O2, and media was changed every 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At day 6 or day 13 cells were harvested and flash frozen in liquid nitrogen and stored at -80c. On the day of RNA extraction, samples were retrived from -80 c and processed using SMARTer chemistry (SMART Seq® v4 Ultra® Low Input RNA Kit for Sequencing, Takara Clontech).
cDNA libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina) with Nextera index kit index 1 (i7) and index 2 (i5) adapters.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
compound description:
Diclofenac Sodium (P1C2)
|
| Data processing |
RNA-sequencing reads were trimmed for Nextera and Illumina adapter sequences using Trim Galore under default parameters. Trimmed reads were then mapped to the human genome build GRCh37 from Ensembl (ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa.gz) using STAR under optimized parameters for single-end sequenced data.
Aligned reads were then counted via featureCounts (47) and piped into DESeq2 (48) for normalization to sequencing depth and downstream analysis. For purposes of producing the PCA plot, count data was transformed via the vst function to eliminate the experiment-wide trend of variance over mean and the plot was produced using ggplot2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw counts
|
| |
|
| Submission date |
Jul 11, 2019 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Min Yu |
| Organization name |
University of Southern California
|
| Department |
USC Norris Comprehensive Cancer Center, Keck School of Medicine
|
| Street address |
1450 Biggy Street, NRT 3507
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE134138 |
A small molecule screen identified N-Acetyl-L-cysteine for promoting ex vivo growth of single circulating tumor cell |
|
| Relations |
| BioSample |
SAMN12255002 |
| SRA |
SRX6431028 |
