|
| Status |
Public on Jul 06, 2023 |
| Title |
MCF7_40_1 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell-line MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell-line: MCF7
treatment: MCF7 Imipramine
rna harvest: 96 hours after treatment
|
| Treatment protocol |
Cells were plated in 6 well plates in complete media. After 24hrs, cells were treated with DMSO or 40µM Imipramine for 96 hours.
|
| Growth protocol |
Cells were maintained in complete medium (DMEM high glucose media supplemented with 10% FBS and 1% Anti-Anti).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from control and MCF7 Imipramine samples (96 hours after treatment), using RNeasy mini kit (Qiagen)
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Dec 13, 2021 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE190814 |
The antidepressant imipramine inhibits breast cancer growth by targeting estrogen receptor signaling and DNA repair events |
|
| Relations |
| BioSample |
SAMN24009666 |
| SRA |
SRX13404273 |
