|
| Status |
Public on Oct 25, 2023 |
| Title |
E4_3_SUM149+ETX |
| Sample type |
SRA |
| |
|
| Source name |
SUM149 breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM149
cell type: breast cancer cell
tissue: Breast
treatment: 100 uM Etomoxir
|
| Treatment protocol |
CPT1 gene was knocked-down by lentiviral shRNA or 100 uM Etomoxir(ETX) was treated for 1 week
|
| Growth protocol |
Cell lines were grown in DMEM containing 5% FBS in T25 flask
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC human reference genome hg38 using STAR.
featureCounts was used to evaluate gene expression level as read counts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each sample
|
| |
|
| Submission date |
Aug 08, 2023 |
| Last update date |
Oct 25, 2023 |
| Contact name |
Benny Abrhaam Kaipparettu |
| E-mail(s) |
kaippare@bcm.edu
|
| Phone |
7137986506
|
| Organization name |
Baylor College Of Medicine
|
| Department |
Department of Molecular and Human Genetics
|
| Lab |
Kaipparettu Lab
|
| Street address |
1 Baylor Plaza T832
|
| City |
HOUSTON |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE240393 |
Metabolomic Rewiring in Endocrine Therapy-Resistant Estrogen Receptor Positive Breast Cancer |
|
| Relations |
| BioSample |
SAMN36892939 |
| SRA |
SRX21301771 |
