|
| Status |
Public on Apr 23, 2020 |
| Title |
siSGK3_1_LETR |
| Sample type |
SRA |
| |
|
| Source name |
letrozole resistant breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7aro cells were long-term exposed to letrozole (>6 months)
transfection: reverse transfection using siPORT NeoFX transfection agent (Ambion)
sirna: the pool of three individual SGK3 siRNA (30nM) (sc-44852, Santa Cruz)
|
| Treatment protocol |
LET-R cells were reversely transfected with 30nM siRNA negative control, AREG siRNA or SGK3 siRNA using siPORT NeoFX transfection agent (Ambion) for 48 h, and then harvested for RNA sequencing.
|
| Growth protocol |
LET-R cells were cultured in MEM medium with 10% CD FBS in the presence of 1nM testesterone and 200nM letrozole.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIZOL reagent (Invitrogen)
TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA)
unstranded 40 bp, 6 bp single-barcode, single-end polyA libraries were sequenced on a HiSeq 2500 (which was a HiSeq 2000, upgraded to have a new camera to be a HiSeq 2500)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-Seq data, siSGK3 Treatment, Replicate 1
RPKM_table.txt
|
| Data processing |
We believe Real Time Analysis (RTA) was used for base calling and bcl2fastq v1 was used to generate FASTQ files.
Reads were aligned using TopHat v2.0.8b
Partek "RNA-Seq" Workflow (in version 6.6, release 6.13.0731) was used mRNA quantification (as well as differential expression, enrichment, and visualization)
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file was exported from Partek for Read Per Kilobase per Million (RPKM) normalized expression values
|
| |
|
| Submission date |
Apr 16, 2020 |
| Last update date |
Apr 23, 2020 |
| Contact name |
Charles David Warden |
| Organization name |
City of Hope
|
| Department |
Department of Molecular and Cellular Biology
|
| Street address |
1500 East Duarte Rd
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE148800 |
The effect of knockdown of amphiregulin or SGK3 on global gene expression in letrozole resistant breast cancer cells |
|
| Relations |
| BioSample |
SAMN14608383 |
| SRA |
SRX8127262 |
