|
| Status |
Public on Dec 20, 2017 |
| Title |
tumor from scrambled siRNA-treated mouse #4959 [miRNA] |
| Sample type |
RNA |
| |
|
| Source name |
patient-derived xenograft tumor from scrambled siRNA-treated mouse #4959
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer tumor tissue
genotype: Triple-negative breast cancer
xenograft type: BCM2665
|
| Treatment protocol |
Groups (0) and (1) (n=10) were treated with 5 µg/mouse DOPC nanoliposomal siRNA IP injection twice a week for 3 weeks. Mice were sacrificed on day 21. Tumors were harvested and snap frozen.
|
| Growth protocol |
In docetaxel-resistant BCM2665 PDX xenografts, tumors were transplanted into the mammary fat pad of SCID-Beige mice. Mice were randomized into 5 groups when tumor volume reached 150-200mm3: (0)scrambled siRNA, (1)HN1L siRNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of miRNA from each frozen tumor sample was performed using miRNeasy Mini kit from Qiagen following manufacturer instruction.
|
| Label |
biotin
|
| Label protocol |
Biotinylated miRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
hybridization,washing and staining were done following Affymetrix protocol for Genechip miRNA 4.0 arrays.
|
| Scan protocol |
Scanning was done on Affymetrix Genechip Scanner model 7G, Affymetrix Genechip command console(AGCC) software was used for instrument control, data acquisition and quality control.
|
| Description |
miRNA expression data from TNBC tumor sample of scramble-siRNA treated mouse model BCM2665
|
| Data processing |
Expression values were processed and normalized using the affy library in R statistical software. Only human probes were isolated, from the multispecies miRNA profiling by the miRNA array 4.0, for the purpose of the analysis. Differential expression analysis was then performed using limma package in R. The most significantly differentially expressed miRNAs were selected based on a cut off log fold change > 1 and FDR < 0.2.
|
| |
|
| Submission date |
Oct 26, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Jenny Chang |
| Organization name |
Houston Methodist Hospital
|
| Department |
Houston Methodist Cancer Center
|
| Street address |
6670 Bertner Ave.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19117 |
| Series (2) |
| GSE106199 |
MicroRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples |
| GSE106200 |
RNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples |
|
