|
| Status |
Public on Dec 20, 2017 |
| Title |
tumor from scrambled siRNA-treated mouse #4967 [mRNA] |
| Sample type |
RNA |
| |
|
| Source name |
patient-derived xenograft tumor from scrambled siRNA-treated mouse #4967
|
| 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 total RNA from each frozen tumor sample was performed using RNeasy Mini kit from Qiagen following manufacturer instruction.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to Ovation Pico WTA system V2 and FL-Ovation cDNABtiotin Module V2 from NUGEN Technologies
|
| |
|
| Hybridization protocol |
Affymetrix Hybridization,cocktail assembly and Fluidics protocol for Standard Array( 49 format) with minor modifications provided by NUGEN's FL-Ovation cDNA biotin module V2 protocol
|
| Scan protocol |
Genechips were scanned using Affymetrix Genechip Scanner model 7G, Genechip command console (AGCC)software provided instrument control, data acquisition and first order data anaylsis
|
| Description |
mRNA expression data from TNBC tumor sample of scramble-siRNA treated mouse model BCM2665
|
| Data processing |
The array data were evaluated using the commercial software suite, Partek Genomics Suite. Specifically, data were normalized by using the RMA (robust multichip averaging) method. Gene-expression levels were analyzed on a logarithmic scale. ANOVA was used to identify differentially expressed genes. Genes with P value less than 0.05 in each comparison were selected for further functional and pathway analyses by Ingenuity Pathway Analysis (IPA) tools.
|
| |
|
| Submission date |
Oct 24, 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 |
GPL570 |
| Series (2) |
| GSE106106 |
mRNA 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 |
|
