|
| Status |
Public on Oct 01, 2023 |
| Title |
PDX09, TGH-treated |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: tumor
treatment: TGH-treated
|
| Treatment protocol |
Tumor volumes were monitored, and mice were stratified and placed into 2 treatment groups of 10 mice. One group was treated with vehicle control (7.5% NMP, 7.5% Solutol HS15, 30% PEG400, and 55% Saline), and one group was treated with TGH. Treatments were administered by daily I.P. injection (100 µL volumes) at a dose of 150mg/kg in the vehicle. Animal weights and tumor volumes were measured.
|
| Growth protocol |
The animal protocol was approved by Mount Sinai Institutional Animal Care and Use Committee (IACUC) (#2018-0064). The PC3 xenograft study was performed by a contractor company OXM Bio (Murray, UT). Aythmic nude mice were purchased through Jackson Laboratory (Strain 002019 52 Male NU/J Homozygous, Male). Mice were fed Teklad irradiated (sterilized) mouse diet and bedded with Teklad irradiated (sterilized) corncob bedding from Envigo (Indianapolis, IN). Mice were housed in Optimice carousel sterile quarters with filtered air supply in disposable cages from Animal Care Systems, Inc. (Centennial, CO). On the day of implantation, PC3 cells were resuspended in 50:50 RPMI (no supplementation): Matrigel at a concentration of 3 x 107 cells / mL. A volume of 100uL was injected into each hind flank of each animal (a total of 3 x 106 cells per injection).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the end of the study, all mice were humanly euthanized. Half of the tumors were harvested in 10% formalin for histological analysis and the other half were snap frozen in liquid nitrogen for RNA extraction. PC3 xenograft RNA was extracted using Automated Robotic System using Beckman's Agencourt RNA dv Advance tissue kit at qPCR core facility at Mount Sinai.
RNA quality was examined by Bioanalyzer nanochips and must have had a minimal RIN of 7. RNA sequencing was performed in the NextSeq core facility at Mount Sinai after in-house RNA library preparation with RiboMinus Eukaryote System v2 and Nextflex Rapid Directional RNA-seq kit.
Ribo-Zero
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H09, M09
|
| Data processing |
Samples were run on an Illumina NextSeq as a single end run.
Assembly: hg19, mm10
Supplementary files format and content: count_human.txt: tab-delimited text file includes counts in each gene for human part of each sample
Supplementary files format and content: count_mouse.txt: tab-delimited text file includes counts in each gene for mouse part of each sample
|
| |
|
| Submission date |
Aug 04, 2023 |
| Last update date |
Oct 01, 2023 |
| Contact name |
William Oh |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Street address |
1 Gustave Levy Place
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL19415 |
| Series (2) |
| GSE240101 |
Starving advanced prostate cancer cells by pharmacological gluose deprivation with a resveratrol trimer trans-Gnetin H [PDX] |
| GSE240104 |
Starving advanced prostate cancer cells by pharmacological gluose deprivation with a resveratrol trimer trans-Gnetin H |
|
| Relations |
| BioSample |
SAMN36844713 |
| SRA |
SRX21257687 |
