|
| Status |
Public on Oct 19, 2020 |
| Title |
BY001-1 |
| Sample type |
RNA |
| |
|
| Source name |
BY001-1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: CT26 tumor
cancer type: colorectal cancer
agent: BY001
|
| Treatment protocol |
CT26 tumor-bearing mouse were treated with vehicle, BY001 ( (75 mg/kg, p.o., daily), anti-PD-1 antibody (50 μg/mouse, i.p., twice a week) or combination of BY001 and anti-PD1 antibody for two weeks. Then total fresh tumor tissues were collected for microarray.
|
| Growth protocol |
The murine colorectal cancer cell lines CT26 were maintained in DMEM medium supplemented with 10% FBS (Gibco, Waltham, MA, USA) and 1% penicillin/streptomycin solution (Gibco) at 37 °C under a humidified atmosphere (5% CO2). 500,000 CT26 tumor cells were suspended in 100 μL PBS and implanted s.c. into the flank of mice. Mice were randomized into four different treatment groups when tumor volumes reached 100-200 mm3 (V = 0.52 × the longest diameter × (the shortest diameter)2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using mirVanaTM miRNA Isolation Kit (ThermoFisher Scientific, Waltham, MA) according to the manufacturer's instructions. RNA was clean-up by RNasey Mini Kit (QIAGEN, Valencia, CA), and quantified by the NanoDrop ND-2000 (Thermo Fisher Scientific). RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3-CTP (Cy3)-labeled cRNA was prepared from 0.2 μg RNA using Agilent One-Color RNA Spike-In Kit (Agilent Technologies) and then purified by Qiagen’s RNeasy mini spin columns following the manufacturer's recommendations. cRNA was quantitated using NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific).
|
| |
|
| Hybridization protocol |
Fragmentation and hybridization were performed using Agilent gene expression Hybridization Kit following the manufacturer's recommendations. 0.6 μg Cy3-labeled linearly amplified cRNA (specific activity > 9.0 pmol Cy3/μg cRNA) was fragmented at 60 °C for 30 min in reaction volume of 25 μL containing 2x Blocking Agent and 1x Fragmentation Buffer and stopped by 25 μL 2x Gene Expression Hybridization Buffer HI-RPM. 40 μL hybridization samples were hybridized to Agilent SurePrint G3 Mouse GE V2.0 microarrays in a rotating Agilent hybridization oven at 65 °C for 17 hours. After hybridization, microarray slides were washed with Gene Expression wash Buffer1 and Gene Expression wash Buffer2 37 °C following the manufacturer's recommendations. Then slowly minimized droplets on the microarray slides.
|
| Scan protocol |
Microarray slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8*60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 μm, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
gene expression data from CT26 tumor with BY001 treatment for two weeks.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent Technologies) to extracting raw data. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data was analyzed and quantile normalized using Genespring 13.1 (Agilent Technologies).
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Oct 19, 2020 |
| Contact name |
lu weiqiang |
| E-mail(s) |
[email protected]
|
| Phone |
13611742737
|
| Organization name |
East China Normal University
|
| Street address |
500 dongchuan
|
| City |
shanghai |
| State/province |
shanghai |
| ZIP/Postal code |
200241 |
| Country |
China |
| |
|
| Platform ID |
GPL21163 |
| Series (1) |
| GSE132004 |
Gene expression profiles in CT26 syngeneic tumor tissues after EP4 antagonist TP-16(BY001), anti-PD-1 antibody or combination treatment |
|
