|
| Status |
Public on Oct 10, 2021 |
| Title |
SW549-cy3-untreated-inflamed-1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SW549
|
| Organism |
Mus musculus |
| Characteristics |
tissue: inflamed
treatment: none
|
| Treatment protocol |
Treated groups received 5-ASA through the experiment.
|
| Growth protocol |
Female Swiss Webster mice (7 weeks of age) were maintained in the animal facility and received food and water ad libitum. Animals were treated with AOM (7.4 mg/kg, i.p.) and 4% DSS for 3 cycles (one cycle = 7 days of DSS plus 21 days of water). At the time of the sacrifice, colons were cut into sections and snap frozen on OCT compound. Frozen sections were cut at 5um at -20oC and kept at -80oC until sample collection by Laser Capture Microdissection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using PicoPure RNA Isolation Kit (Arcturus Bioscience). All RNAs were subjected to DNAse treatment. Quality was assessed on RNA 6000 Pico LabChip and evaluated on Agilent Bioanalyzer 2100 using Eukaryote Total RNA Pico Assay. Total RNA was submitted to two rounds of amplification using RiboAmp Kit (Arcturus Biosciences) and Paradise Reagent System.
|
| Label |
Cy3
|
| Label protocol |
Labeled antisense (aRNA) probes for microarray hybridization were generated in the second round of applification in the presence of UTP after Cy3 fluorescent dye (Amersham Biosciences Corp., Piscataway, NJ) incorporation. 100ng of a mouse universal reference RNA (BD Biosciences Clontech, Palo Alto, CA) was amplified in parallel and labeled with Cy5 fluorescent dye (Amersham Biosciences Corp.)
|
| |
|
| Channel 2 |
| Source name |
Ref
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Ref
treatment: Ref
|
| Treatment protocol |
Treated groups received 5-ASA through the experiment.
|
| Growth protocol |
Female Swiss Webster mice (7 weeks of age) were maintained in the animal facility and received food and water ad libitum. Animals were treated with AOM (7.4 mg/kg, i.p.) and 4% DSS for 3 cycles (one cycle = 7 days of DSS plus 21 days of water). At the time of the sacrifice, colons were cut into sections and snap frozen on OCT compound. Frozen sections were cut at 5um at -20oC and kept at -80oC until sample collection by Laser Capture Microdissection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using PicoPure RNA Isolation Kit (Arcturus Bioscience). All RNAs were subjected to DNAse treatment. Quality was assessed on RNA 6000 Pico LabChip and evaluated on Agilent Bioanalyzer 2100 using Eukaryote Total RNA Pico Assay. Total RNA was submitted to two rounds of amplification using RiboAmp Kit (Arcturus Biosciences) and Paradise Reagent System.
|
| Label |
Cy5
|
| Label protocol |
Labeled antisense (aRNA) probes for microarray hybridization were generated in the second round of applification in the presence of UTP after Cy3 fluorescent dye (Amersham Biosciences Corp., Piscataway, NJ) incorporation. 100ng of a mouse universal reference RNA (BD Biosciences Clontech, Palo Alto, CA) was amplified in parallel and labeled with Cy5 fluorescent dye (Amersham Biosciences Corp.)
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed on Agilent 4x44K mouse genomic arrays. Cy3-labeled aRNA was mixed with Cy5-labeles reference aRNA and hybrized onto Agilent G2545A Hybridization oven using In situ Hybridization Kit Plus (Agilent Technologies).
|
| Scan protocol |
Images were scanned on an Agilent G2505B scanner and quantified using Agilent Feature Extraction (v9.1.1.1)
|
| Data processing |
Agilent Feature Extraction (FE) software (v9.1.1.1) was used to generate Cy3 & Cy5 ProcessedSignal intensities and to flag poor quality spots.
|
| |
|
| Submission date |
Oct 09, 2021 |
| Last update date |
Oct 10, 2021 |
| Contact name |
Mariana Franco Fragoso |
| E-mail(s) |
marifragoso@gmail.com, mariana.fragoso@fccc.edu
|
| Organization name |
Fox Chase Cancer Center
|
| Department |
Cancer Prevention and Control
|
| Street address |
333 Cottman Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19111 |
| Country |
USA |
| |
|
| Platform ID |
GPL7042 |
| Series (1) |
| GSE185599 |
The effect of 5-ASA on colitis-associated carcinogenesis |
|
