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| Status |
Public on Aug 21, 2023 |
| Title |
colorectum_old_AOM+DSS_d10_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
colorectum from old mice,AOM+DSS,d10,replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colorectum
age: old
time point (days): 10
group: wound healing
|
| Treatment protocol |
Mice were injected intraperitoneally (i.p.) with 10 mg/kg azoxymethane (AOM; Sigma-Aldrich, Germany). After 7 days, the mice received drinking water containing 2% DSS for 7 days followed by normal drinking water for 14 days. Totally, three DSS cycles were performed.
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| Growth protocol |
C57 mice (20 g weight, male) were purchased from Beijing HFK Bioscience Co. (Beijing, China) and housed in a specific-pathogen free (SPF) room (25 ˚C) under a 12-h light/dark cycle with ad libitum access to food and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
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| Hybridization protocol |
0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
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| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
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| Description |
gene expression after 10 days in AOM+DSS-treated old mice's colorectum
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
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| |
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| Submission date |
Jan 15, 2020 |
| Last update date |
Aug 21, 2023 |
| Contact name |
Yi Liu |
| E-mail(s) |
[email protected]
|
| Phone |
15108440806
|
| Organization name |
Sichuan University
|
| Lab |
State Key Laboratory of Biotherapy
|
| Street address |
No. 4 keyuan road, gaopeng avenue
|
| City |
Chengdu |
| State/province |
Sichuan Province |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL25663 |
| Series (1) |
| GSE143693 |
Reduced transformation of intestinal smooth muscle cells into fibroblasts inhibit intestinal wound healing and colitis-associated cancer in ageing mice |
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