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| Status |
Public on Jan 11, 2019 |
| Title |
RNA profiles of skin tissues form IRF1 KO mouse following radiation 1 |
| Sample type |
RNA |
| |
|
| Source name |
skin tissue
|
| Organism |
Mus musculus |
| Characteristics |
exposure: 35 Gy radiation
tissue: skin
genotype/variation: IRF1 KO
age: 8 weeks old
Sex: male
strain: C57B L/6
|
| Treatment protocol |
The C57B L/6 IRF1 knockout (IRF-/-) mice were obtained from The Jackson Laboratory (stock number: 002762). IRF1 knockout (IRF-/-) mice and wild-type mice were anesthetized with an intraperitoneal injection of chloral hydrate (360 mg/kg), and the hair on hind limb of the mice was shaved using a razor. Mice were immobilized with adhesive tape on a plastic plate to minimize motion during radiation exposure. A 3-cm-thick piece of lead was used to shield the animals and localize the radiation field on hind leg. Irradiation was administered to the treatment area with 35 Gy at a dose rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems) as reported
|
| Growth protocol |
IRF1 knockout (IRF-/-) mice and wild-type mice were kept in SPF-level animal houses where rats can drink and eat freely.
|
| 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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| |
|
| 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 to Agilent Mouse lncRNA Microrray V3 (4*180K,Design ID:084388) 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.
|
| 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%).
|
| Description |
skin tissue of IRF1 KO-1 with 35 Gy radiation
|
| 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 14.9(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 10, 2019 |
| Last update date |
Jan 11, 2019 |
| Contact name |
zhang shu yu |
| E-mail(s) |
[email protected]
|
| Phone |
+8615851417273
|
| Organization name |
soochow University
|
| Department |
Radiation Medicine
|
| Street address |
199 Ren'ai Rd
|
| City |
suzhou |
| State/province |
Jinagsu |
| ZIP/Postal code |
215123 |
| Country |
China |
| |
|
| Platform ID |
GPL25663 |
| Series (1) |
| GSE124895 |
Differentially expressed RNAs in the skin tissue of IRF1 knockout mice following radiation |
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