|
| Status |
Public on Feb 27, 2018 |
| Title |
Th-05 |
| Sample type |
RNA |
| |
|
| Source name |
thymus
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
age: six weeks old
strain: BALB/c
|
| Treatment protocol |
-
|
| Growth protocol |
The mice were housed in an auto-controlled pathogen-free animal room at 22 ± 2°C under a 12:12 h light/dark cycle, and they were provided with commercial pellets and tap water ad libitum for five weeks. The mice were sacrificed by complete blood collection via the inferior vena cava under anesthesia with ether. The spleen, liver, left kidney, left testis, stomach, thymus, lung, heart, brain, and left rectus femoris muscle were removed in that order and then stored in RNAlater solution at -20°C. Experiments were designed and performed in strict accordance with the Guide for the Care and Use of Laboratory Animals (8TH edition, NIH update 2011) and approved by the Institutional Animal Care and Use Committee of Daejeon University (Animal ethical clearance number: DJUARB 2016-034 to 6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy midi kit according to the manufacturer's instructions. RNA quality and concentration were assessed using an Agilent Bioanalyzer 2100 and a NanoDrop ND-1000 spectrophotometer, respectively. The absorbance ratio at 260:280 nm for all samples was >1.8 and the RIN value was >8. The integrity of RNA samples was also ascertained by the presence of distinct 28S and 18S ribosomal RNA bands in agarose gels after electrophoretic resolution.
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized from total RNA (100 ng) using a T7 oligomer and Superscript RT II kit, and cDNA was purified with a QIAquick PCR Purification Kit. Next, biotin-labeled cRNA was synthesized using an Affymetrix RNA transcription labeling kit.
|
| |
|
| Hybridization protocol |
After cleaning and fragmentation, a total of fifty cDNA samples from each of 10 different tissues collected from the five mice were hybridized using the Mouse gene 1.0 ST array for 16 h.
|
| Scan protocol |
After washing and staining with streptavidin phycoerythrin solution and antibody solution, images were obtained by capturing the fluorescence intensity using a GMS 418 Array Scanner.
|
| Description |
thymus_5 from male BALB/c mouse (six weeks old)
|
| Data processing |
Microarray data were uploaded using GenPlexTM v3.0 (Istech Inc., Korea) and GeneSpring GX 7.3 software (Agilent Technology) and normalized with RMA. Further statistical analyses were performed primarily using tools included in GenPlex and GeneSpring GX 7.3. Functional annotation of genes was performed per the Gene Ontology™ Consortium (http://www.geneontology.org/index.shtml). Gene classification was based on searches using the GeneCards (http://www.genecards.org/), BioCarta (http://www.biocarta.com/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline (http://www.ncbi.nlm.nih.gov/) databases.
|
| |
|
| Submission date |
Feb 26, 2018 |
| Last update date |
Feb 27, 2018 |
| Contact name |
Jung Min Kim |
| E-mail(s) |
jmkim2010@korea.com
|
| Phone |
82-10-3459-4776
|
| Organization name |
NAR Center, Inc. & Genoplan, Inc.
|
| Department |
Department of Health Genomics
|
| Lab |
Genetics & Genomics
|
| Street address |
Gangnam-gu Teheran-ro 216
|
| City |
Seoul |
| ZIP/Postal code |
06221 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE111159 |
Tissue-specific features of oxidative stress-associated gene expression in a healthy mouse model |
|
