|
| Status |
Public on Apr 06, 2022 |
| Title |
Aging-5 |
| Sample type |
RNA |
| |
|
| Source name |
Meniscus_aged
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Meniscus tissue
age: aged
|
| Treatment protocol |
The fresh meniscus tissues were snap-frozen in liquid nitrogen and then stored at -80 degrees Celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen meniscus tissue from Aging and Young patient were cryo pulverized using biopulverizer (Biospec) and homogenized with TRIzol (Invitrogen Life Technologies) by Mini-Bead-Beater-16 (Biospec). RNA was collected from each sample based on the manufacturer’s protocols.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2565BA).
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at The Agilent Feature Extraction Software (version 11.0.1.1) was used to analyze and extract array images. Quantile normalization and subsequent data processing were conducted in GeneSpring GX v12.1 software package (Agilent Technologies). Threshold defined as fold-change > 2.0 (Student’s t test, P < 0.05) was used as a volcano plot filtering for DE lncRNAs and mRNAs.
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| |
|
| Submission date |
Dec 17, 2021 |
| Last update date |
Apr 06, 2022 |
| Contact name |
Jinghua Yang |
| E-mail(s) |
yangjh@xy-data.net
|
| Organization name |
Beijing Zhiyun data technology co. LTD
|
| Street address |
32 North Third Ring Road West, Haidian District, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
100098 |
| Country |
China |
| |
|
| Platform ID |
GPL26963 |
| Series (1) |
| GSE191157 |
Integrated Analysis of lncRNA and mRNA Expression Profiles Indicates Age-related Changes in Meniscus |
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