|
| Status |
Public on Feb 13, 2021 |
| Title |
Sheep 3 S03 Left Caudal lung segment (LC) |
| Sample type |
RNA |
| |
|
| Source name |
Fibrosis_caudal lung
|
| Organism |
Ovis aries |
| Characteristics |
Sex: Female
age: 9 months
histology: Fibrosis
status after 4 weeks: Euthenized
tissue: Caudal Lung
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was done using the miRNeasy Mini Kit according to manufactures instruction (QIAGEN Pty Ltd, Doncaster, Australia. RNA quality was determined by an Agilent Bioanalyzer 2100
|
| Label |
Cy3
|
| Label protocol |
The content of each chip is listed in the layout file named “MRA-1002B1_miRMouse_22” in the main folder. Multiple redundant regions are included. Each region consists of miRNA probes, which detect miRNA transcripts listed in Sanger miRBase Release 22 (http://www.mirbase.org/).
|
| |
|
| Hybridization protocol |
multiple control probes are included on each chip. The control probes are used for quality controls of chip production, sample labeling and assay conditions. Among the control probes, PUC2PM-20B and PUC2MM-20B are the perfect match and single-based match detection probes, respectively, of a 20-mer RNA positive control sequence that is spiked into the RNA samples before labeling. One may assess assay stringency from the intensity ratio of PUC2PM-20B and PUC2MM-20B, which is normally larger than 30.
|
| Scan protocol |
Axon GenePix 4000B Microarray Scanner. Pixel Size 10 µm and sample Gain - 420. Chip images these Cy3 (or Af3) images one may directly read miRNA profiles. The images are displayed in pseudo colors so as to expand visual dynamic range. As signal intensity increases from 1 to 65,535 the corresponding color changes from blue to green, to yellow, and to red.
|
| Description |
S03 3 LC-cy3 Signal
|
| Data processing |
The signal mean values are derived by values of repeating spots after background subtraction. All transcripts that are considered detected are written in black font color. During data processing, “bad spots” that have signal values deviated more than 50% of average values of repeating spots and/or spot CV larger than 0.5 are discarded. Signal p-values are provided to indicate how significantly the signal is differentiated from background. When a signal has a detection p-value larger than 0.01 or is bellow the detection limit, its mean value is written in grey color.
|
| |
|
| Submission date |
Feb 12, 2021 |
| Last update date |
Feb 13, 2021 |
| Contact name |
Udari Eshani Perera |
| E-mail(s) |
udari.perera@unimelb.edu.au, eshani600@yahoo.com
|
| Organization name |
University of Melbourne
|
| Street address |
Corner Flemington Road and Parkdrive, Parkville
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL29715 |
| Series (1) |
| GSE166682 |
Evaluation of microRNA expression in sheep model for lung fibrosis |
|
