|
| Status |
Public on Sep 01, 2021 |
| Title |
nevus tissue 1 (1202425) |
| Sample type |
RNA |
| |
|
| Source name |
nevus tissue 1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: nevus
gender: female
age: 54
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The miRNeasy FFPE Kit (Qiagen, Germany) was used to extract RNA from paraffin-embedded specimens.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug 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.
|
| |
|
| 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 AgilentHuman miRNA 8×60K 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 GenePix 4000B scanner (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
253816610053-2_4
Gene expression
|
| 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.
|
| |
|
| Submission date |
Aug 31, 2021 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Suwei Dong |
| E-mail(s) |
[email protected]
|
| Phone |
+86-19851695256
|
| Organization name |
The Second Affiliated Hospital of Xuzhou Medical University
|
| Street address |
NO.32 Meijian RD
|
| City |
Xuzhou |
| ZIP/Postal code |
221000 |
| Country |
China |
| |
|
| Platform ID |
GPL16543 |
| Series (1) |
| GSE183116 |
Different miRNA expression between melanoma and nevus tissues |
|
