|
| Status |
Public on Sep 23, 2022 |
| Title |
LOXL2 negative rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
LOXL2 negative
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: uterine carcinoma
gender: female
genotype: LOXL2 negative
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. And RNA was prepared using the RNeasy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the One-Color One-Color Quick Amp Labering kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Gene Expression Microarray 4×44K 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 and 1 minute with at room temperature GE Wash buffer 2 , then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).
|
| Description |
Gene expression in LOXL2 negative uterine carcinoma sample rep 3
|
| Data processing |
The scanned images were analyzed with Agilent Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The algorithm used to normalize data: Threshold raw signals to 1.0. Normalization algorithm 75% Percentile shift. Baseline to median of all samples.
|
| |
|
| Submission date |
Sep 21, 2022 |
| Last update date |
Sep 23, 2022 |
| Contact name |
Xufeng Lu |
| E-mail(s) |
luxufeng@wmu.edu.cn
|
| Organization name |
Wenzhou Medical University
|
| Street address |
Caolong Road
|
| City |
Wenzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
325024 |
| Country |
China |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE213868 |
Loss of LOXL2 promotes uterine hypertrophy and tumor progression |
|
