|
| Status |
Public on May 10, 2024 |
| Title |
Adjacent Normal 2 |
| Sample type |
RNA |
| |
|
| Source name |
Tumor 1-adjacent salivary gland tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Adjacent Normal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues or tumors were processed for RNA isolation after snap freezing in liquid nitrogen. Total RNA was extracted using Trizol reagent (Invitrogen) and purified by RNAeasy Mini Column (QIAGEN) NucleoSpin RNA Column.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling was performed based on 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).
|
| |
|
| Hybridization protocol |
The labeled cRNAs were hybridized onto the Mouse LncRNA Array v3.0 (8 x 60K, Arraystar).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting.
|
| Description |
LncRNA/mRNSexpression data
|
| 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 using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
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| |
|
| Submission date |
Jan 07, 2020 |
| Last update date |
May 10, 2024 |
| Contact name |
Lizi Wu |
| Organization name |
University of Florida
|
| Street address |
2033 Mowry Road
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL19286 |
| Series (1) |
| GSE143264 |
Gene expression profiling of mouse CRTC1-MAML2-driven MEC-like tumors |
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