|
| Status |
Public on Sep 01, 2022 |
| Title |
C57/BL6_liver_2-months_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
C57/BL6_liver_2-months
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6
age: 2-months
Sex: male
tissue: liver
|
| Treatment protocol |
No treatment involved
|
| Growth protocol |
All mice were on a C57BL/6 genetic background. Animals were housed in a controlled temperature room maintained under alternating 12 h light and dark cycles and, in between experiments, had free access to food and water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from mouse live tissue using TRIzol™ Plus RNA Purification Kit (ThermoFisher Scientific, Waltham, MA) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 and RNA integrity was assessed by Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling was 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. 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 G2505C).
|
| Description |
LncRNA expression profile of mouse adult liver
Mouse liver lncRNA_01
|
| Data processing |
The raw intensities were first QC flag filtered before next step normalization. The probe signals were QC flagged as Present or Absent based on whether the signals are: 1) Positive and significant; 2) Uniform; 3) Above background; 4) Saturated; 5) Population outlier. The probe signals were additionally flagged as Marginal based on whether their backgrounds are: 1) Uniform; 2) Population outlier. All probes are flagged according to these rules. Probes flagged as Absent are excluded from the Fold Change analysis. Many genes on the array were filtered out primarily because many genes were not expressed across the samples and thus did not have valid intensity values, resulting in the reduced data set.
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 that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs were identified through Fold Change filtering between two samples. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.
|
| |
|
| Submission date |
Jul 23, 2018 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Liuqing Yang |
| E-mail(s) |
lyang7@mdanderson.org
|
| Phone |
713-563-2654
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Molecular and Cellular Oncology
|
| Street address |
1515 Holcombe Blvd.
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19286 |
| Series (1) |
| GSE117540 |
Expression Profile Analysis of Long non-coding RNAs in Mouse Liver |
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