|
| Status |
Public on Mar 24, 2021 |
| Title |
HL2 |
| Sample type |
RNA |
| |
|
| Source name |
Hippocampus of MRL/lpr mouse_replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
strain: MRL/lpr
Sex: female
tissue: Hippocampus
develomental stage: adult
|
| Treatment protocol |
hippocampus was isolated from adult female mice and minced in ice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)
|
| Label |
Cy5
|
| Label protocol |
Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.
|
| |
|
| Hybridization protocol |
825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.
|
| Scan protocol |
The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.
|
| Description |
raw data file:
HL1_HL2_US83300186_252665512245_S01_GE2_1200_Dec17_1_3.txt
Gene expression in cortex of adult female mouse
|
| Data processing |
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
Mar 24, 2021 |
| Contact name |
Dumitru Andrei Iacobas |
| E-mail(s) |
[email protected]
|
| Phone |
936-261-9926
|
| Organization name |
Prairie View A&M University
|
| Department |
Undergraduate Medical Academy
|
| Lab |
Personalized Genomics
|
| Street address |
Ann Preston St
|
| City |
Prairie View |
| State/province |
TX |
| ZIP/Postal code |
77446 |
| Country |
USA |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE169486 |
Remodeling of Mouse Hippocampus Genomic Fabrics in Neuropsychiatric Systemic Lupus Erythematosus |
|
