|
| Status |
Public on Feb 18, 2014 |
| Title |
caudate-HIVpositive_neuroOK3-rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
caudate-HIVpositive_neuroOK3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: caudate
hiv: yes
infection: HIV
neurocognitive abnormal: no
hive: no
|
| Growth protocol |
Postmortem Human Brain Samples
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol + column purification
|
| Label |
Hy3
|
| Label protocol |
Mix: (1) CIP treated RNA sample, (2) Labeling buffer, (3) Hy3™ or Hy5™, (4) DMSO, (5) Enzyme
|
| |
|
| Channel 2 |
| Source name |
caudate-pooled
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: caudate
hiv: all 17 samples pooled
neurocognitive disorder: all 17 samples pooled
hive: all 17 samples pooled
|
| Growth protocol |
Postmortem Human Brain Samples
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol + column purification
|
| Label |
Hy5
|
| Label protocol |
Mix: (1) CIP treated RNA sample, (2) Labeling buffer, (3) Hy3™ or Hy5™, (4) DMSO, (5) Enzyme
|
| |
|
| |
| Hybridization protocol |
Exiqon used miRCURY™ LNA Array Power labeling kit allows highly efficient and uniform labeling of microRNAs with minimal sequence bias. Using Tecan hybridization stations the hybridization and washing steps are fully automated for excellent reproducibility.
|
| Scan protocol |
Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays.
|
| Description |
Hy3: 1_Exiqon_13994548_S01_Cropped.txt
Hy5: 0_Exiqon_13994548_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13
|
| Data processing |
The data obtained is normalized using methods applicable to the performed experiment. Depending on the experimental setup and the size of the project customized data analysis is provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA).
When calling of a particular miRNA failed on an array this is indicated by the acronym null in the row containing this miRNA and in the column corresponding to this array. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 3 or more of the 4 replicated measures of this miRNA were flagged (i.e. the signal is below background) by the image analysis software.
|
| |
|
| Submission date |
Feb 15, 2014 |
| Last update date |
Mar 17, 2015 |
| Contact name |
Howard Fox |
| Organization name |
University of Nebraska Medical Center
|
| Department |
Pharmacology and Experimental Neuroscience
|
| Street address |
985800 Nebraska Medical Center - DRC 3008
|
| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68198-5800 |
| Country |
USA |
| |
|
| Platform ID |
GPL15829 |
| Series (1) |
| GSE55069 |
MicroRNA-21 dysregulates the expression of MEF2C in neurons in monkey and human SIV/HIV neurological disease |
|
