|
| Status |
Public on Aug 10, 2011 |
| Title |
Mouse_sham_1 |
| Sample type |
RNA |
| |
|
| Source name |
whole liver RNA, control
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
tissue: liver
cell type: endothelial cells
treatment: sham surgery
phenoytpe: no cirrhosis
|
| Treatment protocol |
Common bile duct ligation or sham surgery.
|
| Growth protocol |
Standard mouse housing conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miR-VANA miRNA Isolation Kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
GeneChip® One-Cycle Target Labeling.
|
| |
|
| Hybridization protocol |
GeneChip® Hybridization.
|
| Scan protocol |
Affymetrix® GeneChip® Scanner.
|
| Description |
miRNA expression.
|
| Data processing |
Data were analyzed using the Affymetrix® miRNA QC Tool Software using the default analysis.
Probe-specific signal detection calls: Each probe on an array is assayed for detection. For miRNA probes, detection is based on a Wilcoxon Rank-Sum test of the miRNA probe set signals compared to the distribution of signals from GC-content-matched anti-genomic probes. If the resulting p-value for the probes is p=0.06, it is considered “detected above background”.
Background estimation and correction: The same set of anti-genomic probes used to determine detection calls are used to estimate GC-content-matched background signals. Each miRNA probe signal has a GC-content-matched background estimate subtracted from its value. This GC-specific background contribution is estimated by the median signal from the distribution of GC-matched anti-genomic probes. The resulting value may be negative at this stage, if the probe’s signal is less than the median value of the GC-matched anti-genomic probes. The same process can be applied using two other ways to match main content probes to background probes: a) by GC percent and b) by both GC content and probe length.
Constant Variance Stabilization on probes: Probe level constant variance stabilization is based on adding a small constant to all of the intensities. The default value of this constant is 16.
Normalization: Probe-level normalization is provided via quantile, mean array scaling, and mean array scaling (based on normalization probes) normalization algorithms.
Summarization: This process provides the quantification of probe intensities into probe set intensities (via mean, median or RMA methods).
|
| |
|
| Submission date |
Aug 09, 2011 |
| Last update date |
Aug 10, 2011 |
| Contact name |
Robert Christian Huebert |
| Organization name |
Mayo Clinic
|
| Department |
Gastroenterology and Hepatology
|
| Lab |
Vijay Shah
|
| Street address |
200 1st Street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL8786 |
| Series (1) |
| GSE31293 |
MicroRNA Expression Data From Sham or BDL CD1 Mouse Liver |
|
