|
| Status |
Public on May 01, 2013 |
| Title |
Mut+/- rep3 |
| Sample type |
RNA |
| |
|
| Source name |
MMA heterozygote
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
gender: female
genotype/variation: MMA heterozygote
tissue: kidney
diet: high protein diet for 2 months
|
| Treatment protocol |
HP diet for 2 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole kidney tissue total RNA was extracted by Qiagen RNAeazy kit
|
| Label |
Biotin
|
| Label protocol |
Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974) and Affymetrix kit (Cat # 900652).After hybridization, the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
|
| |
|
| Hybridization protocol |
The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human GeneChip 1.0 ST microarrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
|
| Scan protocol |
An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
|
| Description |
CV07_7_(MoGene-1_0-st-v1).rma-gene-default-Signal
|
| Data processing |
Gene expression intensities were calculated using GeneChip Command Console Software (AGCC, v.3.2.4). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software (v.1.2.1) and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
|
| |
|
| Submission date |
Sep 20, 2012 |
| Last update date |
May 01, 2013 |
| Contact name |
abdel elkahloun |
| E-mail(s) |
[email protected]
|
| Organization name |
nih
|
| Street address |
50 south dr
|
| City |
bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE41044 |
Targeting proximal tubule mitochondrial dysfunction attenuates the renal disease of methylmalonic acidemia |
|
