|
| Status |
Public on Jun 27, 2011 |
| Title |
788_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
788_rep3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary Liver
gender: male
age: 7
ancestry: -0.0222
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from tissue homogenized in TRIzol reagent, followed by a clean up on a Qiagen RNAeasy column as per manufacturers’ instructions. The quality of all total RNA samples was assessed with the Agilent Bio-Analyzer. We required a RNA integrity number (RIN) ≥7 to proceed with labeling.
|
| Label |
Cy3
|
| Label protocol |
cRNA was produced using the Agilent Low-Input Linear amplification and labeling kit. Briefly, reverse transcription was performed on 1 µg of total RNA off an oligo dT primer using a modified MMLV-RT. Linear amplification and Cy3-CTP labeling were performed with T7 RNA polymerase. Labeling reactions were cleaned up with RNAeasy columns and total yield and label incorporation were quantified using a nanodrop spectrophotometer. All reactions were performed after addition of Agilent one-color spike-in RNA mix. The spike-in mix contains 10 different in vitro synthesized viral RNAs that are premixed at different concentrations.
|
| |
|
| Hybridization protocol |
Array hybridizations were performed at The University of Chicago, Argonne National Labs high throughput genome analysis core facility. 1.65 µg of Cy3 labeled cRNA were fragmented, hybridized to Agilent-014850 4x44k array.
|
| Scan protocol |
Slides were scanned according the manufacturers instructions.
|
| Description |
Normal human liver gene expression
|
| Data processing |
Feature intensity was adjusted by subtracting background intensity using the minimum method (Ritchie, Silver et al. 2007), as implemented in limma (Smythe 2005). The distribution of background subtracted intensities from each array was adjusted by quantile normalization between arrays (Bolstad, Irizarry et al. 2003), as implemented in limma.
|
| |
|
| Submission date |
Dec 08, 2010 |
| Last update date |
Jun 27, 2011 |
| Contact name |
Christopher David Brown |
| E-mail(s) |
caseybrown@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Kevin P. White
|
| Street address |
920 E. 58th St., R431
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE25935 |
Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue [Agilent] |
| GSE26106 |
Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue |
|
