|
| Status |
Public on Aug 15, 2007 |
| Title |
24 hours rep 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ischemic rat kidney 24 hours; rat = ARF_3
|
| Organism |
Rattus norvegicus |
| Characteristics |
iscemic rat kidney following 45 min of ischemia and 24 hours after reperfusion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
qiagen RNA extraction kit; manufacturers protocol
|
| Label |
Cy5
|
| Label protocol |
Ovation aminallyl labeling kit, manufactureres protocol
|
| |
|
| Channel 2 |
| Source name |
sham operated rat kidney; rat = sham_3
|
| Organism |
Rattus norvegicus |
| Characteristics |
rat kidney from rat 24 hours following sham-operation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
qiagen RNA extraction kit; manufactures protocol
|
| Label |
Cy3
|
| Label protocol |
ovation aminoallyl labeling kit; manufacturers protocol
|
| |
|
| |
| Hybridization protocol |
100 ng of total RNA was labeled with Cy3 or Cy5. Labeled cDNAs were then concentrated using Microcon YM-30 filters (Millipore, Bedford, MA) and hybridized to a microarray at 65°C for 16 h in a hybridization solution containing mouse Cot-1 DNA, 1 µg/µl poly-dA, 1.14 µg/µl
yeast tRNA, 3.4x SSC, and 0.3% SDS. Slides were washed twice in 2Xssc/0.2% SDS/1 mM DTT and once in 0.2X SSC/1 mM
DTT; slides were dried completely in a 60 degree C oven and prepared for scanning.
|
| Scan protocol |
Slides were scanned using a GenePix 4100A gene scanner; signals were obtained at 635 nm for Cy5 and 532 nm for Cy3.
|
| Description |
This data set corresponds to 1 sample kidney following acute renal failure compared with 1 sample from a sham-operated control. A total of 4 comparisons from 4 different pairs of rats were carried out at 24 hours and 4 comparisons from 4 paris of rats carried out at 7 days following surgery. Raw data is expressed per spot. Data for each gene is derived by combining replicate spots corresponding to each gene. These values are found in the corresponding series files.
|
| Data processing |
Raw data were categorized, selected, and adjusted to yield log-transformed, normalized ratios following the systematic method that was described previously by Liang et al, Physiological Genomics 12:229,2003. Log-transformed ratios were obtained from average signal intensities among replicates for each unique element on the array. Hybridizations were carried using kidney RNA derived from 1-sham and 1 post-ischemic rat; ratios for each unique oligonucleotide element were then averaged across multiple 4 hybridizations at each time point post-surgery (ie., 1 day, 7 day). Mathematical manipulation and averaging of microarray data was facilitated using Stata Intercooled 8.2 (Stata Corp, College Station, TX). Determination of differential expression was based on 95 % C.I. of all ratios.
|
| |
|
| Submission date |
Jan 15, 2007 |
| Last update date |
Feb 15, 2007 |
| Contact name |
David Basile |
| E-mail(s) |
dpbasile@iupui.edu
|
| Phone |
317-278-1565
|
| Fax |
317-274-3318
|
| Organization name |
Indiana University
|
| Department |
Cellular & Integrative Physiology
|
| Street address |
635 Barnhill Drive
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL4748 |
| Series (2) |
| GSE6748 |
renal ischemia vs sham - 24h |
| GSE7040 |
Effects of renal ischemia on angiogenic gene expression |
|
