|
| Status |
Public on Dec 15, 2012 |
| Title |
chronic rejection sample 6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
CAN6
|
| Organism |
Homo sapiens |
| Characteristics |
patient sample: chronic rejection sample 6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The blood was drawn in the presence of sodium heparin. PBMC were isolated by density separation over Ficoll solution. Mononuclear cells at the interface were washed twice with phosphate buffered saline (PBS). Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA).
|
| Label |
Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were used.
|
| Label protocol |
Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions.
|
| |
|
| Channel 2 |
| Source name |
negative control
|
| Organism |
Homo sapiens |
| Characteristics |
reference: negative control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The blood was drawn in the presence of sodium heparin. PBMC were isolated by density separation over Ficoll solution. Mononuclear cells at the interface were washed twice with phosphate buffered saline (PBS). Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions.
|
| |
|
| |
| Hybridization protocol |
We followed Agilent’s hybridization protocol. Equal amounts of the exposed and negative control sample (825 ng) were competitively hybridized onto Agilent Whole 4×44K Human oligonucleotide arrays in a hybridization oven at 65°C for 17 hours. Slides were washed according to the manufacturer’s instructions with washing buffers and finally dipped in Stabilization and Drying Solution (Agilent Technologies, Palo Alto, CA) to protect them from environmental ozone.
|
| Scan protocol |
We followed Agilent’s scan protocol. The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies, Palo Alto, CA), and further processed using Agilent Feature Extraction Software.
|
| Description |
chronic rejection sample
|
| Data processing |
GeneSpring for normalization, normalization methods: per spot: devide by control channel, per chip: normalize to 50th percentile, all values are natural log ratio
|
| |
|
| Submission date |
Jul 15, 2009 |
| Last update date |
Dec 15, 2012 |
| Contact name |
Li Li |
| E-mail(s) |
li.li@mssm.edu
|
| Phone |
6507243765
|
| Organization name |
Stanford University
|
| Department |
Pediatric
|
| Lab |
Sarwal Lab
|
| Street address |
300 pastuer dr.,
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE17068 |
Inducing and Predicting Immune Tolerance After Kidney Transplantation |
|
