|
| Status |
Public on May 02, 2017 |
| Title |
GH-70 vs. GH-ref |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
GH-70
|
| Organism |
Canis lupus familiaris |
| Characteristics |
breed: Labrador retriever
subject id: individual-70
tissue: liver biopsy
diagnosis: high copper chronic hepatitis (high copper (hC)cH)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction cellLine
|
| Label |
Cy5
|
| Label protocol |
robot amplification and labeling v1.0
|
| |
|
| Channel 2 |
| Source name |
GH-ref
|
| Organism |
Canis lupus familiaris |
| Characteristics |
breed: Labrador retriever
subject id: Pool of 10 individuals
tissue: liver biopsy
diagnosis: healthy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction cellLine
|
| Label |
Cy3
|
| Label protocol |
robot amplification and labeling v1.0
|
| |
|
| |
| Hybridization protocol |
Tecan HS4800 hybridization
|
| Scan protocol |
Scanning of slides using the Agilent G2565BA scanner.
Features were extracted using Imagene software from Biodiscovery.
|
| Data processing |
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009
|
| |
|
| Submission date |
Sep 14, 2016 |
| Last update date |
May 03, 2017 |
| Contact name |
Marian Groot Koerkamp |
| Organization name |
Princess Maxima Center for Pediatric Oncology
|
| Department |
Research
|
| Lab |
Drostlab
|
| Street address |
Heidelberglaan 25
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CS |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL15184 |
| Series (1) |
| GSE86932 |
HF001-A: Gene expression patterns in the progression towards canine copper-associated chronic hepatitis |
|
