|
| Status |
Public on Jul 08, 2011 |
| Title |
Patient_15 |
| Sample type |
RNA |
| |
|
| Source name |
primary hepatoblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary hepatoblastoma
histology: Epithelial
main epithelial component: Well differentiated
16-gene classifier: C1
sex: M
chemotheraphy: Yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On average, 30 ug of tissue was homogenized in trizol buffer, and RNA extraction was performed according to maunfacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Refer to Liu et al (PNAS 101: 9740-9744 (2004)). 5 ug of total RNA was labeled in reverse transcription at 37C for 90 mins by using biotin-labeled rand-octomer oligo primer. The RT reaction mix was further denatured by using 0.5 N NaOH / 1 mM EDTA at 65C for 15 mins and neutralized by 1 M Tris HCl pH 7.6. Biotin signal was detected with an Alexa 647-Streptavidin conjugate.
|
| |
|
| Hybridization protocol |
The chips were hybridized on Tecan HS 4800 hybridization station. Chips were pre-hybridized at 25C for 30 min in the buffer of 6x SSPE/ 30% formamide/ 1x Denhardt's solution. The chips were further hybridized with labeled target in 6x SSPE/ 30% formamide at 25C for 18 hr. Hybridization, post-hybridization washing in 0.75x TNT (Tris, sodium, Tween 20) (see PNAS) at 37C for 40 mins. The chips were stained by streptavidin-alexa647 (1:500) dilution in TNT for 30 mins. Post-staining washing in 1x TNT FOR 40 min. Rinse with water and spin dry.
|
| Scan protocol |
Arrays were scanned on the GenePix scanner and analyzed using the GenePix Pro software package.
|
| Data processing |
Raw data were normalized by the print-tip loess method (Hua YJ, Genomics 2008)
|
| |
|
| Submission date |
Mar 19, 2010 |
| Last update date |
Jul 09, 2011 |
| Contact name |
stefano cairo |
| E-mail(s) |
stefano.cairo@gmail.com
|
| Organization name |
Xentech
|
| Street address |
4 rue Pierre Fontaine
|
| City |
Evry |
| ZIP/Postal code |
91000 |
| Country |
France |
| |
|
| Platform ID |
GPL10231 |
| Series (2) |
| GSE20971 |
miRNA expression of human samples of hepatoblastoma (HB) and normal and fetal liver |
| GSE21085 |
Analysis of Hepatoblastoma and normal fetal liver miRNA profiles and HepaRG cells that ectopically express miR-371-3 cluster |
|
