|
| Status |
Public on Dec 31, 2012 |
| Title |
Pleural and ascites fluids with chylothorax and an ITGA9 G404S mutation before OK-432 Ind-B |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Pleural fluid
|
| Organism |
Homo sapiens |
| Characteristics |
mutation: ITGA9 G404S
treatment: No OK-432 treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lines were lyzed by Trizol® Reagent (Invitrogen, USA) first, and purified by RNeasy Mini Kit (Qiagen, Germany). RNA isolated was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).
|
| Label |
Cy5
|
| Label protocol |
0.2 mg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer, USA) during the in vitro transcription process.
|
| |
|
| Channel 2 |
| Source name |
Ascites fluid
|
| Organism |
Homo sapiens |
| Characteristics |
mutation: ITGA9 G404S
treatment: No OK-432 treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lines were lyzed by Trizol® Reagent (Invitrogen, USA) first, and purified by RNeasy Mini Kit (Qiagen, Germany). RNA isolated was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).
|
| Label |
Cy3
|
| Label protocol |
0.2 mg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer, USA) during the in vitro transcription process.
|
| |
|
| |
| Hybridization protocol |
0.3 mg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a SurePrint G3 Human GE 8×60K oligo microarray (Agilent Technologies, USA) at 65°C for 17 h.
|
| Scan protocol |
Scanned on an Agilent G2565CA scanner, and images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
|
| Description |
Transcriptional profile comparison of the pleural and ascites fluids in a fetal with chylothorax and an ITGA9 G404S mutation before OK-432 treatment
|
| Data processing |
Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Feb 09, 2012 |
| Last update date |
Dec 31, 2012 |
| Contact name |
Gwo-Chin Ma |
| E-mail(s) |
128729@cch.org.tw
|
| Phone |
886-4-7238595
|
| Fax |
886-4-7249847
|
| Organization name |
Changhua Christian Hospital
|
| Department |
Department of Genomic Medicine
|
| Street address |
3F, 176, Zhanghua Rd.
|
| City |
Changhua |
| ZIP/Postal code |
500 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE33872 |
Human fetal chylothorax: pleural fluid vs. ascites fluid |
|
