|
| Status |
Public on Jan 01, 2013 |
| Title |
BC-BMMSC low-passage injected, zebrafish array |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
BC-BMMSC low in zebrafish
|
| Organisms |
Danio rerio; Mus musculus |
| Characteristics |
cell line: BC-BMMSC
passage: p14
tissue: Mesenchymal stem cells
strain: BALB/C
|
| Growth protocol |
Zebrafish embryos were kept for a maximum of 5 days in egg water at 28.5 degrees celcius.
Cells were cultured in Alpha-MEM supplemented with 10% FBS, 2% Glutamax and 2% Penicillin/Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using miRNeasy Mini Kit (Qiagen) following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
From each sample 500 ng of total RNA was amplified with the Quick Amp Labeling Kit (Agilent Technologies) after adding spike-ins (Two-Colour RNAS Spike-In Kit, Agilent Technologies). After column purification the yield and quality were assessed with Nanodrop ND-1000 (Isogen) and a 2100 Bioanalyzer (Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
Total RNA from pooled zebrafish embryos injected with mouse MSCs
|
| Organisms |
Danio rerio; Mus musculus |
| Characteristics |
strain: Mixed
passage: Mixed
tissue: Pooled embryos and cell lines
|
| Growth protocol |
Zebrafish embryos were kept for a maximum of 5 days in egg water at 28.5 degrees celcius.
Cells were cultured in Alpha-MEM supplemented with 10% FBS, 2% Glutamax and 2% Penicillin/Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using miRNeasy Mini Kit (Qiagen) following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
From each sample 500 ng of total RNA was amplified with the Quick Amp Labeling Kit (Agilent Technologies) after adding spike-ins (Two-Colour RNAS Spike-In Kit, Agilent Technologies). After column purification the yield and quality were assessed with Nanodrop ND-1000 (Isogen) and a 2100 Bioanalyzer (Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
Each zebrafish 4x44k array (Design ID: 021626) was hybridized with 825 ng Cy5-labelled pooled material which was mixed by samples of all injected zebrafish (common reference channel) and 825 ng Cy3-labelled material (test channel). Each mouse 4x44k array (Design ID: 026687) was hybridized with 825 ng Cy5-labelled pooled material which was mixed by samples of different mouse MSCs (common reference channel) and 825 ng Cy3-labelled material for cultured cells or 5x825 ng Cy3-labelled material for zebrafish injected with mouse cells (test channel) because of the low amounts of mouse cells in the injected zebrafish. Hybridization and washing were performed according to the manufacturer’s instruction (Two-Colour Microarray-Based Gene Expression Protocol Manual version 5.5, Agilent Technologies).
|
| Scan protocol |
Slides were scanned with an Agilent G2505C scanner at 2 µm resolution and 20 bit scan-depth.
Data were extracted with Feature Extraction version 10.7.3.1.
|
| Description |
Biological replicate of sample GSM802542
|
| Data processing |
Data analysis was performed using Agilent GeneSpring 11.0 software (Agilent Technologies) for fold change analysis.
|
| |
|
| Submission date |
Sep 27, 2011 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Alex B Mohseny |
| E-mail(s) |
b.mohseny@lumc.nl
|
| Phone |
+31 71 5266528
|
| Fax |
+31 71 5248158
|
| Organization name |
LUMC
|
| Department |
Pathology
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| ZIP/Postal code |
2333 ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL14629 |
| Series (1) |
| GSE32428 |
Mouse and zebrafish genes in vitro and in vivo |
|
