|
| Status |
Public on Mar 30, 2010 |
| Title |
zMNCs, day 4, replicate B, batch 1 |
| Sample type |
RNA |
| |
|
| Source name |
zebrafish mononuclear myogenic cells from day 4 differentiation
|
| Organism |
Danio rerio |
| Characteristics |
tissue: dorsal muscle
cell type: mononuclear myogenic cells
time point: day 4
initial number of cells plated: 500,000
microarray hybridization date: 8-27-09
microarray data quality: good
microarray scanning scale factor: 4.10
microarray scanning target intensity: 500
microarray batch: 1
|
| Treatment protocol |
Zebrafish mononuclear myogenic cells were differentiated in Differentiation media, Promocell human differentiation media, supplemented with 2% horse serum, 1x antibiotics/antimyocotics, 1x Glutamax.
|
| Growth protocol |
Zebrafish mononuclear myogenic cells were expanded in Promocell growth media, supplemented with 20% FBS, 1x antibiotics/antimycotics, 1x Glutamax, 3 ng/ml rhFGF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zebrafish mononuclear myogenic cells were isolated with Tripure (Roche Applied Sciences) following the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
cRNA was biotin-labeled by the Children's Hospital Boston Molecular Genetics Core Facility.
|
| |
|
| Hybridization protocol |
Affymetrix hybridization protocol for the Zebrafish Whole Genome Arrays, 1 µg of cRNA.
|
| Scan protocol |
Scanning was carried out on an Affymetrix GeneChip® Scanner 3000 7G with autoloader. The scanner settings are included in the 'characteristics' field. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
|
| Description |
Zebrafish mononuclear myogenic cells from dorsal muscle from day 4 differentiation.
D4B_082709
|
| Data processing |
CEL files were inputted into Bioconductor/R to derive Affymetrix Microarray Suite version 5.0 (MAS 5.0)-normalized output.
|
| |
|
| Submission date |
Jan 05, 2010 |
| Last update date |
Jan 08, 2010 |
| Contact name |
Alvin T. Kho |
| E-mail(s) |
alvin_kho@hms.harvard.edu
|
| Phone |
617-919-2182
|
| Organization name |
Boston Children's Hospital
|
| Department |
Informatics Program
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE19754 |
Transcriptome analysis of zebrafish mononuclear myogenic cells (zMNCs) during myogenic differentiation |
|
