|
| Status |
Public on Jul 10, 2009 |
| Title |
s854 6dpf GFP+ Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 6 dpf
|
| Organism |
Danio rerio |
| Characteristics |
Strain: Tg(XlEef1a1:GFP)s854
Age: 6 dpf
FACS: GFP positive
|
| Treatment protocol |
Embryos were washed in 3X in PBST, dissociated in HBBS supplemented with 0.25% Trypsin, 0.1% EDTA, 40 µg/ml Proteinase K, and 10 µg/ml Collagenase using a tissue grinder. Cells were resuspended in TMI Buffer (100 mM NaCl, 5 mM KCL, 5 mM HEPES, pH 7.0, and 1% PEG-20000), passed through a 40 µm cell strainer and FAC sorted based on GFP expression.
|
| Growth protocol |
Homozygous Tg(XlEef1a1:GFP)s854 zebrafish embryos were grown in standard embryo media supplemented with 0.003% 1-phenyl-2-thiourea (PTU) at 1 dpf to suppress pigmentation and autofluorescence.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Absolutely RNA micropreps (Stratagene). RNA quality was assessed on an Agilent BioAnalyzer.
|
| Label |
biotin
|
| Label protocol |
RNA was SPIA amplified into cDNA and labeled with biotin using Ovation (NuGEN) as per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Hybridization cocktail contained 2.2 µg fragmented, biotin-labeled and amplified cDNA, as per manufacturer's protocol (NuGEN). Hybridization protocol used was EukGE-WS2v4 on an Affymetrix GeneChip Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned with an Affymetrix scanner according to the manufacturer's protocol.
|
| Description |
Gastrointestinal organogenesis at different time points in Zebrafish
|
| Data processing |
Expression values were extracted using RMA (http://rmaexpress.bmbolstad.com/). Each array was normalized by log2-transformation, subtraction of median, and division by standard deviation.
|
| |
|
| Submission date |
Jul 21, 2008 |
| Last update date |
Jul 10, 2009 |
| Contact name |
Carsten Stuckenholz |
| E-mail(s) |
cstucken@pitt.edu
|
| Phone |
(412) 648-3159
|
| Fax |
(412) 383-5918
|
| Organization name |
University of Pittsburgh
|
| Department |
Department of Medicine, Division of Hematology and Oncology
|
| Lab |
Bahary
|
| Street address |
3501 Fifth Avenue, Room 5065.5B
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15260 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE12189 |
FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development |
|
