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Sample GSM306840 Query DataSets for GSM306840
Status Public on Jul 10, 2009
Title s854 3dpf GFP- Rep2
Sample type RNA
 
Source name Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 3 dpf
Organism Danio rerio
Characteristics Strain: Tg(XlEef1a1:GFP)s854
Age: 3 dpf
FACS: GFP negative
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

Data table header descriptions
ID_REF
VALUE Log2-transformed, centered, and scaled expression values.

Data table
ID_REF VALUE
AFFX-BioB-3_at 2.337707762
AFFX-BioB-5_at 1.977433351
AFFX-BioB-M_at 2.447723119
AFFX-BioC-3_at 2.021801853
AFFX-BioC-5_at 2.655871561
AFFX-BioDn-3_at 3.816665333
AFFX-BioDn-5_at 2.883249555
AFFX-CreX-3_at 4.452825471
AFFX-CreX-5_at 4.032026016
AFFX-DapX-3_at -0.841335418
AFFX-DapX-5_at -0.73929187
AFFX-DapX-M_at -0.69535574
AFFX-Dr-AB076373-1_at -0.661693837
AFFX-Dr-AF292559-1_at -0.473877214
AFFX-Dr-AF292559-2_s_at -0.98275147
AFFX-Dr-AF292559-3_s_at -0.800922731
AFFX-Dr-AF292559-4_s_at -0.628338316
AFFX-Dr-AF292560-1_s_at -0.530910459
AFFX-Dr-AF298789-1_at -0.489850566
AFFX-Dr-AF323980-1_at -0.793888624

Total number of rows: 15617

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM306840.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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