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Sample GSM306838 Query DataSets for GSM306838
Status Public on Jul 10, 2009
Title s854 3dpf GFP- Rep1
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 2.711168024
AFFX-BioB-5_at 2.338756334
AFFX-BioB-M_at 2.848402082
AFFX-BioC-3_at 2.38790363
AFFX-BioC-5_at 3.028839257
AFFX-BioDn-3_at 4.046439983
AFFX-BioDn-5_at 3.230848879
AFFX-CreX-3_at 4.631279827
AFFX-CreX-5_at 4.217394966
AFFX-DapX-3_at -0.826365936
AFFX-DapX-5_at -0.671445758
AFFX-DapX-M_at -0.73815688
AFFX-Dr-AB076373-1_at -0.602953589
AFFX-Dr-AF292559-1_at -0.561966286
AFFX-Dr-AF292559-2_s_at -0.958825365
AFFX-Dr-AF292559-3_s_at -0.846555826
AFFX-Dr-AF292559-4_s_at -0.700190321
AFFX-Dr-AF292560-1_s_at -0.640566427
AFFX-Dr-AF298789-1_at -0.534196101
AFFX-Dr-AF323980-1_at -0.826365936

Total number of rows: 15617

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM306838.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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