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Sample GSM306832 Query DataSets for GSM306832
Status Public on Jul 10, 2009
Title s854 2dpf GFP- Rep1
Sample type RNA
 
Source name Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 2 dpf
Organism Danio rerio
Characteristics Strain: Tg(XlEef1a1:GFP)s854
Age: 2 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 2.392846295
AFFX-BioB-5_at 2.063040559
AFFX-BioB-M_at 2.509309483
AFFX-BioC-3_at 2.077871252
AFFX-BioC-5_at 2.682121192
AFFX-BioDn-3_at 3.84060692
AFFX-BioDn-5_at 2.914828866
AFFX-CreX-3_at 4.398142685
AFFX-CreX-5_at 3.982007533
AFFX-DapX-3_at -0.715395767
AFFX-DapX-5_at -0.690095461
AFFX-DapX-M_at -0.652458708
AFFX-Dr-AB076373-1_at -0.511714611
AFFX-Dr-AF292559-1_at -0.608686465
AFFX-Dr-AF292559-2_s_at -0.825943556
AFFX-Dr-AF292559-3_s_at -0.842883669
AFFX-Dr-AF292559-4_s_at -0.585096311
AFFX-Dr-AF292560-1_s_at -0.554252095
AFFX-Dr-AF298789-1_at -0.460042784
AFFX-Dr-AF323980-1_at -0.824271702

Total number of rows: 15617

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM306832.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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