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Sample GSM306848 Query DataSets for GSM306848
Status Public on Jul 10, 2009
Title s854 4dpf GFP- Rep3
Sample type RNA
 
Source name Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 4 dpf
Organism Danio rerio
Characteristics Strain: Tg(XlEef1a1:GFP)s854
Age: 4 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 2.431378087
AFFX-BioB-5_at 2.102096441
AFFX-BioB-M_at 2.61188035
AFFX-BioC-3_at 2.162941687
AFFX-BioC-5_at 2.729396251
AFFX-BioDn-3_at 3.790225484
AFFX-BioDn-5_at 3.028511209
AFFX-CreX-3_at 4.329811728
AFFX-CreX-5_at 4.014123
AFFX-DapX-3_at -0.798252179
AFFX-DapX-5_at -0.716936426
AFFX-DapX-M_at -0.719758562
AFFX-Dr-AB076373-1_at -0.537330305
AFFX-Dr-AF292559-1_at -0.722592181
AFFX-Dr-AF292559-2_s_at -0.869864854
AFFX-Dr-AF292559-3_s_at -0.823225576
AFFX-Dr-AF292559-4_s_at -0.64794668
AFFX-Dr-AF292560-1_s_at 0.369316437
AFFX-Dr-AF298789-1_at -0.55162077
AFFX-Dr-AF323980-1_at -0.855971906

Total number of rows: 15617

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM306848.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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