NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM306843 Query DataSets for GSM306843
Status Public on Jul 10, 2009
Title s854 4dpf GFP+ Rep1
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 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

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

Data table
ID_REF VALUE
AFFX-BioB-3_at 2.342585647
AFFX-BioB-5_at 2.025045834
AFFX-BioB-M_at 2.508178146
AFFX-BioC-3_at 2.082482223
AFFX-BioC-5_at 2.631116873
AFFX-BioDn-3_at 3.733855222
AFFX-BioDn-5_at 2.845521027
AFFX-CreX-3_at 4.374027361
AFFX-CreX-5_at 3.846350442
AFFX-DapX-3_at -0.724237478
AFFX-DapX-5_at -0.536654273
AFFX-DapX-M_at -0.517288136
AFFX-Dr-AB076373-1_at -0.515499843
AFFX-Dr-AF292559-1_at 0.184017633
AFFX-Dr-AF292559-2_s_at -0.785480605
AFFX-Dr-AF292559-3_s_at -0.523282465
AFFX-Dr-AF292559-4_s_at -0.476711826
AFFX-Dr-AF292560-1_s_at 2.204074401
AFFX-Dr-AF298789-1_at -0.212689599
AFFX-Dr-AF323980-1_at -0.671656853

Total number of rows: 15617

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM306843.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap