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Sample GSM498664 Query DataSets for GSM498664
Status Public on Aug 18, 2010
Title TAIL3_WT
Sample type RNA
 
Source name Zebrafish Tail Mesoderm 21-somite stage
Organism Danio rerio
Characteristics developmental stage: 21-somite
genotype: wild-type
Treatment protocol No treatments were given to the fish -- comparisons were made between wild-type and mutant individuals. Mutants harbored the b104 mutant allele of the transcription factor tbx16/spt.
Growth protocol Fish were grown and cared for following standard techniques (Westerfield M: The zebrafish book: a guide for the laboratory use of zebrafish (Danio rerio): University of Oregon Press Eugene, OR; 1995)
Extracted molecule total RNA
Extraction protocol RNA was extracted using the PicoPure isolation kit (Arcturus)
Label biotin
Label protocol Biotin following standard Affymetrix protocols by the University of Chicago functional genomics core facility
 
Hybridization protocol Following standard Affymetrix protocols by the University of Chicago functional genomics core facility
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
Description Gene expression data from 21-somite stage tail tissue
Data processing Image acquisition and initial array quantification were performed using the Affymetrix Microarray Suite Version 5.0. Subsequent identification of differentially expressed genes between wild-type and mutant tissue was performed using dCHIP with invariant set normalization.
 
Submission date Jan 20, 2010
Last update date Aug 18, 2010
Contact name Rachel Lockridge Mueller
E-mail(s) rlm@colostate.edu
Phone (970) 491-6717
Organization name Colorado State University
Department Biology
Street address 1878 Campus Delivery
City Fort Collins
State/province CO
ZIP/Postal code 80523-1878
Country USA
 
Platform ID GPL1319
Series (1)
GSE19955 Expression data comparing wild-type and spt mutant zebrafish tissues at two developmental time points.

Data table header descriptions
ID_REF
VALUE dCHIP normalized (invariant set) and modeled (PM-only) expression data
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 194.31 P
AFFX-BioB-M_at 174.35 P
AFFX-BioB-3_at 229.15 A
AFFX-BioC-5_at 280.88 P
AFFX-BioC-3_at 411.66 A
AFFX-BioDn-5_at 220.39 P
AFFX-BioDn-3_at 1264.51 P
AFFX-CreX-5_at 1760.96 P
AFFX-CreX-3_at 3832.06 P
AFFX-DapX-5_at 84.59 A
AFFX-DapX-M_at 65.49 A
AFFX-DapX-3_at 61 A
AFFX-LysX-5_at 64.53 A
AFFX-LysX-M_at 137.91 A
AFFX-LysX-3_at 113.35 A
AFFX-PheX-5_at 147.59 A
AFFX-PheX-M_at 70.07 A
AFFX-PheX-3_at 203.78 A
AFFX-ThrX-5_at 126.19 A
AFFX-ThrX-M_at 75.63 A

Total number of rows: 15617

Table truncated, full table size 390 Kbytes.




Supplementary file Size Download File type/resource
GSM498664.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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