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Sample GSM102667 Query DataSets for GSM102667
Status Public on Jul 30, 2006
Title Ruz 3.5dpf zebrafish muscle 3
Sample type RNA
 
Source name Trunk and tail muscle, runzel mutant 3.5 dpf
Organism Danio rerio
Characteristics Runzel homozygous mutant on a TU/TL background
3.5 dpf
Biomaterial provider Tuebingen
Extracted molecule total RNA
Extraction protocol At 3-3.5 dpf (at the onset of the visible phenotype), runzel mutants (ruz) and wildtype siblings (WT) were quickly dissected to remove head, heart and gut from skeletal muscle of the trunk and tail. Pooled muscle was homogenized by douncing in Buffer RLT (Qiagen) and centrifuging through a QiaShredder column (Qiagen). RNA was extracted from homogenate using either the Qiagen RNeasy or RNeasy Micro kit with an on-column DNase step according to manufacturer instructions.
Label Biotin
Label protocol cRNA was produced by the Microarray Core Facility (Children's Hospital, Boston) and hybridized to Affymetrix Zebrafish Genome Arrays as previously described (Shepard et al., 2005).
 
Hybridization protocol cRNA was produced by the Microarray Core Facility (Children's Hospital, Boston) and hybridized to Affymetrix Zebrafish Genome Arrays as previously described (Shepard et al., 2005).
Description Arrays were scanned in an Affymetrix/GeneChip Scanner 3000 and the resulting signals quantified and stored using default parameters of the Affymetrix GeneChip Operating Software Version 1.2. All data were in accordance with set limits provided by Affymetrix.
Data processing Affymetrix default parameters
 
Submission date Mar 30, 2006
Last update date Mar 31, 2006
Contact name Leta S Steffen
E-mail(s) leta_steffen@student.hms.harvard.edu
Organization name Harvard Medical School, Children's Hospital
Department Program in Genomics
Lab Louis M Kunkel
Street address 320 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL1319
Series (1)
GSE4585 The zebrafish runzel mutant results in a novel muscular dystrophy phenotype due to a titin mutation

Data table header descriptions
ID_REF
VALUE GCOSv1.2-calculated Signal intensity
ABS_CALL Automated calls by Affymetrix software for presence/absence/marginal/no_call threshold
DETECTION P-VALUE Affymetrix software call; p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1095.1 P 0.012547
AFFX-BioB-M_at 796.2 P 0.002556
AFFX-BioB-3_at 588.9 M 0.042962
AFFX-BioC-5_at 2473.2 P 0.000169
AFFX-BioC-3_at 2290.8 P 0.00006
AFFX-BioDn-5_at 3873.6 P 0.000044
AFFX-BioDn-3_at 13999.8 P 0.00039
AFFX-CreX-5_at 34261.2 P 0.000052
AFFX-CreX-3_at 45779.7 P 0.000044
AFFX-DapX-5_at 98.3 A 0.313708
AFFX-DapX-M_at 185.8 A 0.287743
AFFX-DapX-3_at 30.1 A 0.932322
AFFX-LysX-5_at 15.5 A 0.941556
AFFX-LysX-M_at 98.7 A 0.645547
AFFX-LysX-3_at 129 A 0.139482
AFFX-PheX-5_at 11.4 A 0.960339
AFFX-PheX-M_at 31.1 A 0.937071
AFFX-PheX-3_at 190.5 A 0.262827
AFFX-ThrX-5_at 73.9 A 0.737173
AFFX-ThrX-M_at 66.5 A 0.5

Total number of rows: 15617

Table truncated, full table size 514 Kbytes.




Supplementary data files not provided

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