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Sample GSM102674 Query DataSets for GSM102674
Status Public on Jul 30, 2006
Title WT 3.5dpf zebrafish muscle 3
Sample type RNA
 
Source name trunk and tail muscle, wildtype siblings 3.5dpf
Organism Danio rerio
Characteristics Wildtype siblings of runzel homozygous mutants on a TU/TL background (mix of homozygous and heterozygous WT)
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 1500.3 P 0.004017
AFFX-BioB-M_at 912.5 P 0.000258
AFFX-BioB-3_at 620.8 P 0.004998
AFFX-BioC-5_at 2552.2 P 0.00011
AFFX-BioC-3_at 2196.8 P 0.00006
AFFX-BioDn-5_at 4140.5 P 0.000044
AFFX-BioDn-3_at 15514.1 P 0.000446
AFFX-CreX-5_at 36664.2 P 0.000044
AFFX-CreX-3_at 37826.2 P 0.000044
AFFX-DapX-5_at 66.8 A 0.327079
AFFX-DapX-M_at 122.5 A 0.354453
AFFX-DapX-3_at 188.1 A 0.368438
AFFX-LysX-5_at 9.7 A 0.945787
AFFX-LysX-M_at 57.2 A 0.686277
AFFX-LysX-3_at 52 A 0.455413
AFFX-PheX-5_at 11.4 A 0.904333
AFFX-PheX-M_at 23.3 A 0.897835
AFFX-PheX-3_at 181.1 A 0.262827
AFFX-ThrX-5_at 58.9 A 0.574038
AFFX-ThrX-M_at 17.1 A 0.645547

Total number of rows: 15617

Table truncated, full table size 514 Kbytes.




Supplementary data files not provided

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