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Sample GSM102665 Query DataSets for GSM102665
Status Public on Jul 30, 2006
Title Ruz 3.5dpf zebrafish muscle 1
Sample type RNA
 
Source name Trunk and tail muscle, runzel mutant, 3.5dpf
Organism Danio rerio
Characteristics Danio rerio Ruz homozygous mutant on a TL/TU background
3.5dpf
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 616.8 A 0.156732
AFFX-BioB-M_at 849.9 P 0.039661
AFFX-BioB-3_at 580 A 0.131361
AFFX-BioC-5_at 2072.4 P 0.000754
AFFX-BioC-3_at 1220.6 P 0.000297
AFFX-BioDn-5_at 2274.6 P 0.000044
AFFX-BioDn-3_at 12325.3 P 0.000857
AFFX-CreX-5_at 27669.7 P 0.000044
AFFX-CreX-3_at 36561.6 P 0.000044
AFFX-DapX-5_at 279.5 M 0.046482
AFFX-DapX-M_at 208.4 A 0.185131
AFFX-DapX-3_at 107.1 A 0.672921
AFFX-LysX-5_at 30.7 A 0.941556
AFFX-LysX-M_at 324.3 A 0.470241
AFFX-LysX-3_at 64.1 A 0.672921
AFFX-PheX-5_at 31.4 A 0.891021
AFFX-PheX-M_at 153.1 A 0.760937
AFFX-PheX-3_at 289.9 A 0.216524
AFFX-ThrX-5_at 55 A 0.772364
AFFX-ThrX-M_at 70.6 A 0.672921

Total number of rows: 15617

Table truncated, full table size 514 Kbytes.




Supplementary data files not provided

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