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Sample GSM450375 Query DataSets for GSM450375
Status Public on Feb 25, 2010
Title Zebrafish regenerating heart after 7 days post-amputation - replicate 1 (7DPA1)
Sample type RNA
 
Source name Zebrafish regenerating heart after 7 days post-amputation
Organism Danio rerio
Characteristics protocol: amputated
tissue: heart
time: 7 day post-amputation
Treatment protocol Wild-type AB line zebrafish were maintained at 28.5ºC by standard methods (Raya et al. 2003) in the animal facilities of the Salk Institute for Biological Studies (La Jolla, San Diego, USA) and the Biomedical Research Park in Barcelona (Spain).
Sham-operated and regenerating hearts at 1, 3, 5 and 7 days post-amputation (dpa) were harvested by pulling from the outflow tract and the sinus venosus and put into PBS. Once in PBS, the outflow tract and the atrium were removed and the ventricles were washed from blood by letting it flow into the buffer and gently pressing the tissue.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol reagent (Invitrogen) after disrupting the tissue with RNAse-free pistons (BioBlock) and further homogenization by passing the suspension through a 25G needle and a 1ml syringe. An additional clean-up protocol including DNAse I digestion was performed using RNeasy Mini Kit (Qiagen).
Label biotin
Label protocol The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturers protocols (Affymetrix, Santa Clara, CA) as descrived previously (Virtaneva et al., 2001).
1 to 2 µg of total RNA was used for biotin-cRNA labeling, fragmentation and hybridization onto the Affymetrix GeneChip® Zebrafish Genome Array (Affymetrix).
 
Hybridization protocol 1 to 2 µg of total RNA was used for biotin-cRNA labeling, fragmentation and hybridization onto the Affymetrix GeneChip® Zebrafish Genome Array (Affymetrix).
Scan protocol Default settings for the Affymetrix GeneChip Scanner (7G upgrade)
Description Heart samples from heart-amputated zebrafish 7 days post-amputation.
Data processing Data were processed using the affy and gcrma packages of Bioconductor (Gentleman et al. 2004) in R. Briefly, data were imported in R, and normalized using the gcrma normalization. As data were obtained in 3 batches, a batch correction procedure (Johnson, W. E., C. Li, et al. 2007) was applied in order to homogenize the data.
 
Submission date Sep 07, 2009
Last update date Mar 29, 2010
Contact name Stephanie Boue
Organization name CMRB
Street address Dr Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL1319
Series (1)
GSE17993 Zebrafish heart regeneration

Data table header descriptions
ID_REF
VALUE GCRMA normalized intensity value after batch correction with Combat

Data table
ID_REF VALUE
AFFX-BioB-3_at 8.2116
AFFX-BioB-5_at 8.6451
AFFX-BioB-M_at 8.9922
AFFX-BioC-3_at 8.7418
AFFX-BioC-5_at 9.394
AFFX-BioDn-3_at 12.3145
AFFX-BioDn-5_at 10.534
AFFX-CreX-3_at 13.8379
AFFX-CreX-5_at 13.3995
AFFX-DapX-3_at 4.0444
AFFX-DapX-5_at 3.6534
AFFX-DapX-M_at 3.9864
AFFX-Dr-AB076373-1_at 1.9022
AFFX-Dr-acta1-3_at 10.6212
AFFX-Dr-acta1-5_at 12.4726
AFFX-Dr-acta1-5_x_at 12.856
AFFX-Dr-acta1-M_at 10.1699
AFFX-Dr-AF292559-1_at 1.9436
AFFX-Dr-AF292559-2_s_at 3.8329
AFFX-Dr-AF292559-3_s_at 2.783

Total number of rows: 15617

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM450375.cel.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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