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Sample GSM280427 Query DataSets for GSM280427
Status Public on Apr 09, 2008
Title Danio_Brain_Control_3 (X2BC3)
Sample type RNA
 
Source name Brain
Organism Danio rerio
Characteristics Strain: Scientific Hatcheries, Sex: Female, N: 3 fish, Birthdate: 8172005, Start date: 432006, Mean Mass: 452.8, Mean Length: 26.4, Mean SGR: 0.148, Mean GSI: 0.123
Treatment protocol Groups of eight females of the same age were randomly assigned to each of twelve 3-L tanks (10 cm wide x 15 cm tall x 25 cm deep) arranged on the same shelf of a flow-through rearing system. Test tanks were assigned to starved or control treatments in an alternating manner so that treatments were uniformly distributed across fish ages and tank location. Fish in the starved treatment received no food for 21 days, while fish in the control treatment continued to be fed to apparent satiety three times daily.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA) following the manufacturer's protocol. After extraction, RNA from three fish was pooled for each tank for analysis.
Label Biotin
Label protocol For each array, up to 10 ug of total RNA were converted to cDNA. Biotinylated cRNA was then produced in vitro using the GeneChip Expression 3' amplification one-cycle target labeling kit (Affymetrix).
 
Hybridization protocol Microarrays were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 r.p.m.), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody. This was followed by another round of SAPE prior to scanning using a GeneChip Scanner 3000 (Affymetrix).
Scan protocol Scanned using a GeneChip Scanner 3000 (Affymetrix).
Description X2BC3
Data processing All analyses of microarray data were conducted using Bioconductor for R (www.R-project.org). Data for brain and liver were normalized and analyzed separately because variances of expression differed considerably between the tissues. The microarray data were filtered as described by Robison et al. (2008). Filtered probesets were then normalized using Robust Multiarray Average (RMA).
 
Submission date Apr 09, 2008
Last update date Apr 09, 2008
Contact name Robert Edward Drew
E-mail(s) rdrew@uidaho.edu
Phone 208-885-8478
Fax 208-885-7905
Organization name University of Idaho
Department Biological Sciences
Lab Robison
Street address Life Sciences South Rm 252
City Moscow
State/province ID
ZIP/Postal code 83844-3051
Country USA
 
Platform ID GPL1319
Series (1)
GSE11107 Effect of starvation on the transcriptomes of the brain and liver in adult female zebrafish (Danio rerio)

Data table header descriptions
ID_REF
VALUE RMA Normalized Log2 data

Data table
ID_REF VALUE
AFFX-BioB-3_at 6.421162787
AFFX-BioB-5_at 7.127647925
AFFX-BioB-M_at 6.880242435
AFFX-BioC-3_at 8.126591177
AFFX-BioC-5_at 7.986209427
AFFX-BioDn-3_at 10.42167501
AFFX-BioDn-5_at 9.495471332
AFFX-CreX-3_at 12.54132005
AFFX-CreX-5_at 11.54343963
AFFX-DapX-3_at 7.893730961
AFFX-DapX-5_at 5.821407009
AFFX-DapX-M_at 6.899803614
AFFX-Dr-AB076373-1_at 3.276672749
AFFX-Dr-acta1-3_at 9.443548887
AFFX-Dr-acta1-5_at 5.025774698
AFFX-Dr-acta1-5_x_at 6.475984889
AFFX-Dr-acta1-M_at 7.920590449
AFFX-Dr-AF292559-1_at 2.943307618
AFFX-Dr-AF292559-2_s_at 2.561970142
AFFX-Dr-AF292559-3_s_at 2.662631348

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM280427.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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