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Sample GSM280429 Query DataSets for GSM280429
Status Public on Apr 09, 2008
Title Danio_Brain_Starved_1 (X2BS1)
Sample type RNA
 
Source name Brain
Organism Danio rerio
Characteristics Strain: Scientific Hatcheries, Sex: Female, N: 3 fish, Birthdate: 10252005, Start date: 432006, Mean Mass: 265.3, Mean Length: 25.7, Mean SGR: -0.907, Mean GSI: 0.055
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 X2BS1
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 6.331305586
AFFX-BioB-5_at 7.025070726
AFFX-BioB-M_at 6.775219464
AFFX-BioC-3_at 7.919071283
AFFX-BioC-5_at 7.869893657
AFFX-BioDn-3_at 10.34389783
AFFX-BioDn-5_at 9.369257635
AFFX-CreX-3_at 12.36302144
AFFX-CreX-5_at 11.43117206
AFFX-DapX-3_at 7.638015835
AFFX-DapX-5_at 5.514439641
AFFX-DapX-M_at 6.761296781
AFFX-Dr-AB076373-1_at 3.402309754
AFFX-Dr-acta1-3_at 7.912037253
AFFX-Dr-acta1-5_at 5.380356016
AFFX-Dr-acta1-5_x_at 6.232400909
AFFX-Dr-acta1-M_at 5.962949338
AFFX-Dr-AF292559-1_at 2.857683585
AFFX-Dr-AF292559-2_s_at 2.611509417
AFFX-Dr-AF292559-3_s_at 2.678852543

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM280429.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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