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Sample GSM912685 Query DataSets for GSM912685
Status Public on Nov 01, 2012
Title Metabolic memory 48h rep 2
Sample type RNA
 
Source name Caudal fin of Danio rerio
Organism Danio rerio
Characteristics disease state: Metabolic memory
time (post amputation): 48h
tissue: caudal fin
Treatment protocol Fish were anesthetized by placing them in 1:1000 2-phenoxyethanol for 1-2 minutes. 0.3% streptozocin solution in 5mM citrate buffer, pH 5.0 to a dose of 350 mg/kg was injected in the dorsal half of the fin with a PLI-90 injector (Harvard Biosciences, Inc., MA). The drug was injected on days 1,3,5, 12 and 19 of the experiment. This was followed by 60 days of keeping the fish without the drug. Control fish were injected with a like volume of citrate buffer.
Growth protocol Wild-type zebrafish were maintained under standard laboratory conditions using a light schedule of 14 h on and 10 h off at a temperature of 28.5°C. Fish were fed twice daily using a combination of dry food and brine shrimp.
Extracted molecule total RNA
Extraction protocol For each time point, triplicate samples from 15 caudal fins were collected and immediately placed into Triazol. The samples were homogenizedand then centrifuged. The RNA was extracted from the supernatant using the purelink RNA mini-kit (Life Technologies Corporation, Carlsbad, CA) according to the manufacturer's protocol.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the GeneChip® Scanner 3000 7G
Description Gene expression data from regenerating caudal fin of Danio rerio
Data processing The data were analyzed with Partek GS 6.5 software (St. Louis, MO) using GCRMA normalization algorithm
 
Submission date Apr 11, 2012
Last update date Nov 01, 2012
Contact name Alexey Aleksandrovich Leontovich
E-mail(s) leontovich.alexey@mayo.edu
Phone 507-284-4850
Organization name Mayo Clinic
Department Health Science Research
Lab Biomedical Statistics and Informatics
Street address 200 First street
City Rochester
State/province MN
ZIP/Postal code 55902
Country USA
 
Platform ID GPL1319
Series (2)
GSE37163 Gene expression data from time course of fin regeneration in Danio rerio (part 1)
GSE37165 Gene expression data from time course of fin regeneration in Danio rerio

Data table header descriptions
ID_REF
VALUE GCRMA normalized, background corrected Log base 2 transformed values

Data table
ID_REF VALUE
AFFX-BioB-3_at 6.3838
AFFX-BioB-5_at 7.00591
AFFX-BioB-M_at 7.88738
AFFX-BioC-3_at 7.87782
AFFX-BioC-5_at 8.24273
AFFX-BioDn-3_at 10.8296
AFFX-BioDn-5_at 10.0235
AFFX-CreX-3_at 13.454
AFFX-CreX-5_at 13.0465
AFFX-DapX-3_at 8.48707
AFFX-DapX-5_at 6.8418
AFFX-DapX-M_at 7.63501
AFFX-Dr-AB076373-1_at 1.73412
AFFX-Dr-AF292559-1_at 1.85351
AFFX-Dr-AF292559-2_s_at 3.71138
AFFX-Dr-AF292559-3_s_at 3.04579
AFFX-Dr-AF292559-4_s_at 1.70392
AFFX-Dr-AF292560-1_s_at 2.66533
AFFX-Dr-AF298789-1_at 1.97669
AFFX-Dr-AF323980-1_at 2.36863

Total number of rows: 15617

Table truncated, full table size 375 Kbytes.




Supplementary file Size Download File type/resource
GSM912685_Jjn010629-Zebrafish.cel.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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