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Sample GSM130398 Query DataSets for GSM130398
Status Public on Jan 31, 2007
Title egy wt sibling embryos at d5, biological rep2
Sample type RNA
 
Source name earl grey embryos at day 4 post fertilization
Organism Danio rerio
Characteristics strain background: AB/WIK, Genotype: egy, Allele: cz3, isolated wt sibling embryos.
Age: 5 days post fertilization
Treatment protocol egy mutant embryos and wild-type siblings were collected in triplicates at the 72 and 120hpf stage and separately processed. After homogenization (Tekmar Tissumizer, Cincinnati, OH), total RNA was extracted by using TRIzol reagent (Invitrogen) and purified on RNeasy resins (Qiagen) according to the manufacturer’s recommendations.
Growth protocol Embryos were obtained by pairwise matings of adult egy heterozygote fish, raised at 28 ºC
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner.
Description Gene expression data from zebrafish wt embryos at day 5 post fertilization.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Aug 24, 2006
Last update date Mar 29, 2007
Contact name Gerhard J Weber
E-mail(s) gweber@enders.tch.harvard.edu
Organization name Children's Hospital Boston, Harvard Medical School
Department Hematology / Oncology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL1319
Series (1)
GSE5586 Expression data from egy wildtype and mutant embryo comparison

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P) or absent (A).

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-3_at 698.3 P
AFFX-BioB-5_at 1101.2 P
AFFX-BioB-M_at 1811.2 P
AFFX-BioC-3_at 1443.5 P
AFFX-BioC-5_at 2073.3 P
AFFX-BioDn-3_at 12049.8 P
AFFX-BioDn-5_at 1890.1 P
AFFX-CreX-3_at 40380.2 P
AFFX-CreX-5_at 21861 P
AFFX-DapX-3_at 17 A
AFFX-DapX-5_at 49.2 A
AFFX-DapX-M_at 48 A
AFFX-Dr-AB076373-1_at 25.8 A
AFFX-Dr-acta1-3_at 127660.1 P
AFFX-Dr-acta1-5_at 23208.5 P
AFFX-Dr-acta1-5_x_at 59794.2 P
AFFX-Dr-acta1-M_at 112482.7 P
AFFX-Dr-AF292559-1_at 34 A
AFFX-Dr-AF292559-2_s_at 1.1 A
AFFX-Dr-AF292559-3_s_at 6.5 A

Total number of rows: 15617

Table truncated, full table size 378 Kbytes.




Supplementary data files not provided

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