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Sample GSM216437 Query DataSets for GSM216437
Status Public on Aug 13, 2007
Title Zebrafish-C
Sample type RNA
 
Source name 24 hours post-fertilization embryos
Organism Danio rerio
Characteristics the uninjected embryos
Treatment protocol Selected embryos were transferred to 2 mL Eppendorf tube, rinsed with DEPC-treated water. After discarding water, the Trizol solution (GibcoBRL) was added to Eppendorf tube containing embryos.
Growth protocol Zebrafish embryos were maintained at 28 ± 0.5 °C
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 (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Fifteen microgram aliquants of the fragmented cRNA were hybridized with the D. rerio Genome AFF-F0027 GeneChip® microarray (Affymetrix, CA) in hybridization cocktail. Hybridization was allowed to proceed overnight (16 h) at 45 °C
Scan protocol The distribution of fluorescent material on the array was obtained using GeneChip® Scanner 3000 (Affymetrix, CA)
Description Gene expression data from the uninjected embryos
Data processing The scanned images were firstly assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. A global scaling factor of 500 was used to normalize the different arrays. The differentially expressed genes were judged according to change p-value calculated by GCOS 1.4, and 2-fold change as an empirical criterion.
 
Submission date Aug 08, 2007
Last update date Aug 14, 2011
Contact name M X Chang
E-mail(s) mingxianchang@ihb.ac.cn
Organization name Institute of Hydrobiology, Chinese Academy of Sciences
Lab Laboratory of Fish Diseases
Street address Luojiaashan
City Wuhan
ZIP/Postal code 430072
Country China
 
Platform ID GPL1319
Series (1)
GSE8724 Gene expression analysis in the zebrafish embryos silenced by zfPGRP-SC

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 599.022 P 6.02111e-05
AFFX-BioB-M_at 532.321 P 4.42873e-05
AFFX-BioB-3_at 373.338 P 0.00687065
AFFX-BioC-5_at 987.895 P 4.42873e-05
AFFX-BioC-3_at 1001.36 P 5.16732e-05
AFFX-BioDn-5_at 2815.77 P 4.42873e-05
AFFX-BioDn-3_at 6054.23 P 5.16732e-05
AFFX-CreX-5_at 14694.4 P 4.42873e-05
AFFX-CreX-3_at 21283.1 P 4.42873e-05
AFFX-DapX-5_at 146.133 P 0.000195116
AFFX-DapX-M_at 447.176 P 0.000581214
AFFX-DapX-3_at 767.243 P 9.4506e-05
AFFX-LysX-5_at 45.4828 P 0.0396608
AFFX-LysX-M_at 118.33 P 0.0219019
AFFX-LysX-3_at 273.287 P 0.000195116
AFFX-PheX-5_at 71.2464 P 0.0113844
AFFX-PheX-M_at 57.9166 M 0.0542134
AFFX-PheX-3_at 253.529 P 0.0012475
AFFX-ThrX-5_at 62.6862 A 0.250796
AFFX-ThrX-M_at 105.074 P 0.000581214

Total number of rows: 15617

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM216437.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM216437.CHP.gz 88.0 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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