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Sample GSM216438 Query DataSets for GSM216438
Status Public on Aug 13, 2007
Title Zebrafish-control siRNA
Sample type RNA
Source name 24 hours post-fertilization embryos
Organism Danio rerio
Characteristics the embryos injected with the control siRNA
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 embryos injected with the control siRNA
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 Jan 04, 2012
Contact name M X Chang
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
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 397.557 P 6.02111e-05
AFFX-BioB-M_at 512.3 P 7.00668e-05
AFFX-BioB-3_at 367.659 P 0.00401721
AFFX-BioC-5_at 909.106 P 5.16732e-05
AFFX-BioC-3_at 783.2 P 4.42873e-05
AFFX-BioDn-5_at 2096.92 P 4.42873e-05
AFFX-BioDn-3_at 4635.5 P 5.16732e-05
AFFX-CreX-5_at 11789 P 4.42873e-05
AFFX-CreX-3_at 17267.6 P 4.42873e-05
AFFX-DapX-5_at 95.0138 P 0.0020226
AFFX-DapX-M_at 476.758 P 0.000195116
AFFX-DapX-3_at 896.624 P 6.02111e-05
AFFX-LysX-5_at 39.568 P 0.0336773
AFFX-LysX-M_at 82.1319 A 0.139482
AFFX-LysX-3_at 215.276 P 4.42873e-05
AFFX-PheX-5_at 74.2836 P 0.036569
AFFX-PheX-M_at 85.7229 P 0.0020226
AFFX-PheX-3_at 149.637 P 0.000972149
AFFX-ThrX-5_at 41.3185 A 0.227636
AFFX-ThrX-M_at 89.7701 P 0.002021

Total number of rows: 15617

Table truncated, full table size 570 Kbytes.

Supplementary file Size Download File type/resource
GSM216438.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM216438.CHP.gz 88.1 Kb (ftp)(http) CHP
GSM216438_control_siRNA_vs_C.CHP 488.9 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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