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Sample GSM216439 Query DataSets for GSM216439
Status Public on Aug 13, 2007
Title Zebrafish-PGRP-SC
Sample type RNA
Source name 24 hours post-fertilization embryos
Organism Danio rerio
Characteristics the embryos injected with zfPGRP-SC
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 zfPGRP-SC
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 476.831 P 9.4506e-05
AFFX-BioB-M_at 613.913 P 4.42873e-05
AFFX-BioB-3_at 439.284 P 0.002867
AFFX-BioC-5_at 928.097 P 4.42873e-05
AFFX-BioC-3_at 1003.11 P 5.16732e-05
AFFX-BioDn-5_at 2853.7 P 4.42873e-05
AFFX-BioDn-3_at 5443.46 P 5.16732e-05
AFFX-CreX-5_at 15058.6 P 4.42873e-05
AFFX-CreX-3_at 24241 P 4.42873e-05
AFFX-DapX-5_at 122.123 P 0.00762003
AFFX-DapX-M_at 535.649 P 0.000340305
AFFX-DapX-3_at 982.461 P 5.16732e-05
AFFX-LysX-5_at 50.7882 P 0.0284573
AFFX-LysX-M_at 116.787 P 0.036569
AFFX-LysX-3_at 224.996 P 0.000169227
AFFX-PheX-5_at 54.9524 A 0.131361
AFFX-PheX-M_at 80.3543 P 0.0032123
AFFX-PheX-3_at 177.552 P 0.0020226
AFFX-ThrX-5_at 48.7948 A 0.175307
AFFX-ThrX-M_at 148.31 P 0.00124642

Total number of rows: 15617

Table truncated, full table size 569 Kbytes.

Supplementary file Size Download File type/resource
GSM216439.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM216439.CHP.gz 88.4 Kb (ftp)(http) CHP
GSM216439_zfPGRP-SC_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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