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Sample GSM218665 Query DataSets for GSM218665
Status Public on Dec 29, 2007
Title MO
Sample type RNA
 
Source name zebrafish embryos at 24 hpf
Organism Danio rerio
Characteristics AB line
Treatment protocol For injection, MOs were at a concentration of about 5ng each embryo. After injection, embryos were incubated at 28.5°C in Embryo Medium. The embryos at 24 hpf were washed with PBS and extracted RNA with Trizol
Growth protocol A breeding colony of zebrafish (Danio rerio) were maintained at 28.5°C on a 14 h (hour) light/10 h dark cycle
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol cRNAs were generated and hybridized on Affymetrix DNA chips according to the Affymetrix protocol, total RNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 37°C on Affymetrix GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneArrayTM scanner 3000.
Description Gene expression data from embryos at 24 hpf injected with DrC1q-like Morpholino
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 500.
 
Submission date Aug 16, 2007
Last update date Aug 14, 2011
Contact name Jie Mei
E-mail(s) kevinmei@ihb.ac.cn
Organization name Institute of Hydrobiology
Department Chinese Academy of Sciences
Lab Wuhan Center for Developmental Biology
Street address 7# Donghu South Road
City Wuhan
State/province Hubei
ZIP/Postal code 430072
Country China
 
Platform ID GPL1319
Series (1)
GSE8800 Expression data from embryos injected with DrC1q-like morpholino and control morpholino

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
Dr.1.1.S1_at 66.0 P 0.001602
Dr.10.1.S1_at 21.5 A 0.267463
Dr.10.4.S1_a_at 26.8 A 0.150527
Dr.100.1.A1_at 72.5 P 0.001602
Dr.1000.1.S1_at 1634.9 P 0.000219
Dr.10000.1.A1_at 7.2 A 0.749276
Dr.10005.1.A1_at 31.8 P 0.039365
Dr.10006.1.A1_at 100.1 P 0.000388
Dr.10010.1.A1_at 25.3 A 0.397994
Dr.10011.1.A1_at 36.2 P 0.017001
Dr.10012.1.A1_at 8.0 A 0.561639
Dr.10014.1.A1_at 6.5 A 0.732537
Dr.10015.1.S1_at 1.5 A 0.978134
Dr.10015.2.S1_a_at 3.4 A 0.901946
Dr.10015.2.S1_at 5.4 A 0.795978
Dr.10016.1.A1_at 125.0 P 0.001602
Dr.10018.1.S1_at 7.8 A 0.641310
Dr.1002.1.S1_at 335.5 P 0.000219
Dr.10022.1.S1_at 25.0 A 0.189687
Dr.10023.1.A1_at 4.1 A 0.872355

Total number of rows: 15502

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM218665.CEL.gz 3.0 Mb (ftp)(http) CEL
GSM218665.EXP.gz 496 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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