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Sample GSM227964 Query DataSets for GSM227964
Status Public on Nov 01, 2007
Title ventral marginal zone explant
Sample type RNA
 
Source name ventral marginal zone explant from stage 10 Xenopus embryo
Organism Xenopus laevis
Characteristics the ventral marginal zone explant contained ventral marginal zone and a ventral portion of the yolk plug.
Biomaterial provider Nasco
Extracted molecule total RNA
Extraction protocol The dissected explants were homogenized in Stat 60 (TEL TEST), RNA was precipitated by isopropanol, treated with DNase I, and purified using the RNeasy kit (Qiagen).
Label biotin
Label protocol Biotinylated probe was prepared from 100 ng total RNA using the OVATION RNA amplification system (Nugen Technologies, Inc)
 
Hybridization protocol 2.2 micrograms of labeled cDNA in a volume of 200 microliters was hybridized to the Affymetrix Xenopus Genecip in a standard Affymetrix Probe Array Cartridge at 45 degrees , using the fluidics protocol EukGE-WS2v4_450 of a Fluidics Station 450 (Affymetrix) for 18hrs.
Scan protocol the hybridized chip was scanned by Affymetrix GeneChip Scanner 3000 and then processed with Genechip Operating Software.
Description gene expression in ventral marginal zone of stage 10 Xenopus embryo
Data processing Hybridiation controls (bioB, bioC, BioD) and oligo B2 were examined to check the quality of the assay. GAPDH and B-actin were used as the internal control to check 3' to 5' ratios. Global scaling was employed for analysis and the target Intensity value (TGT) was set as 500 following the manual form Affymetrix. Genechip Operating Software (Affymetrix) was used to create CEL files from each experiment and further generate Chip file.
 
Submission date Sep 07, 2007
Last update date Aug 14, 2011
Contact name Hui Zhao
E-mail(s) zhaohui@mail.nih.gov
Phone 301-496-9689
Fax 301-496-0243
Organization name NIH
Department NICHD
Lab LMG
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL1318
Series (1)
GSE8990 Regional gene expression in the Xenopus gastrula

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL Detection
DETECTION P-VALUE Detection P-Value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1162.53 P 4.42873e-05
AFFX-BioB-M_at 2078.29 P 5.16732e-05
AFFX-BioB-3_at 1761.3 P 4.42873e-05
AFFX-BioC-5_at 4323.17 P 4.42873e-05
AFFX-BioC-3_at 2328.44 P 4.42873e-05
AFFX-BioDn-5_at 6307.8 P 4.42873e-05
AFFX-BioDn-3_at 12171.6 P 4.42873e-05
AFFX-CreX-5_at 24072.6 P 4.42873e-05
AFFX-CreX-3_at 34315.8 P 4.42873e-05
AFFX-DapX-5_at 10.3586 A 0.712257
AFFX-DapX-M_at 1.04537 A 0.996792
AFFX-DapX-3_at 22.5251 A 0.250777
AFFX-LysX-5_at 4.62006 A 0.852061
AFFX-LysX-M_at 1.90212 A 0.99238
AFFX-LysX-3_at 1.75632 A 0.916593
AFFX-PheX-5_at 1.71848 A 0.98333
AFFX-PheX-M_at 10.3287 A 0.772383
AFFX-PheX-3_at 1.99519 A 0.937153
AFFX-ThrX-5_at 2.623 A 0.868639
AFFX-ThrX-M_at 1.96389 A 0.891041

Total number of rows: 15611

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM227964.CEL.gz 1.7 Mb (ftp)(http) CEL
GSM227964.CHP.gz 2.5 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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