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Sample GSM738308 Query DataSets for GSM738308
Status Public on Dec 01, 2011
Title Embryo-tail-EXP2-rep2
Sample type RNA
 
Source name no treatment_EXP2
Organism Xenopus laevis
Characteristics development stage: St. 18
tissue: tail section
sample origin/type: single embryo
Extracted molecule total RNA
Extraction protocol Total RNA was collected by homogenization in Invitrogen TRIzol reagent and further purified using an Qiagen RNeasy micro kit.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard 2-cycle Affymetrix protocol from 100ng of total RNA (Expression Analysis Technical Manual, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Xenopus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
Scan protocol GeneChips were scanned using the standard Affymetrix protocol.
Description Gene expression data from tail
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 1000.
 
Submission date Jun 07, 2011
Last update date May 10, 2017
Contact name Marcus Breese
Organization name UCSF
Street address 1550 Fourth St, 382
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL1318
Series (2)
GSE29795 Gene expression profile for X.laevis embryo head vs.tail
GSE29816 Identification of putative targets of Nkx2-5 in Xenopus laevis using gene expression analysis and cross-species.

Data table header descriptions
ID_REF
VALUE MAS5.0 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 1683.14 P 0.0044838
AFFX-BioB-M_at 1645.32 P 0.00255552
AFFX-BioB-3_at 1370.75 P 0.000445901
AFFX-BioC-5_at 3186.47 P 0.00159257
AFFX-BioC-3_at 2518.91 P 0.000340305
AFFX-BioDn-5_at 6295.39 P 7.00668e-05
AFFX-BioDn-3_at 14330.7 P 0.000581214
AFFX-CreX-5_at 32494 P 4.42873e-05
AFFX-CreX-3_at 42558.4 P 4.42873e-05
AFFX-DapX-5_at 107.454 A 0.147939
AFFX-DapX-M_at 120.336 A 0.287743
AFFX-DapX-3_at 321.386 A 0.147939
AFFX-LysX-5_at 11.8286 A 0.876448
AFFX-LysX-M_at 29.3889 A 0.883887
AFFX-LysX-3_at 509.436 P 0.000662269
AFFX-PheX-5_at 16.0147 A 0.860518
AFFX-PheX-M_at 16.0031 A 0.986189
AFFX-PheX-3_at 256.712 A 0.195266
AFFX-ThrX-5_at 20.9789 A 0.9273
AFFX-ThrX-M_at 103.283 A 0.52976

Total number of rows: 15611

Table truncated, full table size 559 Kbytes.




Supplementary file Size Download File type/resource
GSM738308_MG04X006.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM738308_MG04X006.CHP.gz 88.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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