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Sample GSM738291 Query DataSets for GSM738291
Status Public on Dec 01, 2011
Title Embryo-control-EXP1-rep1
Sample type RNA
 
Source name GFP injected_EXP1
Organism Xenopus laevis
Characteristics development stage: St. 11.5
tissue: whole embryo
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 whole embryo
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)
GSE29791 Identification of putative targets of Nkx2-5 in Xenopus laevis using gene expression analysis and cross-species annotation
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 459.118 P 0.0012475
AFFX-BioB-M_at 628.645 P 0.000224668
AFFX-BioB-3_at 447.998 P 7.00668e-05
AFFX-BioC-5_at 1155.57 P 8.14279e-05
AFFX-BioC-3_at 1050.14 P 5.16732e-05
AFFX-BioDn-5_at 2827.09 P 4.42873e-05
AFFX-BioDn-3_at 4422.94 P 6.02111e-05
AFFX-CreX-5_at 15514.7 P 4.42873e-05
AFFX-CreX-3_at 22850.1 P 4.42873e-05
AFFX-DapX-5_at 27.2035 A 0.340648
AFFX-DapX-M_at 109.437 P 0.0113844
AFFX-DapX-3_at 439.609 P 0.000753643
AFFX-LysX-5_at 12.3961 A 0.631562
AFFX-LysX-M_at 93.2604 A 0.108979
AFFX-LysX-3_at 293.068 P 9.4506e-05
AFFX-PheX-5_at 2.27503 A 0.937071
AFFX-PheX-M_at 5.46814 A 0.843268
AFFX-PheX-3_at 133.5 P 0.00933744
AFFX-ThrX-5_at 7.7138 A 0.910522
AFFX-ThrX-M_at 52.3261 A 0.382599

Total number of rows: 15611

Table truncated, full table size 569 Kbytes.




Supplementary file Size Download File type/resource
GSM738291_MG03X001.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM738291_MG03X001.CHP.gz 86.6 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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