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Sample GSM738293 Query DataSets for GSM738293
Status Public on Dec 01, 2011
Title Embryo-control-EXP1-rep3
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
VALUE MAS5.0 signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 387.845 P 0.000753643
AFFX-BioB-M_at 625.041 P 0.00010954
AFFX-BioB-3_at 524.888 P 4.42873e-05
AFFX-BioC-5_at 1221.63 P 7.00668e-05
AFFX-BioC-3_at 1244.04 P 4.42873e-05
AFFX-BioDn-5_at 2642.59 P 4.42873e-05
AFFX-BioDn-3_at 4332.56 P 7.00668e-05
AFFX-CreX-5_at 15424.4 P 4.42873e-05
AFFX-CreX-3_at 22496.7 P 5.16732e-05
AFFX-DapX-5_at 17.531 A 0.60308
AFFX-DapX-M_at 111.941 P 0.00762003
AFFX-DapX-3_at 512.891 P 0.000224668
AFFX-LysX-5_at 16.7347 A 0.645547
AFFX-LysX-M_at 92.2171 A 0.165861
AFFX-LysX-3_at 292.033 P 0.000169227
AFFX-PheX-5_at 18.9257 A 0.48511
AFFX-PheX-M_at 4.76593 A 0.860518
AFFX-PheX-3_at 201.577 P 0.0020226
AFFX-ThrX-5_at 6.93545 A 0.984817
AFFX-ThrX-M_at 13.1902 A 0.804734

Total number of rows: 15611

Table truncated, full table size 569 Kbytes.

Supplementary file Size Download File type/resource
GSM738293_MG03X004.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM738293_MG03X004.CHP.gz 86.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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