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Sample GSM738309 Query DataSets for GSM738309
Status Public on Dec 01, 2011
Title Embryo-tail-EXP2-rep3
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
VALUE MAS5.0 signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 819.924 P 0.00110197
AFFX-BioB-M_at 1365.64 P 0.000972149
AFFX-BioB-3_at 851.953 P 7.00668e-05
AFFX-BioC-5_at 2195.69 P 0.00010954
AFFX-BioC-3_at 1881.57 P 5.16732e-05
AFFX-BioDn-5_at 4940.11 P 4.42873e-05
AFFX-BioDn-3_at 10285 P 9.4506e-05
AFFX-CreX-5_at 26095.1 P 4.42873e-05
AFFX-CreX-3_at 42371.5 P 4.42873e-05
AFFX-DapX-5_at 85.4275 A 0.175328
AFFX-DapX-M_at 166.388 P 0.0396608
AFFX-DapX-3_at 476.492 P 0.00401721
AFFX-LysX-5_at 11.0008 A 0.897835
AFFX-LysX-M_at 57.8181 A 0.672921
AFFX-LysX-3_at 707.576 P 0.000146581
AFFX-PheX-5_at 6.11893 A 0.876428
AFFX-PheX-M_at 6.99342 A 0.976071
AFFX-PheX-3_at 332.021 M 0.0429619
AFFX-ThrX-5_at 16.135 A 0.986189
AFFX-ThrX-M_at 51.0849 A 0.617401

Total number of rows: 15611

Table truncated, full table size 564 Kbytes.

Supplementary file Size Download File type/resource
GSM738309_MG04X007.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM738309_MG04X007.CHP.gz 87.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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