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Sample GSM738307 Query DataSets for GSM738307
Status Public on Dec 01, 2011
Title Embryo-tail-EXP2-rep1
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 1045.68 P 0.00499819
AFFX-BioB-M_at 1283.08 P 0.00179591
AFFX-BioB-3_at 996.105 P 0.000146581
AFFX-BioC-5_at 2618.39 P 0.000581214
AFFX-BioC-3_at 2047.71 P 0.00010954
AFFX-BioDn-5_at 5272.4 P 4.42873e-05
AFFX-BioDn-3_at 10866.9 P 0.000340305
AFFX-CreX-5_at 27757.6 P 5.16732e-05
AFFX-CreX-3_at 45845.6 P 4.42873e-05
AFFX-DapX-5_at 143.821 P 0.0125468
AFFX-DapX-M_at 136.655 A 0.147939
AFFX-DapX-3_at 427.559 P 0.0200219
AFFX-LysX-5_at 16.1447 A 0.645547
AFFX-LysX-M_at 62.0405 A 0.772364
AFFX-LysX-3_at 532.746 P 0.000169227
AFFX-PheX-5_at 8.94267 A 0.814869
AFFX-PheX-M_at 13.1934 A 0.979978
AFFX-PheX-3_at 286.886 A 0.0956669
AFFX-ThrX-5_at 21.6888 A 0.976071
AFFX-ThrX-M_at 85.4168 A 0.645547

Total number of rows: 15611

Table truncated, full table size 561 Kbytes.

Supplementary file Size Download File type/resource
GSM738307_MG04X005.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM738307_MG04X005.CHP.gz 88.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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