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Sample GSM738297 Query DataSets for GSM738297
Status Public on Dec 01, 2011
Title Embryo-injected-EXP1-rep1
Sample type RNA
Source name Nkx2-5/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 453.878 P 0.000753643
AFFX-BioB-M_at 555.338 P 0.000258358
AFFX-BioB-3_at 454.216 P 5.16732e-05
AFFX-BioC-5_at 1144.76 P 0.00010954
AFFX-BioC-3_at 946.402 P 5.16732e-05
AFFX-BioDn-5_at 2906.55 P 4.42873e-05
AFFX-BioDn-3_at 4287.88 P 6.02111e-05
AFFX-CreX-5_at 14248.1 P 4.42873e-05
AFFX-CreX-3_at 19400.8 P 4.42873e-05
AFFX-DapX-5_at 26.9534 A 0.131361
AFFX-DapX-M_at 110.074 P 0.00499819
AFFX-DapX-3_at 473.344 P 0.000224668
AFFX-LysX-5_at 3.55139 A 0.957038
AFFX-LysX-M_at 58.9309 A 0.275146
AFFX-LysX-3_at 248.914 P 0.000340305
AFFX-PheX-5_at 3.94219 A 0.794288
AFFX-PheX-M_at 4.76879 A 0.904333
AFFX-PheX-3_at 170.315 P 0.00401447
AFFX-ThrX-5_at 7.25289 A 0.921998
AFFX-ThrX-M_at 4.5648 A 0.860518

Total number of rows: 15611

Table truncated, full table size 570 Kbytes.

Supplementary file Size Download File type/resource
GSM738297_MG03X009.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM738297_MG03X009.CHP.gz 86.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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