GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM738310 Query DataSets for GSM738310
Status Public on Dec 01, 2011
Title Embryo-tail-EXP2-rep4-pooled
Sample type RNA
Source name no treatment_EXP2
Organism Xenopus laevis
Characteristics development stage: St. 18
tissue: tail section
sample origin/type: pooled embryos
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 pooled tails
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 798.6 P 0.000753643
AFFX-BioB-M_at 1165.17 P 0.000753643
AFFX-BioB-3_at 989.791 P 8.14279e-05
AFFX-BioC-5_at 2063.53 P 0.000195116
AFFX-BioC-3_at 1982.67 P 4.42873e-05
AFFX-BioDn-5_at 4780.75 P 4.42873e-05
AFFX-BioDn-3_at 10561.1 P 8.14279e-05
AFFX-CreX-5_at 27401.8 P 4.42873e-05
AFFX-CreX-3_at 39927.1 P 4.42873e-05
AFFX-DapX-5_at 14.0213 A 0.645547
AFFX-DapX-M_at 138.927 M 0.0464673
AFFX-DapX-3_at 341.745 P 0.0138105
AFFX-LysX-5_at 15.5843 A 0.737173
AFFX-LysX-M_at 71.5204 A 0.5
AFFX-LysX-3_at 468.316 P 7.00668e-05
AFFX-PheX-5_at 3.24713 A 0.98333
AFFX-PheX-M_at 13.5009 A 0.910522
AFFX-PheX-3_at 261.748 A 0.0726999
AFFX-ThrX-5_at 14.1563 A 0.960339
AFFX-ThrX-M_at 72.7893 A 0.51489

Total number of rows: 15611

Table truncated, full table size 565 Kbytes.

Supplementary file Size Download File type/resource
GSM738310_MG04X008.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM738310_MG04X008.CHP.gz 86.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap