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Sample GSM305690 Query DataSets for GSM305690
Status Public on Jul 01, 2009
Title Ectodermal explant after treatment with beta globin (control), 1st biological replicate
Sample type RNA
Source name Neuralized ectodermal explants from zic1 and beta globin (control) injected embryos
Organism Xenopus laevis
Characteristics Neuralized ectodermal explants free from mesoderm
Treatment protocol Ectodermal explants were harvested from stage 9 embryos injected at the 2 cell stage with hormone-inducible zic1 or beta globin as control, each plus noggin to neuralize the explants. After incubation to the equivalent of stage 12 they were incubated with cycloheximide for 30 min to prevent further protein synthesis, followed by addition of dexamethasone to activate injected hormone-inducible zic1. Three hours later ectodermal explants were harvested and treated with proteinase K.
Extracted molecule total RNA
Extraction protocol RNA extracted with phenol/chloroform and purified by alcohol and sodium acetate precipitation
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol from 2 micrograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Hybridization protocol Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip Xenopus laevis GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GCOS Scanner 3000.
Description gene expression of ectodermal explant expression of zic1 or beta globin control.
Data processing Data was analyzed with Agilent Genespring GX v. 7.3.1 using Affymetrix GCOS generated flag data from scaled CHP files, and RMA-normalized CEL files.
Submission date Jul 15, 2008
Last update date Jul 18, 2008
Contact name Kate McInnerney
Phone 406-994-5666
Fax 406-994-4926
Organization name Montana State University
Department Microbiology
Lab Functional Genomics Facility
Street address 109 Lewis Hall
City Bozeman
State/province MT
ZIP/Postal code 59717
Country USA
Platform ID GPL1318
Series (1)
GSE12128 Expression data from ectodermal explants following activation of hormone-inducible zic1

Data table header descriptions
VALUE RMA normalized

Data table
AFFX-r2-TagA_at 1.152
AFFX-r2-TagB_at 0.988
AFFX-r2-TagC_at 1
AFFX-r2-TagD_at 1
AFFX-r2-TagE_at 1.034
AFFX-r2-TagF_at 1.106
AFFX-r2-TagG_at 1
AFFX-r2-TagH_at 0.884
AFFX-r2-TagIN-3_at 1.055
AFFX-r2-TagIN-5_at 1
AFFX-r2-TagIN-M_at 0.9
AFFX-r2-TagJ-3_at 1
AFFX-r2-TagJ-5_at 1
AFFX-r2-TagO-3_at 1
AFFX-r2-TagO-5_at 0.994
AFFX-r2-TagQ-3_at 1.122
AFFX-r2-TagQ-5_at 1.041
AFFX-ThrX-3_at 0.676
AFFX-ThrX-5_at 0.679
AFFX-ThrX-M_at 0.668

Total number of rows: 15572

Table truncated, full table size 325 Kbytes.

Supplementary file Size Download File type/resource
GSM305690.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM305690.CHP.gz 86.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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