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Sample GSM325454 Query DataSets for GSM325454
Status Public on Feb 01, 2010
Title Cdx2_E1
Sample type RNA
Source name Cdx2 overexpression
Organism Mus musculus
Characteristics R1 ES cells expressing mouse Cdx2 T2ER fusion
Treatment protocol To induce transgene activity, cells were treated with induction medium (TS medium + 1 µg/mL tamoxifen (Sigma)). For microarray analysis, ES cells were seeded at densities of 2 x 105 cells per gelatinized 35-mm well in ES medium, switched to induction medium the following day, and fed daily for the indicated time period.
Growth protocol To create stably transformed lines, 1-3 x 107 ES cells were electroporated with 20-30 µg plasmid (pCAG-mCdx2ER-ires-puror (Niwa et al., 2005), pCAG-hCdx2ERT2-ires-puror, or pCAG-hGata3ERT2-ires-puror), and seeded on two 10 cm gelatinized plates. Cells were fed with plasmid selection medium (ES medium + 1.2 µg/mL puromycin) until colonies were visible by eye. Colonies were picked and individually expanded on gelatin.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. A second clean up step was done using the RNEasy kit from QIAGEN according to manufactures instructions
Label biotin
Label protocol as per facility protocols
Hybridization protocol as per facility protocols
Scan protocol Gene Chips were scanned using the Hewlett-Packard Gene Array Scanner G2500A.
Description Cdx2 overexpression replicate 1
Data processing The data were analyzed with Expression Console (Affymetrix) using the quartile normalization and PLIER algorithm
Submission date Sep 30, 2008
Last update date Nov 23, 2009
Contact name Brian Joseph Cox
Organization name University of Toronto
Department Physiology
Lab Cox System Biology
Street address 1 King's College Circle, Rm 3360
City Toronto
State/province Ontario
ZIP/Postal code M5S1A8
Country Canada
Platform ID GPL1261
Series (2)
GSE12986 Expression of Cdx2 or Gata3 in R1 mouse embryonic stem cells
GSE12999 Gata3 acts alongside Cdx2 to promote trophoblast gene expression downstream of Tead4 during mouse development

Data table header descriptions
VALUE Quantification

Data table
AFFX-BioB-5_at 886.894
AFFX-BioB-M_at 1022.5
AFFX-BioB-3_at 757.527
AFFX-BioC-5_at 1532.03
AFFX-BioC-3_at 1488.96
AFFX-BioDn-5_at 2867.19
AFFX-BioDn-3_at 6109.64
AFFX-CreX-5_at 15695.5
AFFX-CreX-3_at 14933.8
AFFX-DapX-5_at 34.8487
AFFX-DapX-M_at 48.6431
AFFX-DapX-3_at 12.7672
AFFX-LysX-5_at 13.3416
AFFX-LysX-M_at 57.1041
AFFX-LysX-3_at 35.51
AFFX-PheX-5_at 45.0776
AFFX-PheX-M_at 125.714
AFFX-PheX-3_at 104.048
AFFX-ThrX-5_at 33.4231
AFFX-ThrX-M_at 114.313

Total number of rows: 45101

Table truncated, full table size 850 Kbytes.

Supplementary file Size Download File type/resource
GSM325454.CEL.gz 3.9 Mb (ftp)(http) CEL
GSM325454.chp.gz 325.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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