E-GEOD-2204 - Transcription profiling of mouse ES cells versus XEN cells

Submitted on 28 January 2005, released on 12 June 2008, last updated on 27 March 2012
Mus musculus
Samples (4)
Array (1)
Protocols (2)
Comparison of mouse ES cells and three different XEN cell cultures. Three XEN cell cultures: Two different strains (IM8A1 is PO, and XEN1-3 is ICR). And two different culture conditions (IM8A1-I versus IM8A1-II). Three biological replicates of XEN cell RNA were submitted to the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada) for preparation of cRNA and hybridization to the mouse U74Av2 Affymetrix gene array. QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA) was used to extract total RNA from all samples according to manufacturer's instructions. The samples were (1) XEN1-3 cells at passage 18 (ICR strain, male) cultured on gelatin with 70% EMFI-CM, (2) IM8A1 cells at passage 27 (PO strain) cultured on gelatin with 70% EMFI-CM, (3) IM8A1 cells at passage 27 cultured on tissue culture plastic in RPMI 1640 (Gibco) supplemented with 20% FBS (CanSera, Rexdale, Canada), 1 mM sodium pyruvate, 2 mM L-glutamine, 50 mg/ml each of penicillin/streptomycin (all from Gibco), 100 uM b-mercaptoethanol (Sigma) for 4 days. RNA was also obtained from R1 ES cells grown in the absence of EMFIs in the above medium with LIF.
Experiment types
transcription profiling by array, cell type comparison, growth condition, strain or line
Imprinted X-inactivation in extra-embryonic endoderm cell lines from mouse blastocysts. Tilo Kunath, Danielle Arnaud, Gary D Uy, Ikuhiro Okamoto, Corinne Chureau, Yojiro Yamanaka, Edith Heard, Richard L Gardner, Philip Avner, Janet Rossant. Development 132(7):1649-61 (2005)
Investigation descriptionE-GEOD-2204.idf.txt
Sample and data relationshipE-GEOD-2204.sdrf.txt
Raw data (1)E-GEOD-2204.raw.1.zip
Processed data (1)E-GEOD-2204.processed.1.zip
Array designA-AFFY-6.adf.txt
R ExpressionSetE-GEOD-2204.eSet.r