E-TABM-163 - Transcription profiling of murine presomitic mesoderms of 17 samples at various time points to identify cyclic genes of the mouse segmentation clock

Status
Released on 6 November 2006, last updated on 2 May 2014
Organism
Mus musculus
Samples (23)
Arrays (2)
Protocols (6)
Description
A microarray time series was generated to identify cyclic genes of the segmentation clock in the mouse. The right posterior half presomitic mesoderms (PSM) from 17 mouse embryos were dissected while the contralateral side of the embryo containing the left PSM was immediately fixed to be analyzed by in situ hybridization using a Lfng probe to order the samples along the segmentation clock oscillation cycle. Probes were produced from RNA extracted from the 17 dissected posterior half PSMs using a two-step amplification protocol and were hybridized to Affymetrix GeneChip MOE430A. The reproducibility of the amplification procedure was initially assessed by comparing array data generated from the right and the left posterior PSM from the same embryo. Because of the symmetry of the paraxial mesoderm along the left-right axis, left and right samples are expected to show overtly similar gene expression. RNA was amplified from three such sample pairs (1, a and b; 2, a and b; 3, a and b) and hybridized on Murine Genome U74Av2 array (MG-U74Av2)
Experiment types
transcription profiling by array, co-expression, development or differentiation, time series
Contact
Citations
A complex oscillating network of signaling genes underlies the mouse segmentation clock. Mary-Lee Dequeant, Earl Glynn, Karin Gaudenz, Matthias Wahl, Jie Chen, Arcady Mushegian, Olivier Pourquie.
Comparison of pattern detection methods in microarray time series of the segmentation clock. Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquié O. :e2856 (2008), Europe PMC 18682743
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-TABM-163.idf.txt
Sample and data relationshipE-TABM-163.sdrf.txt
Raw data (1)E-TABM-163.raw.1.zip
Processed data (1)E-TABM-163.processed.1.zip
Array designsA-AFFY-23.adf.txt, A-AFFY-6.adf.txt
R ExpressionSetE-TABM-163.eSet.r
Links