Transcriptomics

Dataset Information

62

Kidney development time course


ABSTRACT: Array Design; Mouse Compugen 22K Spotted Oligo Author; Sean Grimmond Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene) Concentration; 100 Data processing/normalization; Lowess Normalisation GeneSpring) Developmental Stage; embryonic Diseased/Normal; normal Dye Swap; red/green Experiment Type; time course Genetic Characteristic; Wild type Image Analysis Software; Imagene5.5 (Biodiscovery) Labeling Protocol; Amino Allyl Message Amp- Ambion Organ/Organism part; kidney Organism; Mus Musculus RNA type; aRNA Message Amp-ambion Tissue Type; Pool of whole organs Organization; IMB, Uni of QLD, Brisbane Australia Sample Source; primary tissue Sampling Method; Dissection of whole organ Sex; Pool of both sexes Strain/Cell-line; CD1 Series_overall_design: To account for dye swap, the signal channel and control channel measurements for each sample were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Specific samples were normalized to one another: sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples. Keywords: time-course

ORGANISM(S): Musculus  

SUBMITTER: Daniela E Myers   Ana del Pilar Cintron  Sean M Grimmond  Penglin Ma  Darrin F Taylor  Kelly J Sittler  Shuibang Wang  Robert L Danner  Xiaolin Cui  Peter J Munson  Jianhua Zhang  Ilana G Goldberg  Jennifer J Barb  J. Philip McCoy 

PROVIDER: E-GEOD-2282 | ArrayExpress | 2010-06-09

SECONDARY ACCESSION(S): GSE2282PRJNA91337

REPOSITORIES: GEO, ArrayExpress

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Publications

Temporal and spatial transcriptional programs in murine kidney development.

Challen G   Gardiner B   Caruana G   Kostoulias X   Martinez G   Crowe M   Taylor DF   Bertram J   Little M   Grimmond SM  

Physiological genomics 20050705 2


We have performed a systematic temporal and spatial expression profiling of the developing mouse kidney using Compugen long-oligonucleotide microarrays. The activity of 18,000 genes was monitored at 24-h intervals from 10.5-day-postcoitum (dpc) metanephric mesenchyme (MM) through to neonatal kidney, and a cohort of 3,600 dynamically expressed genes was identified. Early metanephric development was further surveyed by directly comparing RNA from 10.5 vs. 11.5 vs. 13.5dpc kidneys. These data showe  ...[more]

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