Journal: Nucleic Acids Research

Article Title: AgBase: supporting functional modeling in agricultural organisms

doi: 10.1093/nar/gkq1115

Figure Lengend Snippet: Publication of agricultural microarray data. On average, less than half of the agricultural microarray data sets submitted to the NCBI GEO database are published. These statistics are based upon gene expression data submitted to the NCBI GEO database. Records are shown for as at 9 September 2010. For each species the number of expression data sets linked to a PubMed record was used to determine the proportion of unpublished data sets. Note that this approach is likely to under-estimate the amount of unpublished data sets as it does not include data not submitted to this database.

Article Snippet: We worked directly with microarray users and developers to provide ID mapping and GO annotations for the FHCRC chicken 13K (GPL2863) and Equine Whole Genome Oligonucleotide microarrays ( ) and are currently working to provide the same data for the 15K Agilent Sheep Gene Expression microarray (019921).

Techniques: Microarray, Expressing

Journal: Nucleic Acids Research

Article Title: AgBase: supporting functional modeling in agricultural organisms

doi: 10.1093/nar/gkq1115

Figure Lengend Snippet: Annotation updates for agricultural arrays

Article Snippet: We worked directly with microarray users and developers to provide ID mapping and GO annotations for the FHCRC chicken 13K (GPL2863) and Equine Whole Genome Oligonucleotide microarrays ( ) and are currently working to provide the same data for the 15K Agilent Sheep Gene Expression microarray (019921).

Techniques: Microarray, Expressing

Journal: Physiological Genomics

Article Title: Patterns of gene expression in the sheep heart during the perinatal period revealed by transcriptomic modeling

doi: 10.1152/physiolgenomics.00027.2015

Figure Lengend Snippet: Top: principal component plot showing the distribution of gene expression in cardiac septum along the first 2 principal components of the variance in the data identified in the unsupervised analysis of the normalized, background corrected gene expression levels detected on the microarrays. 130-days gestation = blue, term = red, and 2 wk old = green circles. Bottom: heat map representation of the unsupervised gene expression data for each animal, the closer their data are on the y-axis, the more closely related their gene expression levels. 130_1 through 130_6 are the 6 130-day gestation samples, 140_1 through 140_8 the 8 term samples, and Lamb_1 through Lamb_8 are the 2-wk-old samples. The colored scale for the heat maps, bottom right, shows the fold change in expression levels of the gene from the normalization point, where green is decreased, and red increased, expression.

Article Snippet: Septa from sheep hearts at 130 days gestation, term, and 14-day-old lambs were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays.

Techniques: Expressing