Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits

Additional File 1:

Top tables of differentially expressed probes (q-value < 0.015) identified in contrast All WL vs. All, RJ, and in corresponding sex-specific contrasts. Positive M-values indicate higher expression in WL, whereas negative M-values indicated more expression in RJ.

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Additional File 2:

Hierarchical clustering of microarray data for 837 probes, corresponding to 779 differentially expressed in three contrasts between WL and RJ.

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Additional File 3:

Along x-axis, individuals included in experiment are presented (1–5 = WL males, 6–10 = WL females, 11–15 = RJ males and 16–20 = RJ females) On the y-axis, mean M-value for sample vs. reference is presented. Mean M-values are based on signal from 124 separate spots on microarray all containing a probe targeting GAPDH (used as an endogenous control in the microarray experiment)

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Additional File 7:

Overrepresented Gene Ontologies (GOs) among 3372 probes showing differential expression (q-values < 0.015) in contrast between ten males and ten females (all males compared to all females). Presented are GO-terms which obtained EASE-score < 0.05 and which comprised six or more DE probes on the microarray. Top-level Gene Ontologies are denoted: P = biological process, C = cellular component, F = molecular function. List Hits to Category indicates numbers of DE probes on microarray belonging to specific GO-IDs. Total numbers of occurrences of C, P and F among 3372 DE probes were: C = 2226, P = 2283 and F = 2224. Total Hits to Category indicates total numbers of probes on microarray belonging to specific GO-ID. Total numbers of occurrences of C, P and F among all probes on microarray were: C = 13074, P = 17435 and F = 13433. The EASE-Score indicates the statistical significance of the observed overrepresentation

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Additional File 4:

Metaphyseal images of female femurs from which RNA was derived for the microarray study. Images were derived from phenotyping of the femoral metaphysis by peripheral Quantitative Computerized Tomography (pQCT). The same femoral bones, from which RNA was prepared from the midshaft, were phenotyped in the distal metaphysis by one pQCT-scan at approximately 5% of bone length. Arrows indicate appearance of trabecular bone and medullary bone as well as the absence of medullary bone from red junglefowl female number 19. The noncortical bone mineral density (BMD) in mg/cm³ which in the female metaphysis represents the density of a mix between trabecular and medullary bone is presented below the images corresponding to each individual. The number corresponding to each individual is presented above the images.

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Additional File 5:

Metaphyseal images of male femurs from which RNA was derived for the microarray study. Images were derived from phenotyping of the femoral metaphysis by peripheral Quantitative Computerized Tomography (pQCT). The same femoral bones, from which RNA was prepared from the midshaft, were phenotyped in the distal metaphysis by one pQCT-scan at approximately 5% of bone length. The number corresponding to each individual is presented above the images.

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Additional File 6:

Correlation between noncortical BMD of the distal femoral metaphysis and medullary BMD of the femoral midshaft. Results are based on an independent sample consisting of 313 female chicken studied at 200 days of age. Phenotyping was performed by peripheral Quantitative Computerized Tomography and noncortical bone was defined by setting the inner thresholds to 600 mg/cm³ and 1000 mg/cm³ at the distal metaphysis and midshaft, respectively.

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