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Analysis of the turkey skeletal muscle transcriptome between genetic lines within a developmental stage (Experiment 2)

ABSTRACT: The purpose of Experiment 2 was two-fold: a) to evaluate a unique set of negative, distance, and mismatch control probes on the newly designed 6K TSKMLO microarray, and b) to identify differences in gene expression between two genetic lines of turkeys that phenotypically display differences in growth. Negative and mismatch controls confirmed specific hybridization using this array, and genes identified as differentially expressed between developmental stages by microarray analysis were confirmed by qRT-PCR. Novel candidate genes and pathways were identified as playing potentially crucial roles in skeletal muscle development between 2 distinct lines of turkeys with implications for improving turkey meat quality defects and growth-induced myopathies long-term.

ORGANISM(S): Meleagris gallopavo

PROVIDER: GSE19538 | GEO | 2010/02/01

SECONDARY ACCESSION(S): PRJNA123945

REPOSITORIES: GEO

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Analysis of the turkey skeletal muscle transcriptome through development within a genetic line (Experiment 1)

2010-02-01 | GSE19531 | GEO

Analysis of the turkey skeletal muscle transcriptome between genetic lines within a developmental stage (Experiment 2)

Project description:The purpose of Experiment 2 was two-fold: a) to evaluate a unique set of negative, distance, and mismatch control probes on the newly designed 6K TSKMLO microarray, and b) to identify differences in gene expression between two genetic lines of turkeys that phenotypically display differences in growth. Negative and mismatch controls confirmed specific hybridization using this array, and genes identified as differentially expressed between developmental stages by microarray analysis were confirmed by qRT-PCR. Novel candidate genes and pathways were identified as playing potentially crucial roles in skeletal muscle development between 2 distinct lines of turkeys with implications for improving turkey meat quality defects and growth-induced myopathies long-term. This experiment utilized turkeys from two genetic lines: RBC2, a randomly bred control line representative of a 1,967 commercial turkey, and F, a subline genetically selected from the RBC2 line for increased 16-week body weight. Skeletal muscle was collected at three critical developmental stages: 18-day embryo (18de; peak of hyperplasia), 1-day post-hatch (1d; shift from myoblast-mediated growth to satellite cell modulated growth by hypertrophy), and 16-week-old birds (16wk; completion of muscle formation and approximate age of commercial slaughter). Experiment 2 was designed to directly compare the two genetic lines, RBC2 vs. F, for each of the three stages of skeletal muscle development: 18de, 1d, and 16wk. Experiment 2 contained 10 arrays per comparison, therefore, it contained 30 arrays total. Birds were randomly assigned to an array, and hybridizations were performed in random order.

2010-01-31 | E-GEOD-19538 | biostudies-arrayexpress

Analysis of the turkey skeletal muscle transcriptome through development within a genetic line (Experiment 1)

Project description:The purpose of Experiment 1 was two-fold: a) to evaluate a unique set of negative, distance, and mismatch control probes on the newly designed 6K TSKMLO microarray, and b) to identify patterns of gene expression in skeletal muscle during development. Negative and mismatch controls confirmed specific hybridization using this array, and genes identified as differentially expressed between developmental stages by microarray analysis were confirmed by qRT-PCR. Novel candidate genes and pathways were identified as playing potentially crucial roles in turkey skeletal muscle development with implications for improving turkey meat quality defects and growth-induced myopathies long-term. This experiment utilized turkeys from two genetic lines: RBC2, a randomly bred control line representative of a 1,967 commercial turkey, and F, a subline genetically selected from the RBC2 line for increased 16-week body weight. Skeletal muscle was collected at three critical developmental stages: 18-day embryo (18de; peak of hyperplasia), 1-day post-hatch (1d; shift from myoblast-mediated growth to satellite cell modulated growth by hypertrophy), and 16-week-old birds (16wk; completion of muscle formation and approximate age of commercial slaughter). Experiment 1 was designed to directly compare the three stages of skeletal muscle development: 18de vs. 1d, or 1d vs. 16wk, for each of the genetic lines. Experiment 1 contained 10 arrays per comparison, therefore, it contained 40 arrays total. Birds were randomly assigned to an array, and hybridizations were performed in random order.

2010-01-31 | E-GEOD-19531 | biostudies-arrayexpress

Transcriptional profiling of turkey muscle satellite cells transfected with versican-siRNA during proliferation and differentiation

2012-06-01 | GSE36365 | GEO

Transcriptional profiling of turkey muscle satellite cells transfected with MGP-siRNA during proliferation and differentiation

2012-06-01 | GSE36362 | GEO

Transcriptional profiling of turkey muscle satellite cells transfected with DAP-siRNA during proliferation and differentiation

2012-06-01 | GSE35660 | GEO

Transcriptional profiling of turkey muscle satellite cells transfected with MGP-siRNA during proliferation and differentiation

Project description:In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene Matrix Gla Protein (MGP) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788). The MGP gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the MGP-mediated effects on the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted). This experiment was designed to investigate the role of MGP expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation. Satellite cells were isolated from 7-week-old turkeys from the RBC2 line. Cells were transfected with either MGP siRNA or a lipofectamine control; MGP expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted). Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction. Microarrays directly compared the MGP -knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of MGP expression in satellite cell development and function. Hybridizations were performed in random order.

2012-05-31 | E-GEOD-36362 | biostudies-arrayexpress

Transcriptional profiling of turkey muscle satellite cells transfected with versican-siRNA during proliferation and differentiation

Project description:In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene versican (VCAN) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788). The VCAN gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the VCAN-mediated effects on the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted). This experiment was designed to investigate the role of VCAN expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation. Satellite cells were isolated from 7-week-old turkeys from the RBC2 line. Cells were transfected with either VCAN siRNA or a lipofectamine control; VCAN expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted). Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction. Microarrays directly compared the VCAN-knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of VCAN expression in satellite cell development and function. Hybridizations were performed in random order.

2012-05-31 | E-GEOD-36365 | biostudies-arrayexpress

Transcriptional profiling of turkey muscle satellite cells transfected with DAP-siRNA during proliferation and differentiation

Project description:In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene Death-Associated Protein (DAP) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788). The DAP gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the DAP-mediated attenuation of the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted). This experiment was designed to investigate the role of DAP expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation. Satellite cells were isolated from 7-week-old turkeys from the RBC2 line. Cells were transfected with either DAP siRNA or a lipofectamine control; DAP expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted). Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction. Microarrays directly compared the DAP-knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of DAP expression in satellite cell development and function. Hybridizations were performed in random order.

2012-05-31 | E-GEOD-35660 | biostudies-arrayexpress

TSKMLO microarray validation experiment

Project description:A 6K oligonucleotide microarray (TSKMLO) was designed as a community resource for researchers interested in domestic turkey muscle biology as it pertains to growth and development and their association with downstream meat quality. A series of quality control experiments performed to assess the functionality of the newly constructed array, which included a set of validation hybridizations performed in order to initially assess the functionality and repeatability of the newly designed TSKMLO array. Strong correlations between these test comparisons confirmed that the array was able to hybridize fluorescently-labeled aRNA samples from turkey skeletal muscle at different developmental stages, that there was little dye bias, and that results were repeatable.

2010-02-01 | GSE19452 | GEO

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