Ontology highlight
ABSTRACT:
PROVIDER: PRJNA341399 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4106460_1.fastq.gz | Fastqsanger.gz | |||
| SRR4106460_2.fastq.gz | Fastqsanger.gz | |||
| SRR4106431_1.fastq.gz | Fastqsanger.gz | |||
| SRR4106431_2.fastq.gz | Fastqsanger.gz | |||
| SRR4106461_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 49 |
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Project description:Response of Commercial Turkey Muscle Satellite Cells to Thermal Challenge
| PRJNA842679 | ENA
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).
2012-06-01 | GSE36365 | GEO
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).
2012-06-01 | GSE36362 | GEO
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).
2012-06-01 | GSE35660 | GEO
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
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
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
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
Project description:Because of its high plasticity and rapid growth rate, turkey skeletal muscle is an important model for studying mechanisms responsible for vertebrate skeletal muscle development and function. Skeletal muscle is composed of metabolically heterogeneous myofibers that exhibit high plasticity at both the morphological and transcriptional levels. The objective of this study was to employ microarray analysis to elucidate the differential gene expression between the tonic- “red” Anterior latissimus dorsi (ALD) muscle, the phasic- “white” Posterior latissimus dorsi (PLD), and “mixed”-phenotype Biceps femoris (BF) in 1-week and 19-week old male turkeys. A total of 170 differentially expressed genes were identified in the analyzed muscle samples (P<0.05). Gene Go analysis software was utilized to identify top gene networks and metabolic pathways involving differentially expressed genes. The largest differences were observed between ALD and PLD muscles, where 32 genes were over-expressed and 82 genes were under-expressed in ALD1-PLD1 comparison; and 70 genes were over-expressed and 70 under-expressed in ALD19-PLD19 comparison. The largest number of genes over-expressed in ALD muscles as compared to other muscles, code for extracellular matrix proteins such as dystroglycan and collagen. Furthermore, a number of genes involved in glycolytic metabolism were under-expressed in ALD muscles as compared to BF and PLD muscles. The gene analysis revealed that phenotypically “red” BF muscle has high expression of glycolytic genes usually associated with “white” muscle phenotype. Muscle-specific differences were observed in expression levels of genes coding for proteins involved in mRNA processing and translation regulation, proteosomal degradation, apoptosis, and insulin resistance. The study utilized Nicholas turkey males at two different stages of growth (1 week old: high satellite cell mitotic activity; 19 weeks old: low satellite cell mitotic activity, hypertrophy, market age). Six 1-week-old and six 19-week-old Nicholas turkey males (Meleagris gallopavo) were randomly selected from a single flock. The experiments were designed to compare genes characterizing muscle fiber phenotype at each time point, and to elucidate age-related differences in gene expression levels. Each analyzed cDNA sample was derived from six pooled RNA samples, resulting with six cDNA samples per muscle (one cDNA per bird). To minimize dye bias, the cDNA samples were labeled either with Cy3 or Cy5. A total of 17 Turkey Skeletal Muscle Long Oligo (TKSMLO) microarrays were utilized. Birds were randomly assigned to each array and the cDNA hybridizations we performed at random. The array data was Log2 transformed and then normalized by using locally weighed regression and smoothing within each array and across all arrays. Mixed model ANOVA with Bonferroni correction of P=0.05 for multiple testing was performed to increase the sensitivity of detected differences in gene expression levels.
2011-01-13 | E-GEOD-23354 | biostudies-arrayexpress
Project description:In response to skeletal muscle injury, adult myogenic stem cells, known as satellite cells, are activated and undergo proliferation and differentiation to regenerate new muscle fibers. The skeletal muscle-specific microRNA, miR-206, is up-regulated in satellite cells following muscle injury, but its role in muscle regeneration has not been defined. Here we show that skeletal muscle regeneration in response to cardiotoxin injury is impaired in mice lacking miR-206. Loss of miR-206 also accelerates and exacerbates the dystrophic phenotype of mdx mice, a model for Duchenne muscular dystrophy. MiR-206 promotes satellite cell differentiation and fusion to form multinucleated myofibers by suppressing a collection of negative regulators of myogenesis. Our findings reveal an essential role for miR-206 in satellite cell differentiation during skeletal muscle regeneration and as a modulator of Duchenne muscular dystrophy. total RNA obtained from TA muscle of mdx and 3 miR-206 KO; mdx mice at 3 months of age.
2012-04-30 | E-GEOD-36077 | biostudies-arrayexpress