Identification of miRNAs involved in embyonic chicken muscle development
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE20947 | GEO | 2011/03/18
SECONDARY ACCESSION(S): PRJNA129645
REPOSITORIES: GEO
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Project description:In the current study, we expanded our previous work to identify miRNAs implicated in the myogenesis regulation through the comparison of miRNAs transcriptome in skeletal muscle tissues between broilers and layers. miRNA expression studies of two different intra-species breeds
2011-03-18 | E-GEOD-20947 | biostudies-arrayexpress
Project description:The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms determining the divergent muscle growth rates and muscle fiber sizes in different chicken lines, we systematically identified differentially expressed genes between broilers and layers during muscle development (embyonic day 10, 12, 14 and 18) by microarray hybridization experiment.
2011-03-18 | GSE20990 | GEO
Project description:In the current study, we expanded our previous work to identify miRNAs implicated in the myogenesis regulation through the comparison of miRNAs transcriptome in skeletal muscle tissues between broilers and layers. To address that, we firstly performed Solexa deep sequencing to profile miRNAs expressed in chicken skeletal muscle tissues. Sequence tags analyses not only enable us to report a group of highly abundant known miRNAs expressed in skeletal muscles but most importantly to identify novel putative chicken miRNAs from skeletal muscle tissue. Further miRNA transcriptome comparison and real-time RT-PCR validation experiments revealed seveal differentially expressed miRNAs between broilers and layers. Examination of miRNA transcriptome in skeletal muscle of two kinds of chickens
2011-03-18 | E-GEOD-20942 | biostudies-arrayexpress
Project description:The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms determining the divergent muscle growth rates and muscle fiber sizes in different chicken lines, we systematically identified differentially expressed genes between broilers and layers during muscle development (embyonic day 10, 12, 14 and 18) by microarray hybridization experiment. Time-course studies of two different intra-species breeds
2011-03-18 | E-GEOD-20990 | biostudies-arrayexpress
Project description:In the current study, we expanded our previous work to identify miRNAs implicated in the myogenesis regulation through the comparison of miRNAs transcriptome in skeletal muscle tissues between broilers and layers. To address that, we firstly performed Solexa deep sequencing to profile miRNAs expressed in chicken skeletal muscle tissues. Sequence tags analyses not only enable us to report a group of highly abundant known miRNAs expressed in skeletal muscles but most importantly to identify novel putative chicken miRNAs from skeletal muscle tissue. Further miRNA transcriptome comparison and real-time RT-PCR validation experiments revealed seveal differentially expressed miRNAs between broilers and layers.
2011-03-18 | GSE20942 | GEO
Project description:The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms determining the divergent muscle growth rates and muscle fiber sizes in different chicken lines, we systematically identified differentially expressed genes between broilers and layers during muscle development (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks) by microarray hybridization experiment. Taken together, 543 differentially expressed probe sets were found between broilers and layers across different developmental stages, including genes related to muscle growth and hypertrophy, fatty acid transportation and metabolism, protein degradation, and several important signaling pathways. The expression profiles of a few differentially expressed genes were highly correlated with the growth rates of broilers and layers. We also identified SNPs within upstream transcription factor binding sites of a few differentially expressed genes, indicating that these SNPs might be the causing factor of the expression differences of these genes between broilers and layers. These studies provided new clues for deciphering mechanisms underlining muscle development and organ size control in different chicken lines, will shed light on the study of human muscle related disease as well. Keywords: Time-course studies of two different intra-species breeds
2009-01-01 | GSE9251 | GEO
Project description:The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms determining the divergent muscle growth rates and muscle fiber sizes in different chicken lines, we systematically identified differentially expressed genes between broilers and layers during muscle development (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks) by microarray hybridization experiment. Taken together, 543 differentially expressed probe sets were found between broilers and layers across different developmental stages, including genes related to muscle growth and hypertrophy, fatty acid transportation and metabolism, protein degradation, and several important signaling pathways. The expression profiles of a few differentially expressed genes were highly correlated with the growth rates of broilers and layers. We also identified SNPs within upstream transcription factor binding sites of a few differentially expressed genes, indicating that these SNPs might be the causing factor of the expression differences of these genes between broilers and layers. These studies provided new clues for deciphering mechanisms underlining muscle development and organ size control in different chicken lines, will shed light on the study of human muscle related disease as well. Experiment Overall Design: Pectoralis major muscles were sampled from broilers and layers at indicated developmental stage (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks). Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. Affymetrix Gene Chip array hybridization was carried out according to Affymetrix Expression Analysis Technical Manual by GeneTech Biotechnology Limited Company (Shanghai, China). Following labeled cRNA fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45â on Affymetrix Chicken Genome Array. After standard washing and staining, GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
2009-01-14 | E-GEOD-9251 | biostudies-arrayexpress
Project description:Domestic chicken has been intensively studied because of its role as an efficient source of lean meat. However, commercial broilers resulting from genetic selection for rapid growth demonstrate detrimental traits, such as excess deposition of abdominal adipose tissue, metabolic disorders, and reduced reproduction. Therefore fast-growing broilers represent “obese” chickens compared to slow-growing egg layers (e.g, Leghorn) or wild strain of meat-type chickens (e.g., Fayoumi). Fayoumi chickens, originating from Egypt, represent a harder stain of chickens, which are more resistant to diseases. Leghorn chickens are the original breed of commercial U.S layers. Both lines were maintained highly inbred by Iowa State University poultry geneticists with an inbreeding coefficient higher than 0.95. Both Fayoumi and Leghorn demonstrated lean phenotype compared to broilers, and these three lines of chickens are genetically distant from each other. In this study, we used affymetrix microarray to profile global gene expression of three distinct genetic lines of chickens to identify functional pathways associated with leanness of domestic chickens.
2013-12-23 | E-GEOD-44394 | biostudies-arrayexpress
Project description:Proctor2017 - Identifying microRNA for muscle regeneration during ageing (Mir1_in_muscle)
This model is described in the article:
Using computer simulation
models to investigate the most promising microRNAs to improve
muscle regeneration during ageing
Carole J. Proctor & Katarzyna
Goljanek-Whysall
Nature Scientific Reports
Abstract:
MicroRNAs (miRNAs) regulate gene expression through
interactions with target sites within mRNAs, leading to
enhanced degradation of the mRNA or inhibition of translation.
Skeletal muscle expresses many different miRNAs with important
roles in adulthood myogenesis (regeneration) and myofibre
hypertrophy and atrophy, processes associated with muscle
ageing. However, the large number of miRNAs and their targets
mean that a complex network of pathways exists, making it
difficult to predict the effect of selected miRNAs on
age-related muscle wasting. Computational modelling has the
potential to aid this process as it is possible to combine
models of individual miRNA:target interactions to form an
integrated network. As yet, no models of these interactions in
muscle exist. We created the first model of miRNA:target
interactions in myogenesis based on experimental evidence of
individual miRNAs which were next validated and used to make
testable predictions. Our model confirms that miRNAs regulate
key interactions during myogenesis and can act by promoting the
switch between quiescent/proliferating/differentiating
myoblasts and by maintaining the differentiation process. We
propose that a threshold level of miR-1 acts in the initial
switch to differentiation, with miR-181 keeping the switch on
and miR-378 maintaining the differentiation and miR-143
inhibiting myogenesis.
This model is hosted on
BioModels Database
and identified by:
MODEL1704110000.
To cite BioModels Database, please use:
Chelliah V et al. BioModels: ten-year
anniversary. Nucl. Acids Res. 2015, 43(Database
issue):D542-8.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-09-26 | MODEL1704110000 | BioModels
Project description:Proctor2017 - Identifying microRNA for muscle regeneration during ageing (Mir378_in_muscle)
This model is described in the article:
Using computer simulation
models to investigate the most promising microRNAs to improve
muscle regeneration during ageing
Carole J. Proctor & Katarzyna
Goljanek-Whysall
Scientific Reports
Abstract:
MicroRNAs (miRNAs) regulate gene expression through
interactions with target sites within mRNAs, leading to
enhanced degradation of the mRNA or inhibition of translation.
Skeletal muscle expresses many different miRNAs with important
roles in adulthood myogenesis (regeneration) and myofibre
hypertrophy and atrophy, processes associated with muscle
ageing. However, the large number of miRNAs and their targets
mean that a complex network of pathways exists, making it
difficult to predict the effect of selected miRNAs on
age-related muscle wasting. Computational modelling has the
potential to aid this process as it is possible to combine
models of individual miRNA:target interactions to form an
integrated network. As yet, no models of these interactions in
muscle exist. We created the first model of miRNA:target
interactions in myogenesis based on experimental evidence of
individual miRNAs which were next validated and used to make
testable predictions. Our model confirms that miRNAs regulate
key interactions during myogenesis and can act by promoting the
switch between quiescent/proliferating/differentiating
myoblasts and by maintaining the differentiation process. We
propose that a threshold level of miR-1 acts in the initial
switch to differentiation, with miR-181 keeping the switch on
and miR-378 maintaining the differentiation and miR-143
inhibiting myogenesis.
This model is hosted on
BioModels Database
and identified by:
MODEL1704110002.
To cite BioModels Database, please use:
Chelliah V et al. BioModels: ten-year
anniversary. Nucl. Acids Res. 2015, 43(Database
issue):D542-8.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-09-26 | MODEL1704110002 | BioModels