Ontology highlight
ABSTRACT:
PROVIDER: PRJNA862644 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20662906_1.fastq.gz | Fastqsanger.gz | |||
| SRR20662906_2.fastq.gz | Fastqsanger.gz | |||
| SRR20662907_1.fastq.gz | Fastqsanger.gz | |||
| SRR20662907_2.fastq.gz | Fastqsanger.gz | |||
| SRR20662908_1.fastq.gz | Fastqsanger.gz |
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Project description:Deep sequencing as a high-throughput technology has been widely used in the transcriptome profiling in mammals. In the present study, we aimed to identify chicken lncRNAs ranging from 300-1600 nt long. Total RNAs from chicken skeletal muscle at the embryonic stage were fractionated by 6% urea PAGE. Selected RNA fractions (300-1600 nt) were sequenced by Solexa technology.
2012-02-20 | GSE28080 | 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.
2011-03-18 | GSE20942 | GEO
Project description:Deep sequencing as a high-throughput technology has been widely used in the transcriptome profiling in mammals. In the present study, we aimed to identify chicken lncRNAs ranging from 300-1600 nt long. Total RNAs from chicken skeletal muscle at the embryonic stage were fractionated by 6% urea PAGE. Selected RNA fractions (300-1600 nt) were sequenced by Solexa technology. Chicken eggs (White Leghorn) were incubated at 37.5°C for 10 days (E10), 12 days (E12), 14 days (E14), 18 days (E18). Skeletal muscles (pectoralis) were collected from chicken embryo incubated at above four stages. All muscle samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA isolation. All embryonic manipulations were conducted in accordance with the protocols of the Chinese Academy of Medical Sciences and the Institutional Animal Care and Use Committee of Peking Union Medical College. The single 'Chicken_muscle' Sample represents muscle pooled from all four stages.
2012-02-20 | E-GEOD-28080 | 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. Examination of miRNA transcriptome in skeletal muscle of two kinds of chickens
2011-03-18 | E-GEOD-20942 | biostudies-arrayexpress
Project description:We have used RNA-seq to examine circular RNAs from RNase R treated and ribo- RNAs in chicken leg muscle of three different development stages (11 embryo age, 16 embryo age, and 1 days post hatch). Our study reveals the prevalence of circRNAs in chicken, and has identified circRNAs differentially abundant in different stage of embryonic skeletal muscle, suggesting its important functions during poultry muscle development.
2016-11-01 | GSE89355 | GEO
Project description:The PDZ-LIM superfamily member is present in the nucleus of many cells and consists of one PDZ domain at the N-terminus and one or more LIM domains at the C-terminus. The family includes 10 genes, of which PDLIM3, PDLIM5 and LMO7 genes have been shown to promote mouse myoblast differentiation and participate in the regulation of skeletal muscle growth and development. To explore whether chicken PDLIM3, PDLIM5 and LMO7 genes have the same function, this study explored the expression of these genes in the before and after birth of chicken, and after the chicken skeletal muscle satellite cells cultured in vitro interfered with the expression of these genes. The proliferation and differentiation of satellite cells were finally analyzed by transcriptome sequencing. The molecular pathways involved in the regulation of cell proliferation and differentiation were analyzed. The main results are as follows: Transcriptome sequencing revealed that the differentially expressed genes of chicken skeletal muscle satellite cells interfering with PDLIM3 gene expression were mainly enriched in cGMP-PKG, Oxytocin, MAPK, Tight junction and other signaling pathways, and involved in cytoskeletal protein binding, actin binding, muscle tissue regeneration and development, adhesion and other functions. Transcriptome sequencing revealed that compared with the control group, the differentially expressed genes of chicken skeletal muscle satellite cells that interfered with PDLIM5 gene expression were mainly enriched in signaling pathways such as Tight junction, Oxytocin, p53, MAPK, and involved in myocyte production and muscle contraction. Muscle cell differentiation, and participate in cytoskeletal protein binding, actin cytoskeleton formation, actin and actin binding.
2020-05-30 | GSE151450 | GEO
Project description:We have used RNA-seq to examine long non-coding RNA (lncRNA) and mRNA from rRNA depleted in chicken leg musle of three different development stages (11 embryo age, 16 embryo age, and 1 days post hatch). Our study reveals the prevalence of lncRNA in chicken, and has identified lncRNA differentially abundant in different stage of embryonic skeletal muscle, suggesting its important functions during poultry muscle development.
2016-12-13 | GSE91060 | GEO
Project description:Different chicken breeds exhibit distinct muscle phenotypes resulting from selective breeding, but little is known about the molecular mechanisms responsible for this phenotypic difference. Skeletal muscle is composed of a large number of heterogeneous cell populations. Differences in differentiation and interaction of cell populations play a key role in the difference of skeletal muscle phenotype. Here, skeletal muscle single-cell RNA sequencing in three developmental stages was performed on Daheng broiler (cultivated breed) and Tibetan chicken (native breed).
2023-12-25 | GSE251682 | GEO
Project description:Purpose:We have used RNA-seq to examine of differentially expressed miRNAs in chicken leg muscle of three different development stages (11 embryo ages, 16 embryo ages, and 1 day old post hatch chick).The aims of this study are characterization of miRNAs differentially expressed in different developmental stage of chicken embryo, using RNA sequence sample. Methods: On this study we used two embryonic stage and one post hatch chick leg muscle of Xinghua chicken breed. Total RNA from E11 day embryo, E16 day embryo and 1 day post hatch chick was isolated by TRIzol following the manufacturer’s protocol (Invitrogen, CA, USA). Each stages were designed two samples, and the total samples were six (three group × two sample/group) and RNA samples of six individuals were pooled with equal amounts, and then were subjected to Illumina deep sequencing. Results: After eliminating adaptor and low-quality reads, a total of 5,302,700, 6,556,747, 5,359,793, 4,213,112, 7,112,885 and 7,469,939 clean reads were obtained in group E11 (E11.1-E11.2), group E16 (E16.1-E16.2) and group P1 (P1.1–P1.2) libraries, respectively. The clean reads were aligned to the chicken genome databases, miRBase, Rfam, RepBase and mRNA. Conclusions:To assess miRNA expression during chicken embryo skeletal muscle development, we sequenced and analyzed leg muscle at 11 day embryo age, 16 day embryo age, and 1 days post hatch.
2017-06-22 | GSE100321 | GEO
Project description:As muscle function is relevant for the stress response, and as gene array and proteomics analyses have not been conducted to investigate muscle response in stress paradigm in birds, we developed generic approaches to assess molecular bases of muscle response to stress in chicken. Restraint test was chosen as stress situation because this treatment has previously been shown to be a high stressful situation in birds and mammals. Keywords: comparative genomic expression, skeletal muscle, restraint-transport stress, chicken
2010-03-26 | GSE19644 | GEO