GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus

Type:

Expression profiling by array; Non-coding RNA profiling by array; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10225 GPL10234 GPL10223

32 Samples

Download data: CEL, TXT, XLS

(Submitter supplied) 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.

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL10234

24 Samples

Download data: CEL

(Submitter supplied) 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.

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by array

Platform:

GPL10225

6 Samples

Download data: XLS

(Submitter supplied) 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. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10223

2 Samples

Download data: BED, TXT

(Submitter supplied) To determine the transcriptional response to Salmonella enterica serovar Enteritidis (SE) infection, a newly developed chicken 44K Agilent array was used to analyze total RNA of heterophils from SE-resistant (line A) and SE–susceptible chickens (line B), treated with in vitro infection of SE (I) or non SE medium (N) for 1 hr. A dual-color balanced design was used to provide a direct comparison between SE-infected and non-infected groups (AI/AN, BI/BN) and between line A and line B (AN/BN, AI/BI). more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL4993

16 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3213

30 Samples

Download data: CEL

(Submitter supplied) Purpose: MicroRNAs (miRNAs) are non-coding small miRNA ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and theses difference are programmed during prenatal muscle development.To shed directly light on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by array

Platform:

GPL15455

6 Samples

Download data: TXT

(Submitter supplied) A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by array

Platform:

GPL15455

3 Samples

Download data: TXT

(Submitter supplied) A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by array

Platform:

GPL15455

3 Samples

Download data: TXT

(Submitter supplied) To investigate specific miRNA expression profiles of Marek's disease virus (MDV)-infected samples, we performed deep sequencing for miRNAs in four small RNA libraries, including MDV-infected tumorous spleen, MD lymphoma from liver, and non-infected spleen and lymphocytes from controls. A total of 7.76x106, 6.36x106, 6.36x106, and 7.60x106 counts were obtained in four libraries, respectively. The sequences were blasted with chicken and MDV genomes and miRBase 16.0 to identify known and novel miRNAs. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10223

4 Samples

Download data: TXT

(Submitter supplied) Alternative splicing (AS) is a post-transcriptional gene regulatory mechanism that contributes to proteome diversity. Aberrant splicing mechanisms (mutations, polymorphisms, insertion/deletion etc.) contribute to various cancers and muscle related conditions such as Duchenne muscular dystrophy. However, dysregulation of AS in Cancer Cachexia (CC) patients remains unexplored. Our objectives were (i) to profile alternatively spliced genes (ASGs) on a genome-wide scale, and (ii) to identify DE alternatively spliced genes (DASGs) associated with CC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17585

40 Samples

Download data: CEL

(Submitter supplied) Background: MicroRNAs (miRs) are small non-coding RNAs that regulate gene (mRNA) expression. Although pathological role of miRs have been studied in muscle wasting conditions such as age, obesity, starvation and muscular dystrophy, their roles in Cancer Cachexia CC are still emerging. Objectives: (i) to profile human skeletal muscle expressed miRs; (ii) to identify differentially expressed (DE) miRs between cachectic and non-cachectic cancer patients; (iii) to identify mRNA targets for the DE miRs to gain mechanistic insights and (iv) to investigate if miRs show potential prognostic and predictive value. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

43 Samples

Download data: TXT

(Submitter supplied) Obese and lean pig show breed-specific traits in muscle growth and meat quality. However, the mechanisms underlying remains unclear. Here, we reported the first genome-wide muscle development research from embryonic to 6 months old between Lantang (obese) and Landrace (lean) using Solexa/Illumina’s Genome Analyzer. We obtained 4.22±0.9×107 total reads per sample with approximately 5×106 distinct tags. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9126

20 Samples

Download data: TXT

(Submitter supplied) Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. more...

Organism:

Salicornia europaea

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19315

6 Samples

Download data: FA

(Submitter supplied) 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.

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9385

1 Sample

Download data: BED, BEDGRAPH

(Submitter supplied) Gene expression data of micro RNA from skeletal muscle samples of F2 population based DL and Pi F2 63 days post conception (dpc).

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL14969

118 Samples

Download data: CEL

(Submitter supplied) 47,845 probe-sets were screened, in the first part of this study pig embryos at 63 days post conception (dpc)

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL16569

118 Samples

Download data: CEL

(Submitter supplied) MicroRNAs (miRNAs) are small non-coding regulatory RNAs that play key roles in many diverse biological processes such as spermatogenesis. However, no study has been performed on the miRNA transcriptome of developing porcine testes. Here, we employed Solexa deep sequencing technology to extend the repertoire of porcine testis miRNAs and extensively compare the expression patterns of the sexually immature and mature porcine testes. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9126

2 Samples

Download data: TXT

(Submitter supplied) The present study provides the first large-scale characterization of miRNAs in M. amblycephala and miRNA profile of M. amblycephala with different growth performance. The discovery of miRNA resource from this study is expected to contribute to a better understanding of the miRNAs roles playing in regulating the growth biological processes in fish and the study of miRNA function and phenotype-associated miRNA identification in fish.

Organism:

Megalobrama amblycephala

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17832

2 Samples

Download data: FASTA, TXT