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Items: 1 to 20 of 119

1.

Exon Level Machine Learning Analyses Elucidate Novel Candidate miRNA Targets in an Avian Model of Fetal Alcohol Spectrum Disorder

(Submitter supplied) An RNA-seq dataset obtained from neural fold-stage chicken (Gallus gallus, strain Special Black) embryos that were exposed to a pharmacologically-relevant alcohol concentration (52 mM for 90 min) or isotonic saline. The cranial headfolds were isolated 6 hours following the initial alcohol exposure. Following RNA isolation, cDNA synthesis, and quality assurance (20), paired-end reads (75 bp) were generated on an Illumina Genome Analyzer IIx (University of Wisconsin Biotechnology Center).
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13797
4 Samples
Download data: CSV, TXT
Series
Accession:
GSE115383
ID:
200115383
2.

Morphological and transcriptomic effects of endocrine modulators on the gonadal differentiation of chicken embryos: the case of tributyltin (TBT)

(Submitter supplied) Chicken eggs (Gallus gallus domesticus) were incubated, after 24 h of incubation either non-injected (control, C), or injected with the solvent sesame oil (Oleum Sesame Raffinatum, solvent control, SC), and the substances Tributyltin (TBT, 10pg TBT-SN/g egg) or 17alpha-Methyltestosteron (MT, 30 pg/g egg). Animals were decapitated on breeding day 19, 2 days before anticipated hatching. Right and left gonads of female and male chicken were accurately separated from adhesing tissues, stored in RNA lysis buffer (Promega) at -80°C until until RNA isolation with the SV Total RNA Isolation System Kit according to manual 048 (Promega). more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13797
16 Samples
Download data: XLSX
Series
Accession:
GSE108141
ID:
200108141
3.

miRNA expression profiling in liver of juvenile and egg-laying hens

(Submitter supplied) A total of 565 miRNAs annotated in miRBase 20.0 were identified to be expressed in the liver of hen by high-throughput sequencing three biological reduplication libraries in juvenile and egg-laying hens, respectively. Compared with juvenile hen, 80 miRNAs (67 down-regulated and 13 up-regulated) were verified to be significant differential expression (SDE) in egg-laying physiological stage. Among these, miR-22-3p has the highest abundant expression, and miR-146b-5p has the highest fold-change. more...
Organism:
Gallus gallus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13797
6 Samples
Download data: TXT
Series
Accession:
GSE74242
ID:
200074242
4.

MicroRNA expression in chicken cecum following Campylobacter jejuni infection

(Submitter supplied) SPF leghorn chickens were infected with C. jejuni. The cecum were collected at 8h post infection for total RNA isolation. The significantly expressed microRNAs between infected and non-infected chickens were identified through Solexa sequencing technology.
Organism:
Gallus gallus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13797
4 Samples
Download data: TXT
Series
Accession:
GSE58767
ID:
200058767
5.

Expression profiling of DT40 chicken B cell line by RNA-seq

(Submitter supplied) A single replicate of exponentially growing DT40 CL18 chicken B lymphoma cells were harvested and extracted RNA was subjected to Illumina GAIIx paired-end sequencing to determine global gene expression.
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13797
1 Sample
Download data: BW
Series
Accession:
GSE58766
ID:
200058766
6.

Extrachromosomal DNA (microDNA) in Human, Mouse and Chicken

(Submitter supplied) MicroDNAs are <400-base long extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs were found in all tissue types, including sperm. MicroDNAs arose preferentially from areas with high gene density, high GC content, high exon density, promoters with activating chromatin modifications and in sperm from the 5'UTR of full-length LINE-1 elements, but were depleted from lamin-associated heterochromatin. more...
Organism:
Gallus gallus; Mus musculus; Homo sapiens
Type:
Genome variation profiling by high throughput sequencing
4 related Platforms
24 Samples
Download data: TXT
Series
Accession:
GSE68644
ID:
200068644
7.

Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to J Subgroup Avian Leukosis Virus (ALV-J) Infection.

(Submitter supplied) Purpose: The goals of this study are to investigate the differentially expressed genes between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing. Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13797
2 Samples
Download data: XLS
Series
Accession:
GSE63226
ID:
200063226
8.

Differentiation state-specific mitochondrial dynamic regulatory networks are revealed by global transcriptional analysis of the developing chicken lens.

(Submitter supplied) The mature eye lens contains a surface layer of epithelial cells called the lens epithelium that require a functional mitochondrial population to maintain the homeostasis and transparency of the entire lens. The lens epithelium overlies a core of terminally differentiated fiber cells that must degrade their mitochondria to achieve lens transparency. These distinct mitochondrial populations make the lens a useful model system to identify those genes that regulate the balance between mitochondrial homeostasis and elimination. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13797
8 Samples
Download data: TXT
Series
Accession:
GSE53976
ID:
200053976
9.

The evolution of lncRNA repertoires and expression patterns in tetrapods

(Submitter supplied) Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. more...
Organism:
Monodelphis domestica; Gallus gallus; Ornithorhynchus anatinus; Xenopus tropicalis; Macaca mulatta; Gorilla gorilla; Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
15 related Platforms
55 Samples
Download data: BEDGRAPH, TXT
Series
Accession:
GSE43520
ID:
200043520
10.

Systematic discovery of spleen miRNAs involved in host response to avian pathogenic Escherichia coli (APEC) by deep sequencing and integrated analysis

(Submitter supplied) Avian pathogenic Escherichia coli (APEC) is considered one of the most common infectious bacterial diseases resulting in significant economic losses in poultry industry worldwide. In order to investigate the association between host immune resistance and miRNA expression in the pathogenic process induced by APEC, miRNA expression profiles in broilers spleen were performed by Solexa deep sequencing from three different treatment groups including non-challenged (NC), challenged-mild pathology (MD), and challenged-severe pathology (SV).In total, 3 462 706, 3 586 689, and 3 591 027 clean reads were obtained for NC, MD, and SV, respectively. more...
Organism:
Gallus gallus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13797
3 Samples
Download data: TXT
Series
Accession:
GSE51396
ID:
200051396
11.

Distinct Global Shifts in Genomic Binding Profiles of Limb Malformation Associated HOXD13 Mutations

(Submitter supplied) We applied ChIP-seq to explore the effect of missense mutations in TFs on their genome wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype. The glutamine at position 317 (position 50 of the homeodomain) is conserved in most homeodomains, a notable exception being bicoid-type homeodomains that have K at this position. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL13797
13 Samples
Download data: BED, TXT
Series
Accession:
GSE44799
ID:
200044799
12.

Marek's Disease Virus Infection Induces Differential Chromatin Marks and Tissue-specific effects in inbred chicken lines

(Submitter supplied) Marek’s disease (MD) is a viral neoplastic disease in chickens caused by the MD virus (MDV). Successful vaccination strategies against MD have resulted in a progressive increase in the virulence of MDV and therefore, the understanding of genetic resistance to MD is considered crucial to the long-term control of the disease. Here we examine whether MDV infection induces changes in the epigenetic status of genes and whether this response is dependent on the host genotype. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13797
8 Samples
Download data: BED, PROBSCOREISLAND, TXT
Series
Accession:
GSE33541
ID:
200033541
13.

Evolution of mammalian miRNA genes

(Submitter supplied) MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species that represent all main mammalian lineages and birds (the evolutionary outgroup), with the aim to unravel the evolution of mammalian miRNAs. more...
Organism:
Gallus gallus; Ornithorhynchus anatinus; Didelphis virginiana; Mus musculus; Macaca mulatta; Homo sapiens; Monodelphis domestica
Type:
Non-coding RNA profiling by high throughput sequencing
7 related Platforms
38 Samples
Download data: TXT
Series
Accession:
GSE40499
ID:
200040499
14.

Epigenomic profiling of enhancers identifies orphan nuclear receptors NR2F1 and NR2F2 as novel regulators of human neural crest.

(Submitter supplied) Combining an in vitro hNCC differentiation protocol with epigenomic profiling, we provide the first whole-genome characterization of cis-regulatory elements in this highly relevant cell type. With this data at hand, we have characterized the chromatin state and dynamics of all human gene promoters during the course of NCC in vitro differentiation. Most importantly, we have identified a large cohort of active and NCC-specific enhancers, which we showed to be functionally relevant in vivo, in the context of embryonic development. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13797
4 Samples
Download data: BED
Series
Accession:
GSE38066
ID:
200038066
15.

A cross-species analysis of microRNAs in the developing avian face

(Submitter supplied) Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation. To determine the molecular basis of avian craniofacial patterning, we have used Next-Generation sequencing to profile all 20-40nt microRNAs from micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks). more...
Organism:
Gallus gallus; Anas platyrhynchos; Coturnix japonica
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13797 GPL13932 GPL13931
11 Samples
Download data: TXT
Series
Accession:
GSE30716
ID:
200030716
16.

The evolution of gene expression levels in mammalian organs

(Submitter supplied) Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. more...
Organism:
Monodelphis domestica; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Gorilla gorilla; Homo sapiens; Mus musculus; Pan troglodytes; Pongo pygmaeus
Type:
Expression profiling by high throughput sequencing
10 related Platforms
131 Samples
Download data
Series
Accession:
GSE30352
ID:
200030352
17.

Illumina Genome Analyzer IIx (Gallus gallus)

Organism:
Gallus gallus
16 Series
102 Samples
Download data
Platform
Accession:
GPL13797
ID:
100013797
18.

run183.SB-15perc-ETOH_L006

Organism:
Gallus gallus
Source name:
cranial headfolds_ETOH
Platform:
GPL13797
Series:
GSE115383
Download data
Sample
Accession:
GSM3177100
ID:
303177100
19.

run183.SB-15perc-ETOH_L005

Organism:
Gallus gallus
Source name:
cranial headfolds_ETOH
Platform:
GPL13797
Series:
GSE115383
Download data
Sample
Accession:
GSM3177099
ID:
303177099
20.

run182.SB-Saline_L007

Organism:
Gallus gallus
Source name:
cranial headfolds_saline
Platform:
GPL13797
Series:
GSE115383
Download data
Sample
Accession:
GSM3177098
ID:
303177098
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