GEO DataSets

(Submitter supplied) In mice, genome-wide DNA methylation is actively erased at the onset of fertilisation, followed by remethylation in epiblasts after implantation, leading to inactive chromatin formation as a preliminary step to somatic cell differentiation, and then demethylation again during primitive streak formation and the determination of primordial germ cells (PGCs). This sequence of DNA methylation changes is accompanied by dynamic epigenetic reprogramming, including nuclear structure, histone modification, and intranuclear re-localisation of chromosomes, during totipotency acquisition of the fertilised egg and germline development. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16133

16 Samples

Download data: BW

(Submitter supplied) Chicken infectious anaemia (CIA) is an immunosuppressive disease caused by chicken infectious anaemia virus (CIAV). Due to immunosuppression, the disease is often leads to mixed infections and secondary infections, exacerbating viral, bacterial, and fungal infections, which can be highly detrimental. Therefore, it is imperative to identify the immune genes involved in regulating CIAV infection. In this study, comprehensive transcriptome sequencing was employed to determine the expression levels of regulated immune genes including mRNAs, microRNAs, lncRNAs, and circRNAs in CIAV-infected MDCC-MSB1 cells. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16133

6 Samples

Download data: XLSX

(Submitter supplied) Eimeria (E.) maxima parasite infects the midgut disrupting the jejunal and ileal mucosal lining causing high morbidity and mortality in chickens. Heat stress (HS) is a seasonal stressor that affects biological functions leading to poor performance. Our objective was to elucidate how HS, E. maxima infection, and their combination affect the ileum transcriptome. Two-hundred and forty 2-week-old males Ross708 chickens were randomly allocated into four treatment groups: thermoneutral control (TNc), thermoneutral infected (TNi), heat stress control (HSc), and heat stress infected (HSi), with 6 replicates each of 10 birds. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

20 Samples

Download data: TXT

(Submitter supplied) Avian reovirus (ARV) infection is prevalent in farmed poultry, causes viral arthritis and severe immunosuppression. The spleen plays an important role in host defense against pathogen infection. In this study, transcriptome and translatome sequencing technology were combined to investigate the mechanisms of transcriptional and translational regulation in the spleen after ARV infection. On a genome-wide scale, ARV infection can significantly reduce the translation efficiency (TE) of splenic genes. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16133

8 Samples

Download data: TXT

(Submitter supplied) Distal limb mesenchyme cells were collected from embryonic chickens at Hamburger Hamilton (HH) stages HH24 and HH27, and from samples that had been grafted from HH20 to HH24 and left to develop for 24 hours. Bioinformatics and clustering analyses were then performed to determine whether grafted cells are more similar to HH24 (graft stage) or HH27 (host stage).

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

8 Samples

Download data: CSV

(Submitter supplied) Comparison of transcriptomic profiles of primordial germ cells and derived fibroblast cell lines from homozygous, CRISPR/Cas9 gene-edited, ANP32A knockout and mutant chickens

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

32 Samples

Download data: TXT

(Submitter supplied) We applied high-throughput sequencing on rooster testis samples.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Other

Platforms:

GPL29297 GPL16133

123 Samples

Download data: BIGWIG, CSV, SF, TXT

(Submitter supplied) The transcription factors ERR2 and ERR3 promote promote the development of functional properties in gamma motor neurons necessary for executing precise movements.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

19 Samples

Download data: XLSX

(Submitter supplied) Previously FGF signalling has been shown to specify otic fate from multipotent pre-placodal ectoderm. Though many FGF target genes have been identified in subsequent studies, none of them is sufficient to induce otic lineage. Profiling and analysing the transcriptome and epigenomical signature during otic specification, we predicted and confirmed Sox8 as an otic master regulator, able to specify otic fate in the pre-placodal ectoderm. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16133

5 Samples

Download data: BW

(Submitter supplied) In order to found the target genes of ALV-miR-p19-01 which encoded by ALV-J, we used RNA-pull down and RNA-seq. The resulted showed there were 917 potential target genes of ALV-miRNA-p19-01 had been identified

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

2 Samples

Download data: XLSX

(Submitter supplied) Purpose:In order to assess the toxicity of AFB1 in chicken liver and the mechanism of curcumin alleviating AFB1-induced liver toxicity in chicken, we established a co-administered model to investigate LncRNA and mRNA profiles of chicken liver. Methods: RNA extracted by Total RNA Extractor (Trizol) was utilized to construct the final library. Libraries were pooled and sequenced on a 150-bp paired-end Illumina HiSeq™ 2000 run. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

9 Samples

Download data: CSV

(Submitter supplied) Avian sex is determined by various factors, such as the dosage of DMRT1 and cell-autonomous mechanisms. While the sex-determination mechanism in gonads is well analyzed, the mechanism in germ cells remains unclear. In this study, we explored the gene expression profiles of male and female primordial germ cells (PGCs) during embryogenesis in chickens to predict the mechanism of sex-determination. Male and female PGCs were isolated from blood and gonads with a purity > 96% using flow cytometry and analyzed using RNA-seq. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

12 Samples

Download data: TXT

(Submitter supplied) Broiler breeder hens given ad libitum access to feed have excessive ovarian follicle development with poor reproductive outcome. One strategy to improve their reproductive capacity is by restricting their feed intake. In this study, we sequenced the liver transcriptomes of hens fed ad libitum (FF, n=3) and hens given a restricted fed diet (RF, n=3) to get insight into possible signaling pathways affected by dietary treatment. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

5 Samples

Download data: XLSX

(Submitter supplied) Purpose: The aim of this study is to analyse and compare the differentially expressed genes between the developmental stages and to construct heat maps with the data generated. Methods: The trancriptome sequencing was performed using Illumina HiSeq 2000 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 75 database. Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

4 Samples

Download data: XLSX

(Submitter supplied) This manuscript is about our recent work on investigating the effective mechanism of Zinc oxide Nanoparticles on the malformation of craniofacial skeleton. Briefly, we focused on addressing the phenotype of destroyed cranial neural crest cells’ development where the effect of oxidant stress was explored when developing early embryos were exposed to Zinc oxide Nanoparticles during the embryogenesis.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

6 Samples

Download data: TXT

(Submitter supplied) piRNAs can derive from transposable elements (TEs), long non-coding RNAs, or the 3'UTR of mRNAs, the last being the least characterized out of the three piRNA classes. In this study, we systematically defined the regulation, biogenesis and function of the 3'UTR piRNAs that are expressed throughout mouse spermatogenesis. These piRNAs are regulated by A-MYB transcription factors, and their precursors are bifunctional mRNAs which are processed into piRNAs after pioneer rounds of translation. more...

Organism:

Mus musculus; Gallus gallus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL16133

27 Samples

Download data: BIGWIG, TXT

(Submitter supplied) HOX transcription factors are members of an evolutionarily conserved family of proteins required for the establishment of the anteroposterior body axis during bilaterian development. Although they are often deregulated in cancers, the molecular mechanisms by which they act as oncogenes or tumor suppressor genes are only partially understood. Since the MAPK/ERK signaling pathway is deregulated in most cancers, we aimed at apprehending if and how Hox proteins interact with ERK oncogenicity. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

6 Samples

Download data: XLSX

(Submitter supplied) Most human cancers demonstrate activated MAPK/ERK pathway signaling as a key tumor initiation step, but the immediate steps of further oncogenic progression are poorly understood due to a lack of appropriate models. Spinal cord differentiation follows caudal elongation in vertebrate embryos; both processes are regulated by a FGF8 gradient highest in neuromesodermal progenitors (NMP), where kinase effectors ERK1/2 maintain an undifferentiated state. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

4 Samples

Download data: XLSX

(Submitter supplied) Animals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16133 GPL19787

16 Samples

Download data: TXT

(Submitter supplied) SmallRNA seq and longRNA seq of chicken kidney and testis

Organism:

Gallus gallus

Type:

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

Platform:

GPL16133

20 Samples

Download data: BED2, SF