Project description: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).
Project description:We report the transcriptomes of 10 different chicken (Gallus gallus) cell/tissue types. The goal of this project was to determine similarities and differences between different cell/tissue types, with respect to protein coding genes, lncRNA, isoform counts, and differential gene expression. We provide raw data and bigWig files for UCSC visualization. The findings described here will be useful towards a complete annotation of chicken tissue and cellular transcriptomes.
Project description:Copy number variation profiles comparing control female Dehong chiken blood DNA with 11 different chicken breeds(Silkie, Tibetan Chicken, Gallus gallus spadiceus, Bearded Chicken, Jinhu Chicken, Anak Chicken, Beijing Fatty Chicken, Langshan Chicken, Qingyuan partridge Chicken, Shek-Ki Chicken, Wenchang Chicken) blood DNA. Each test breeds had one male and one female sample, totally 22 test DNA samples.Goal is to get the golbal copy number variation profile between chicken breeds.
Project description:We present the first Hi-C map of non-mammalian vertebrate, Gallus gallus (domestic chicken). We show the presence of TADs in chicken embryonic fibroblast genome, distributed in accordance with gene density, transcriptional activity, and CTCF binding sites localization. In contrast to mammals, where all examined cell types display relatively similar chromatin architecture profile, in mature and immature chicken erythrocytes we identify unique chromatin spatial organization strongly differed from fibroblasts. Comparing mammalian and chicken genome architectures, we provide evidence highlighting evolutionary role of spatial organization and their significance in genome activity and regulation.
Project description:Generation of genetically uniformed individuals from somatic cells is an effective approach for large-scale reproduction of elite varieties and a powerful tool for restoration of endangered species. However, this technique has never been realized in avian due to their oviparous reproduction pattern. In this study, we produced cloned-like chicken by allogeneic transplantation of somatic cells induced primordial germ cells (PGCs). Oct4, Sox2, Nanog and Lin28A (OSNL) factors were employed to reprogram primary chicken embryo fibroblasts (CEF) to pluripotent stem cells (iPS), in which DNA demethylation and histone acetylation were found to increase the efficiency to 13.00%. The obtained iPS presented embryonic stem cell like characters and were further induced to PGCs by BMP4/BMP8b/EGF, in which histone acetylation and glycolysis inhibition elevated the induction rate to 17.30% and 16.41%, respectively. With the optimized system, we induced Black Langshan Chicken (Gallus domestiaus, black feather) donated CEF to PGCs and transplanted them into the Recessive White Chicken (white feather) embryos. The transplanted cells migrated into the genital ridges and produced functional sperm or oocytes. The sexual matured recipients were self-crossed, with 189/509 (37.13%) cloned-like chicken produced. Microsatellite analysis confirmed their DNA inheritance from the black donor chicken. Thus, we demonstrated, for the first time, the feasibility of avian cloning from somatic cells.
Project description: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. Here we used an RNA sequencing and bioinformatics approach to identify the transcript levels of all genes expressed by distinct regions of the lens epithelium and maturing fiber cells of the embryonic Gallus gallus (chicken) lens. Our analysis detected over 15,000 unique transcripts expressed by the embryonic chicken lens. Of these, over 3000 transcripts exhibited significant differences in expression between lens epithelial cells and fiber cells. Multiple transcripts coding for separate mitochondrial homeostatic and degradation mechanisms were identified to exhibit preferred patterns of expression in lens epithelial cells that require mitochondria relative to lens fiber cells that require mitochondrial elimination. These included differences in the expression levels of metabolic, autophagy, and mitophagy transcripts between lens epithelial cells and lens fiber cells. These data provide a comprehensive window into all genes transcribed by the lens and those mitochondrial regulatory and degradation pathways that function to maintain mitochondrial populations in the lens epithelium and to eliminate mitochondria in maturing lens fiber cells. Differentiation-state transcriptional analysis of embryonic chicken lenses was performed following microdissection of 100 embryonic day 13 (E13) chicken lenses into four distinct regions that represent a continuum of lens cell differentiation states: lens central epithelium (EC), equatorial epithelium (EQ), cortical fibers (FP), and central fibers (FC). Further analysis of the transcriptional content of biologically replicate samples was performed by Illumina directional mRNA sequencing and resulting reads mapped by TopHat and assembled with Cufflinks.
Project description:Cerebrospinal fluid (CSF) proteins regulate neurogenesis, homeostasis and participate in active signalling during neuroinflammation. Components of CSF are mostly blood-derived, but partially also secreted from the brain cells. While various birds may represent suitable models for the investigation of adult constitutive neurogenesis, proteomic studies of the avian CSF examined so far solely chicken embryos. On this basis, we explored the proteomic composition of CSF and plasma in adult parrots, budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus) and chickens (Gallus gallus) using liquid chromatography–tandem mass spectrometry (nLC-MS/MS). To overcome the lack of a complete cockatiel genome information, we compared the MS/MS identification success rates after mapping all spectra from all three species against the reference proteomes of three model avian species: chicken, budgerigar and zebra finch. We show highest efficiency (8.8-4.7%) for the closest reference proteome, although part of the proteins (7.2-18%) were mapped only with other references. After filtering the selected datasets, we identified up to 746 proteins represented in the CSF and plasma of chicken, budgerigar and cockatiel. Enrichment analysis of the core proteome of these datasets revealed various metabolic and signalling pathways. Comparative analysis of CSF and plasma for each species then indicated clusters of proteins preferentially upregulated into CSF that were involved in neurogenesis, neural development and neural differentiation pathways. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel molecular evidence supporting the adult neurogenesis in birds.
Project description:DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).