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:Purpose:In order to assess the respiratory toxicity of co-infection in chicken lung, we established a co-infection model to investigate transcriptome profiles of chicken lung. Methods: RNA extracted by Trizol reagent (Invitrogen) was utilized to construct the final library (BGISEQ-500 RNA-Seq Library) based on the manufacturer’s instructions. Library was validated on the Agilent Technologies 2100 bioanalyzer. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecule. The DNBs were load into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by synthesis. Whole transcriptome sequencing data was filtered and mapped to Chicken genome (Gallus genome Version 5.0.1 NCBI). DEG-seq method was based on Poisson distribution (Fold Change > 2 and Adjusted P value < 0.001) Results: Sampling directly from the lung yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 18,043 Gallus gallus genes. Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-infection (MG and E.coli) and their underlying mechanisms.
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: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).
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:The change in the plasma proteome in chicken (Gallus gallus) challenged with lipopolysaccharide (endotoxin) derived from E. coli was determined by relative quantitation using a TMT label-based approach. This study provides insights into different factors contributing to innate immune response to experimental infection during 72 hours with special emphasis on acute phase proteins (APPs). Apart from APPs, several pathways endopeptidase activation and vasoconstriction were found to be significant.
Project description:The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology. During chick development, embryonic day 8 (E8) retina are packed with multipotent neuronal precursors on the cusp of differentiation into all retinal cell types. By E18 the retina is nearly fully mature with all major retinal cell types differentiated and expressing cell type-specific genes. Whole retina were harvested from embryonic day 8 (E8), E16, and E18 developing chicken embryos. Whole cornea were also collected from E18 embryos as a reference tissue. Duplicates were obtained for each time point and total RNA was extracted from samples using a Qiagen AllPrep Mini Kit. To characterize differential gene expression in these tissues, Illumina stranded TrueSeq RNA-Seq libraries were prepared from total RNA and 125 PE sequencing reads were obtained. These data will be used to characterize retina-specific patters of gene expression as well as global changes in gene expression between critical developmental time points in the chicken retina.
