Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1149711 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2015-03-13 | GSE36504 | GEO
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.
2017-03-10 | GSE96037 | GEO
Project description:Expression of known and predicted genes in tissues of Gallus gallus (chicken) pooled from multiple healthy individuals.
2009-04-16 | GSE12974 | GEO
Project description: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. The sequencing data obtained from Illumina Hiseq™ was filtered to get clean reads using Trimmomatic. The reads themselves and their matching reads which length was less than 35nt were removed. Clean reads were aligned to the reference sequence (Gallus_gallus-5.0, NCBI) using HISAT2. Results: Sampling directly from the liver yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 24,883 Gallus gallus genes. Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-administered (AFB1 and curcumin) and their underlying mechanisms.
2022-04-02 | GSE148014 | GEO
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.
2019-04-19 | GSE130015 | GEO
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.
2021-04-26 | GSE166257 | GEO
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).
2019-05-25 | GSE131764 | GEO
Project description:RNA samples from chicken (Gallus gallus) embryonic fibroblasts (sample ID: ES90) as well as from the HD11 chicken macrophage cell line (sample ID: ES91) were sequenced at the National Institutes of Health Intramural Sequencing Center (NISC) using the Illumina GAIIx technology running the standard CASAVA/ELAND pipeline.
2013-08-01 | E-MTAB-1479 | biostudies-arrayexpress