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Chicken Enteroids

ABSTRACT: Transcriptome of chicken (Gallus gallus) enteroids

PROVIDER: PRJEB37491 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR4017930_1.fastq.gz	Fastqsanger.gz
	ERR4017930_2.fastq.gz	Fastqsanger.gz
	ERR4017940_1.fastq.gz	Fastqsanger.gz
	ERR4017940_2.fastq.gz	Fastqsanger.gz
	ERR4017931_1.fastq.gz	Fastqsanger.gz

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Chicken Enteroids 2

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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.

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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.

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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).

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