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Gallus gallus

ABSTRACT: Quantitative Analysis of differentially expressed genes between HH10-HH13 stages of chick embryo

PROVIDER: PRJNA258415 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1553301_1.fastq.gz	Fastqsanger.gz
	SRR1553301_2.fastq.gz	Fastqsanger.gz
	SRR1553302_1.fastq.gz	Fastqsanger.gz
	SRR1553302_2.fastq.gz	Fastqsanger.gz
	SRR1553303_1.fastq.gz	Fastqsanger.gz

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Project description:Purpose:We have used RNA-seq to examine of differentially expressed miRNAs in chicken leg muscle of three different development stages (11 embryo ages, 16 embryo ages, and 1 day old post hatch chick).The aims of this study are characterization of miRNAs differentially expressed in different developmental stage of chicken embryo, using RNA sequence sample. Methods: On this study we used two embryonic stage and one post hatch chick leg muscle of Xinghua chicken breed. Total RNA from E11 day embryo, E16 day embryo and 1 day post hatch chick was isolated by TRIzol following the manufacturer’s protocol (Invitrogen, CA, USA). Each stages were designed two samples, and the total samples were six (three group × two sample/group) and RNA samples of six individuals were pooled with equal amounts, and then were subjected to Illumina deep sequencing. Results: After eliminating adaptor and low-quality reads, a total of 5,302,700, 6,556,747, 5,359,793, 4,213,112, 7,112,885 and 7,469,939 clean reads were obtained in group E11 (E11.1-E11.2), group E16 (E16.1-E16.2) and group P1 (P1.1–P1.2) libraries, respectively. The clean reads were aligned to the chicken genome databases, miRBase, Rfam, RepBase and mRNA. Conclusions:To assess miRNA expression during chicken embryo skeletal muscle development, we sequenced and analyzed leg muscle at 11 day embryo age, 16 day embryo age, and 1 days post hatch.

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Project description:Newly-hatched domestic chick serves as an important model for studies of neural and behavioral plasticity, particularly with respect to learning and memory such as filial imprinting. Imprinting is assumed to be a unique case of recognition learning with some characteristic features, such as sensitive period and irreversibility. However, the molecules involved in the memory process are yet to be fully identified. To address this issue, we attempted to identify the genes differentially expressed at an earlier phase of filial imprinting than described in our previous report (Brain Res. Bull.76, 275-281 (2008)). One-day-old chicks were trained for imprinting for 1 h and whole brains were collected and used for cDNA microarray analysis and quantitative RT-PCR. We identified 18 genes upregulated accompanying filial imprinting. These results suggested that the increase of these 18 genes associated with filial imprinting might play an important role in the acquisition of memory in the filial imprinting. Total RNA was extracted from whole brains of trained chicks (n=16) and control dark-reared chicks (n=16). Using these total RNAs, we performed RT-PCR to distinguish male chicks from females. Then total RNAs were separated and mixed in four groups (1, male trained (n=8); 2, female trained (n=8); 3, male dark-reared (n=8); and 4, female dark-reared chicks (n=8)), and we performed cDNA microarray expression analysis to identify the upregulated genes following imprinting (1 versus 3 and 2 versus 4).

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