Dataset Information

The proteomics analyses of different silkworm tissues(fat body)

ABSTRACT: We collected a total of 9.8 million mass spectra data generated in the laboratory from the proteomics analyses of different silkworm tissues.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Bombyx Mori (silk Moth)

TISSUE(S): Fat Body

SUBMITTER: Boxiong Zhong

LAB HEAD: Boxiong Zhong

PROVIDER: PXD009695 | Pride | 2019-07-01

REPOSITORIES: Pride

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Publications

Improving Silkworm Genome Annotation Using a Proteogenomics Approach.

Ye Xiaogang X Tang Xiaoli X Wang Xiaoxiao X Che Jiaqian J Wu Meiyu M Liang Jianshe J Ye Lupeng L Qian Qiujie Q Li Jianying J You Zhengying Z Zhang Yuyu Y Wang Shaohua S Zhong Boxiong B

Journal of proteome research 20190702 8

The silkworm genome has been deeply sequenced and assembled, but accurate genome annotation, which is important for modern biological research, remains far from complete. To improve silkworm genome annotation, we carried out a proteogenomics analysis using 9.8 million mass spectra collected from different tissues and developmental stages of the silkworm. The results confirmed the translational products of 4307 existing gene models and identified 1701 novel genome search-specific peptides (GSSPs) ...[more]

PMID: 31250652

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Project description:Single-base resolution DNA methylomes have been accomplished for both Arabidopsis and human cells which have high genome methylation levels by Illumina ultra-high-throughput bisulfite sequencing technology (MethylC-Seq). Here by combining MethylC-Seq and biological replicate strategies we generated single-base resolution methylome for the silkworm which has low genome methylation levels like other insects. Our conservative estimation showed that methylcytosines (mCs) accout for about 0.11% of genomic cytosines, exclusively in CG context. The CG methylation is significantly enriched in gene bodies and positively correlated with gene expression levels, suggesting its positive role in gene transcription in silkworms. However, the well-documented functions of methylation on promoters and rDNAs in plants and mammals do not seem to have effects in insects. Methylated genes are enriched in functions involved in cellular metabolism and biosynthesis. Small RNA (smRNA) loci are also significantly enriched in gene bodies, and moreover, the smRNA loci and the predicted target sites of microRNA have high level of CG methylation, indicating functional involvement of smRNAs in the genic methylation This first methylome for silkworms provides a foundation for further studies on the epigenetic gene regulation of silkworms’ or even insects’ gene methylation. Each silk gland of 5th instar larvae of two individuals (called Biological Replicate 1 and 2, respectively) of the silkworm (Bombyx mori) strain Dazao was ground into powder in liquid nitrogen. Half of the powder from each silk gland was used to extract total DNAs using DNeasy Blood & Tissue Kit (Qiagen) and another half was used to extract total RNAs using RNeasy Mini Kit (Qiagen). We sequenced bisulfite-treated total DNA extracted from the silk glands of the two individuals, using Illumina Ultra-High-Throughput Sequencing, generating the Single-Base Resolution Methylomes. To reveal functional consequences of gene body methylation, we generated expression profiles for the two individuals’ silk glands using Digital Gene Expression tag profiling (DGE) technology, which combines classic SAGE (Serial Analysis of Gene Expression) and Illumina ultra-high-throughput sequencing technology.

			Action	DRS
	ZB10-Drosophila.dat	Other
	ZB10-bombyx.dat	Other
	ZB10.dat	Other
	fatbody.adult.raw.rar	Raw
	fatbody.larva.raw.rar	Raw