Browse
Submit Data
Databases
API
Help

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MicroRNA of the fifth-instar posterior silk gland of silkworm identified by Solexa sequencing.

ABSTRACT: No special studies have been focused on the microRNA (miRNA) in the fifth-instar posterior silk gland of Bombyx mori. Here, using next-generation sequencing, we acquired 93.2 million processed reads from 10 small RNA libraries. In this paper, we tried to thoroughly describe how our dataset generated from deep sequencing which was recently published in BMC genomics. Results showed that our findings are largely enriched silkworm miRNA depository and may benefit us to reveal the miRNA functions in the process of silk production.

SUBMITTER: Li J

PROVIDER: S-EPMC4535748 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

MicroRNA of the fifth-instar posterior silk gland of silkworm identified by Solexa sequencing.

Li Jisheng J Ye Lupeng L Wang Shaohua S Che Jiaqian J You Zhengying Z Zhong Boxiong B

Genomics data 20141007

No special studies have been focused on the microRNA (miRNA) in the fifth-instar posterior silk gland of Bombyx mori. Here, using next-generation sequencing, we acquired 93.2 million processed reads from 10 small RNA libraries. In this paper, we tried to thoroughly describe how our dataset generated from deep sequencing which was recently published in BMC genomics. Results showed that our findings are largely enriched silkworm miRNA depository and may benefit us to reveal the miRNA functions in ...[more]

PMID: 26484119

Similar Datasets

MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori.

Project description:BackgroundThe growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production.ResultsHere, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, of the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs. Functional categorization classifies the targets into complex pathways that include both cellular and metabolic processes, especially protein synthesis and processing.ConclusionThe enrichment of target genes in the ribosome-related pathway indicates that miRNAs may directly regulate translation. Our findings pave a way for further functional elucidation of these miRNAs and their targets in silk production.

| S-EPMC4045974 | biostudies-literature

MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori

2014-07-30 | GSE56380 | GEO

MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori

Project description:Background: The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. Results: Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, from the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs. Functional categorization classifies the genes into complex pathways that include both cellular and metabolic processes, especially protein synthesis and processing. Conclusion: The enrichment of target genes in the ribosome-related pathway indicates that miRNAs may directly regulate translation. Our findings pave a way for further functional elucidation of these miRNAs in silk production. Sequencing 10 total RNA samples from the posterior silk gland of different strains and developmental stage using Illumina Solexa technology. Four strains of silkworm (Q, B, QB and BQ) with different two development stages (stage 1: fourth instar molting to day 2 of fifth instar; stage 2: fifth instar day 3 to day 8 before spinning, according to our previous genes expression cluster analysis), and two strains (R1 and J1) from entire period (stage 1 + stage 2).

2014-07-30 | E-GEOD-56380 | biostudies-arrayexpress

Analysis of Transcripts Expressed in One-Day-Old Larvae and Fifth Instar Silk Glands of Tasar Silkworm, Antheraea mylitta.

Project description:Antheraea mylitta is one of the wild nonmulberry silkworms, which produces tasar silk. An EST project has been undertaken to understand the gene expression profile of A. mylitta silk gland. Two cDNA libraries, one from the whole bodies of one-day-old larvae and the other from the silkglands of fifth instar larvae, were constructed and sequenced. A total of 2476 good-quality ESTs (1239 clones) were obtained and grouped into 648 clusters containing 390 contigs and 258 singletons to represent 467 potential unigenes. Forty-five sequences contained putative coding region, and represented potentially novel genes. Among the 648 clusters, 241 were categorized according to Gene Ontology hierarchy and showed presence of several silk and immune-related genes. The A. mylitta ESTs have been organized into a freely available online database "AmyBASE". These data provide an initial insight into the A. mylitta transcriptome and help to understand the molecular mechanism of silk protein production in a Lepidopteran species.

| S-EPMC2864506 | biostudies-literature

The proteomics analyses of different silkworm tissues(posterior silk gland)

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

2019-07-01 | PXD009869 | Pride

The fourth instar in the silk gland of silkworm LC-MSMS

Project description:In the present study, the silk gland proteomes of the fourth instar and fourth molt were analyzed using liquid chromatography−tandem mass spectrometry. In total, 2654 proteins were identified from the silk gland. High abundance of ribosomal proteins and RR-motif chitin-binding proteins were identified during day 2 of the fourth instar (IV-2) larval developmental stage, and the expression of cuticular proteins analogous to peritrophin (CPAP)-motif chitin-binding proteins was higher during the fourth molt (IV-M). In all, nine enzymes were found to be involved in the chitin regeneration pathway in the silk gland. Among them, two chitinase and two chitin deacetylases were identified as CPAP-motif proteins.

2018-06-04 | PXD008677 | Pride

Circular transcriptome sequencing of the middle silk gland and posterior silk gland in the Bombyx mori.

Project description:Circular transcriptome sequencing of the middle silk gland (MSG) and posterior silk gland (PSG) in the Bombyx mori are presented. The middle silk gland and posterior silk gland were collected from the third day of fifth-instar B.mori larvae. The circular RNAs enriched by using RNase R to degrade the linear RNA molecules, and circular RNA sequencing (circRNA-seq) was performed using an Illumina Hiseq. 2500 sequencing platform. Samples are described in the SRA portal (SRP100385) and FASTQ files have been deposited in Sequence Read Archive (accession numbers: SRX2577343 and SRX2577342). The interpretation of these data is presented in the following research article: "Identification of circular RNA in the Bombyx mori silk gland" [1] (Gan et al., 2017).

| S-EPMC5671477 | biostudies-literature

Proteomic analysis of posterior silk gland of wild silkworm during developmental stages

Project description:We performed shotgun proteomic analysis of the posterior silk glands (PSGs) of wild silkworms on the 3rd and 5th days of the fifth instar.

2017-08-25 | PXD006655 | Pride

Proteome identification of the silkworm middle silk gland.

Project description:To investigate the functional differentiation among the anterior (A), middle (M), and posterior (P) regions of silkworm middle silk gland (MSG), their proteomes were characterized by shotgun LC-MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014) [1] via the PRIDE partner repository (Vizcaino, 2013) [2] with the dataset identifier PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP) after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015) [3].

| S-EPMC4753389 | biostudies-literature

The proteomics analyses of different tissues(the posterior silk gland of wild silkworm)

Project description:We collected a total of 9.8 million mass spectra data generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland (29), middle silk gland (30), ovary and testis (31), head (32), brain, prothoracic glands, subesophageal ganglion (33), hemolymph (34), fat body (35) and embryo (36,37) of domestic silkworm, and the posterior silk gland of wild silkworm (38).

2019-07-01 | PXD009671 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data