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Expression data from silkworm posterior silk glands at the late larval stages

ABSTRACT: The silkworm silk gland is one of the most efficient protein synthesis systems among all organisms. Its amazingly efficient protein synthesis makes the silk gland a desirable object for basic studies on gene expression and regulation and for biotechnological applications. At the early stages of the fifth (final) instar, the cellular structures necessary for the synthesis of fibroin are rapidly formed, and at the later stage the synthesis of fibroin proceeds at a maximum rate. The posterior silk gland (PSG) is the longest suborgan and is responsible for the synthesis of the silk core protein fibroin, which is composed of heavy (H) and light (L) chains plus P25. We used microarrays to detail the global programme of gene expression in silkworm PSG during the late larval stages, including the fourth molting (M4) and day 1 (V1), day 3 (V3), day 5 (V5), and day 7 (wandering stage, W) of the fifth instar, and to reveal the correlations of differential expression genes with the PSG development and fibroin synthesis.

ORGANISM(S): Bombyx mori

PROVIDER: GSE26172 | GEO | 2012/12/05

SECONDARY ACCESSION(S): PRJNA135253

REPOSITORIES: GEO

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Expression data from silkworm posterior silk glands at the late larval stages

Project description:The silkworm silk gland is one of the most efficient protein synthesis systems among all organisms. Its amazingly efficient protein synthesis makes the silk gland a desirable object for basic studies on gene expression and regulation and for biotechnological applications. At the early stages of the fifth (final) instar, the cellular structures necessary for the synthesis of fibroin are rapidly formed, and at the later stage the synthesis of fibroin proceeds at a maximum rate. The posterior silk gland (PSG) is the longest suborgan and is responsible for the synthesis of the silk core protein fibroin, which is composed of heavy (H) and light (L) chains plus P25. We used microarrays to detail the global programme of gene expression in silkworm PSG during the late larval stages, including the fourth molting (M4) and day 1 (V1), day 3 (V3), day 5 (V5), and day 7 (wandering stage, W) of the fifth instar, and to reveal the correlations of differential expression genes with the PSG development and fibroin synthesis. Silkworm PSGs were collected at M4, V1, V3, V5, and W stages for RNA extraction and hybridization on 23K Silkworm Genome Arrays (CapitalBio Corp., Beijing, China). Three groups of biological replicates were prepared at each time point.Dual-dye experiments were performed for the PSG at M4, V1, V3, V5, and W; a total of 15 samples were tested including three biological replicates at each stage. Aliquots of each test sample were pooled as a common reference sample (CKA). The test samples and CKA were labeled with Cy3 and Cy5, respectively.

2012-12-05 | E-GEOD-26172 | biostudies-arrayexpress

Proteome identification of the silkworm middle silk gland

Project description:The middle silk gland (MSG) is an important silkworm sub-organ for synthesis and secretion of sericin proteins. To investigate the proteome differences among the anterior, middle, and posterior regions of silkworm MSG at the third day of the fifth instar, the extracted tissue proteins were digested in gel with trypsin followed by shotgun LC-MS/MS analysis with a LTQ-Orbitrap mass spectrometer.

2016-03-11 | PXD003371 | Pride

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

Bombyx mori anterior silk gland LC-MS/MS

Project description:The anterior silk gland in the silkworm plays an important role in the process of liquid fibroin to solid silk fiber .In view of this,the proteomics analysis was applied to to study the relationship between the function of proteins in the anterior silk gland and the mechanism of spinning. The anterior silk glands on the 3rd day of fifth instar were dissected.Aftter 1D SDS-PAGE ,one gel lane was cut into 10 bands and each band further sliced into small pieces was subjected to in-gel tryptic digestion for 20 hours.The digested peptides were separated by RP nanoscale capillary liquid chromatography and analyzed using a surveyor LC system (Thermo Figgigan, San Jose, CA).The eluate from the RP column was analyzed by Finnigan LTQ(Thermo Electron Corporation）linear ion trap Mass equipped with a nanospray souce in the positive ion mode. The MS analysis was performed with one full MS scan followed by three MS/MS scans on the most intense ions from the MS spectrum with the dynamic exclusion settings: repeat count 2, repeat duration 30s, exclusion duration 90s. Data were acquired in data-dependent mode using Xcalibur software.Ten raw datasets from LC-MS/MS were searched against the predicted silkworm database by Xia.et al which consists of 21312 silkworm proteins.The searching was carried out with the Turbo SEQUEST(Bioworks version 3.2, Thermo Electron).

2014-03-26 | PXD000090 | Pride

Improving silkworm genome annotation using a proteogenomics approach

Project description:We collected a total of 9.8 million mass spectra generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland (PSG) 30, middle silk gland 31, ovary and testis 32, head 33, brain, prothoracic glands, subesophageal ganglion 34, hemolymph 35, fat body 36 and embryo 37,38 of domestic silkworm, and the posterior silk gland of wild silkworm 39.

2019-07-01 | PXD009697 | Pride

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

2014-07-30 | GSE56380 | GEO

Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori

Project description:We designed and constructed a genome-wide microarray with 22,987 70-mer oligonucleotides covering the presently known and predicted genes in the silkworm genome, and surveyed the gene expression in multiple silkworm tissues on day 3 of the fifth instar. Clusters of tissue-prevalent and tissue-specific genes and genes that are differentially expressed in different tissues were identified, and they reflect well major tissue-specific functions on the molecular level. The data presented in this study provide a new resource for annotating the silkworm genome. In the present study, we surveyed gene expression in the A/MSG, the PSG, testis, ovary, fat body, midgut, integument, hemocyte, malpighian tubule, and head from silkworm individuals on day 3 of the fifth instar. In order to establish gene expression differences between sexes, we prepared male and female samples of the same tissue. In addition, we also selectively performed the biological replicates at least twice for five tissues including testis, ovary, A/MSG, PSG and malpighian tubule, to evaluate biological reproducibility. In all, we prepared 30 two-channel hybridizations across the selected tissues for study. We extracted the single channel intensity instead of the ratio value from each two-channel hybridization for further analysis, a strategy that has been reported as being more flexible and valid previously.

2009-08-28 | E-GEOD-17571 | biostudies-arrayexpress

Bombyx mori Posterior and Median Silk Gland SAGE transcriptome

Project description:To identify functions that distinguish the posterior and median cells producing fibroin and sericin in the silk gland of Bombyx mori, serial analysis of gene expression (SAGE) profiles from both silk gland regions were analyzed and compared. The construction of a B. mori reference tag collection extracted from a set of 38000 Bombyx EST sequenced from the 3’ side, helped annotating the SAGE libraries. Most of the tags appeared at similar relative concentration in the two libraries except for those corresponding to silk proteins that were found region-specific and highly abundant. Strikingly, besides tags from silk protein mRNAs, 19 tags were found in the class of high abundance in the median cell library, which were absent in the posterior cell tag collection. Except tags from SP1 mRNA, no PSG specific tags were found in the same class of abundance. The analysis of MSG-specific different transcripts led to suggest that middle silk gland cell realizes more diversified functions as those already known, of synthesis and secretion of the silk sericins.

2010-12-22 | GSE23098 | GEO

Project description:small RNA sequencing for silk gland of silkworm on 3-day of fifth instar

| PRJNA393492 | ENA

Silkworm spinneret LC-MSMS - Proteome profile of spinneret from the silkworm, Bombyx mori

Project description:Spinneret, which locates at the end of the silk gland, is an important tissue for silk spinning. Although it has been discovered for hundreds of years, its particular roles in silk spinning and fiber formation are still unclear. Here we report the first proteome profile of silkworm spinnerets by LC-MS/MS. Totally, 1572 non-redundant proteins and 232 differential expressed proteins were identified in the spinneret from the spinning larvae and the third day of fifth instar larvae. Silk fiber formation related proteins, such as cuticle proteins, ion-transporting proteins, muscular proteins, and energy metabolic proteins, were abundant in the spinneret. By analyzing the signal pathways, we discovered that the processes associated with energy metabolism were active in spinneret. GO enrichment analysis revealed that the differential expressed proteins were involved in energy metabolism, chitin binding, and cuticle construction. The active energy metabolism might provide abundant energy for the muscle contraction, ion and water transporting. The chitin binding and cuticle construction process might provide sufficient shear forces for silk formation. This dataset suggests that the spinneret provided a suitable physiological and biochemical environment for silk formation, and will be helpful for elucidating the functions of spinneret.

2017-05-08 | PXD004455 | Pride

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