Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

69 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Host reponse of silkworm, Control vs. Nb infected

ABSTRACT: Microsporidia have attracted much attention because they infect a variety of species ranging from protists to mammals, including immunocompromised patients with AIDS or cancer. Aside from the study on Nosema ceranae, few works have focused on elucidating the mechanism in host response to microsporidia infection. Nosema bombycis is a pathogen of silkworm pM-CM-)brine that causes great economic losses to the silkworm industry. Detailed understanding of the host (Bombyx mori) response to infection by N. bombycis is helpful for prevention of this disease. The 23 K silkworm genome array was used to investigate host responses (i.e., Bombyx mori) occurring at 2, 4, 6 and 8 d post-infection by Nosema bombycis.We focused on elucidating the mechanism of the host response to microsporidia infection, especially for the investigation of host immune response . The third instar molted silkworm larvae were in oral infected by Nosema bombycis. In order to known the silkworm host response to Nosema bombycis infection at different time points, samples of infected larvae (i.e., the treatment set) and uninfected larvae (i.e., the control set) were collected at 2, 4, 6 and 8 dpi for RNA extraction and array hybridization. The obtained data were usd to investigate on the interplay of the genome-wide expression profile of hosts.

ORGANISM(S): Bombyx mori

SUBMITTER: Tian Li

PROVIDER: E-GEOD-51247 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Juvenile hormone (JH) response in integuments of silkworm larvae

Project description:Expression changes in silkworm integuments after JH analogue (JHA) methoprene treatment. Two-condition experiments, namely JH analogue (JHA) methoprene treatment (Test) and acetone treatment (Control). Time course: 12 hours after treatment (Hat), 24 Hat, 36 Hat, and 48 Hat.

2014-06-29 | E-GEOD-53374 | biostudies-arrayexpress

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

Expression profile of cuticular genes of silkworm, Bombyx mori

Project description:Insect cuticle plays essential roles in multiple physiological functions. During molting and metamorphosis, tremendous changes occur in silkworm cuticles. Silkworm is a model of Lepidoptera insects; however, little is known about the stage expression profiles of genes in cuticles of silkworm. In the present study, we selected 16 developmental stages, ranging from day 1 of the first instar larvae to day 8 of pupae, to perform microarray-based expression profiles. The data told us that various functions and physiological pathways were activated in the cuticle. Moreover, the expression profiles of cuticular protein genes, as the important components of cuticle, were investigated. The current study provides important insights for the functional study of insect cuticle and the regulation of insect cuticular protein genes. Transcription profiling experiments, 16 developmental stages (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. Common reference sample was used for data normalization. One biological replicate. No dye-swaps.

2009-11-04 | E-GEOD-18878 | biostudies-arrayexpress

Microarray-based gene expression profiles of silkworm brains

Project description:Molecular genetic studies of Bombyx mori have led to profound advances in understanding the regulation of development. Bombyx mori brain, as a main endocrine organ, plays important regulatory roles in various biological processes. The microarray technology will allow the genome-wide analysis of gene expression patterns in silkworm brains. We reported microarray-based gene expression profiles in silkworm brains at four stages including V7, P1, P2 and P3. A total of 4,550 genes were transcribed in at least one selected stage. Of these, clustering algorithms separated the expressed genes into stable expressed genes and variable expressed genes. The results of the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis of stable expressed genes showed that the ribosomal and oxidative phosphorylation pathways were principal pathways. Secondly, four clusters of genes with significantly different expression patterns were observed in the 1,175 variable expressed genes. Thirdly, thirty-two neuropeptide hormones genes, nine neuropeptide-like precursor genes, and 117 cuticular protein genes were expressed in selected developmental stages. The present study deﬁned major characteristics of the transcriptional profiles in the brains of Bombyx mori at the specific development stages. Our data will provide abundant information that will be useful in future research. Transcription profiling experiments, 4 developmental stages (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. Common reference sample was used for data normalization. One Biological replicate. No dye-swaps.

2010-11-16 | E-GEOD-25342 | biostudies-arrayexpress

Knockdown of BmSoxE gene in silkworm BmN4-SID1 cells

Project description:Transcriptional profiling of silkworm BmN4-SID1 cells comparing the test of BmSoxE knockdown with the control of EGFP Knockdown. Two-condition experiment, BmSoxE knockdown vs EGFP Knockdown. Biological replicates: 3. One replicate per array.

2014-06-28 | E-GEOD-53240 | biostudies-arrayexpress

The midgut of domestic silkworm: Control vs. phoxim treated

Project description:Transcriptional characteristics of genes in the midgut of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray. Transcription profiling experiments, phoxim-treated midgut (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and control samples labeled by Cy3. Three Biological replicate. No dye-swaps.

2012-10-13 | E-GEOD-41550 | biostudies-arrayexpress

Genome-wide Identification of Polycomb Target Genes Reveals a Functional Association of Pho with Scm in Bombyx mori

Project description:Polycomb group (PcG) proteins are involved in chromatin modifications for maintaining gene repression that play important roles in the regulation of gene expression, tumorigenesis, chromosome X-inactivation, and genomic imprinting in Drosophila melanogaster, mammals, and even plants. PcG proteins act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1), Polycomb repressive complex 2 (PRC2), and Pleiohomeotic repressive complex (PhoRC), to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori using genome-wide expression screening based on the knockdown of the BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, most genes were up-regulated after knocking down these four PcG genes, which indicated a potential epigenetic mechanism on the regulation of these genes expression by the PcG system. The further analysis of our data will provide some important information for the regulation mediated by PcG proteins in Bombyx mori. Transcription profiling experiments, knockdowns of four Polycomb genes (four samples) in silkworm BmN4-SID1 cells, were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. The common reference sample, knockdown of the EGFP gene in BmN4-SID1 cells, was used for data normalization. One biological replicate. No dye-swaps.

2012-04-17 | E-GEOD-34246 | biostudies-arrayexpress

Gene expression profiling of the fat body of Bombyx mori exposed to phoxim insecticide

Project description:Transcriptional characteristics of genes in the fat body of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray. Transcriptional profiling of fat body in the domestic silkworms comparing control untreated fat body with phoxim-treated fat body Transcription profiling experiments, phoxim-treated fat body (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and control samples labeled by Cy3. Three Biological replicate. No dye-swaps.

2016-07-03 | E-GEOD-60877 | biostudies-arrayexpress

MicroRNAs of Bombyx mori identified by Solexa sequencing

Project description:Background: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three total RNA libraries prepared from the whole body, and the anterior and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. Results: With the aid of large-scale Solexa sequencing technology, we validated 244 unique miRNA genes, including 191 novel and 53 previously reported genes, corresponding to 309 loci in the silkworm genome. Interestingly, 24 unique miRNAs were widely conserved from invertebrates to vertebrates; 12 unique ones were limited to invertebrates and 33 were confined to insects; whereas the majority of the newly identified miRNAs were silkworm-specific. We identified 21 clusters and 42 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters are not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs are located in transposable elements, and display significant differences in abundance between the anterior and posterior silk glands. Conclusions: Conservative analysis revealed that miRNAs serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enriched the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior and posterior silk glands supports their involvement as new layers in the regulation of the silkworm silk gland. Sequencing three total RNA pools of the whole silkworm body from 5th-instar day-3 larvae, and anterior and posterior silkworm silk glands, using the latest sequencing Solexa technology

2010-02-01 | E-GEOD-17965 | biostudies-arrayexpress

Host reponse of silkworm, Control vs. Nb infected

Project description:Microsporidia have attracted much attention because they infect a variety of species ranging from protists to mammals, including immunocompromised patients with AIDS or cancer. Aside from the study on Nosema ceranae, few works have focused on elucidating the mechanism in host response to microsporidia infection. Nosema bombycis is a pathogen of silkworm pébrine that causes great economic losses to the silkworm industry. Detailed understanding of the host (Bombyx mori) response to infection by N. bombycis is helpful for prevention of this disease. The 23 K silkworm genome array was used to investigate host responses (i.e., Bombyx mori) occurring at 2, 4, 6 and 8 d post-infection by Nosema bombycis.We focused on elucidating the mechanism of the host response to microsporidia infection, especially for the investigation of host immune response .

2013-09-27 | GSE51247 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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