Lepidoptera
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REPOSITORIES: ENA
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Project description:Comparative transcriptome analysis of silkgland-expressed genes between mulberry feeders and nonmulberry feeders
| PRJDB3803 | ENA
Project description:Embryonic stem cells from B6 and NOD backgrounds were derived freshly in the presence of 2i. After 3-5 passages on feeders, ES cells were cultured in 2i media without any feeders for several passages. In order to identify differentially expressed genes and proteins, we performed RNA-Seq and mass spectromety analysis respectively. Among the differentially expressed genes, we identified several important players in innate and adaptive immunity. Several of these genes had been linked to onset of type-1 diabetes. Proteomics analysis was able to quantitative differences in protein expression among the B6 and NOD ES cell lines.
2020-08-31 | PXD020055 | Pride
Project description:We assembled larval transcriptome of D. arcuata using RNA-seq data from both social and solitary instars, and then conducted differential gene expression analysis between the two behavioural instars. This revealed a large number of transcripts that were differential expressed between the two behavioral states, including some transcripts coding for gene products that have been previously implicated in social behaviour in other insects.
2020-06-22 | GSE146351 | GEO
Project description:We investigate the functional complexity of the Plutella xylostella transcriptome in defending against a Bt toxin using Illumina sequencing technology. Over 2,900 differentially expressed unigenes were obtained in resistant P. xylostella comparison to their susceptible counterpart. All the P. xylostella were maintained on cabbage.The susceptible strain (MM) was cultured without exposure to any Bt toxins.Before the sample collected, Cry1Ac-resistant P. xylostella were treated with 750μg/mL Bt toxin Cry1Ac to eliminate the heterozygous individuals. Then the survivors were collected after 48 hours and designed as the resistant sample (MK and GK). Then fourth-instars larvae midgut tissues of MK,GK and MM were collected, respectively, The RNA was extracted and sequenced using Illunima HiSeq 2000.
2014-05-01 | E-GEOD-46399 | biostudies-arrayexpress
Project description:Autotetraploid carries several phenotypic changes with larger leaves and fruit compared to diploid. To analysis of phenotypic changes in mulberry autotetraploids on the transcriptome, we performed RNA-Seq analyses on mulberry leaf samples of diploid and autotetraploids using Illumina HiSEq 2000.
2017-02-09 | GSE70428 | GEO
Project description:In Europe, ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information and functional annotation of proteins of the most important European tick, Ixodes ricinus, is limited. Here we present the first analysis of the I. ricinus genome and of the transcriptome of the unfed I. ricinus midgut. We combined and integrated data from genome, transcriptome and proteome. The de novo assembly of 1 billion paired-end sequences identified 6,415 putative genes providing an unprecedented insight into the I. ricinus genome. Mapping of our midgut mRNA reads to the assembled contigs let us estimate to cover around two third of the unique genomic sequences. In addition, more than 10,000 transcripts from naïve midgut were annotated functionally and/or locally. By combining the alignment-based with a motif-search based annotation approach, we could double the number of annotations throughout all groups without shifting the dataset. Moreover, 1,175 proteins expressed in the naïve midgut were identified by mass spectrometry confirming the high completeness of our transcriptome database, and 608 were significantly annotated for function and/or localization. This multiple-omics study vastly extends the publicly available DNA, RNA and protein databases for I. ricinus and ticks in general.
2015-11-04 | PXD001796 | Pride
Project description:This study seeks to understand the mechanism of midgut escape and identify candidate genes and potential biochemical pathways involved in the midgut infection of chikungunya virus (CHIKV) in vector mosquito Aedes aegypti. We conducted a comparative transcriptomic analysis of midgut samples of female mosquitoes,after feeding a saline meal (SM) or a protein meal (PM) containing CHIKV. Our results allow the conclusion that midgut-expressed genes not involved in blood or protein digestion can be identified by substituting either a bloodmeal or PM for a SM. In presence of orally acquired CHIKV in midguts of SM fed mosquitoes, the majority of the upregulated DE genes belonged to the categories immune system and catalytic activity. These genes included several serine-type endopeptidases, trypsins, collagenases, and M1 zinc metalloproteases, which potentially could be involved in the midgut escape mechanism of CHIKV. One of the serine metalloproteinase genes, AeLT, was further analyzed showing strong (MMP) collagenase activity in vitro. Our results present a set of candidate genes potentially responsible for overcoming the arbovirus midgut escape barrier (MEB) in Ae. aegypti.
2017-05-17 | GSE95378 | GEO
Project description:Purpose: We isolated Drosophila midgut cells : Delta+ intestinal stem cells (ISCs), Su(H)+enteroblasts (EBs), Esg+ cells (ISC+EB), Myo1A+Enterocytes (ECs), Pros+Enteroendocrine cells (EEs) and How+Visceral muscle cells (VM) from whole midguts to identify stem cell specific genes and study cell type specificities of midgut cells. We also isolated all the cell types from the 5 major regions (R1-R5) of the Drosophila midgut to study differences in cells in different regions. Methods: 3-7 day old female flies were dissected. Flies with GFP/YFP marking different cell types (using the GAL4-UAS system) were used to separate cells of the midgut.The midguts were dissociated with Elastase and FACS sorted using FACS AriaIII. RNA was extracted, amplified and sequenced. Whole midgut samples were sequenced on Illumina GAIIX and regional cell populations were sequenced on HiSeq2000. Methods:Raw fastqc reads were mapped to the Drosophila genome (Drosophila_melanogaster.BDGP5.70.dna.toplevel.fa) using Tophat 2.0.9 at default (using boost_1_54_0, bowtie2-2.1.0, samtools-0.1.19). Methods: For differential expression analysis, DESeq (p-value adjustment 0.05 by method Benjamini-Hochberg) was used. The reads were normalized also to Reads per kilobase of transcript per million mapped reads (RPKM). Results: More than 50% of the genome is expressed in the adult midgut (FlyAtlas- Chintapalli et al., 2007), of these genes about 50% (2457) were differentially expressed (DE) between all 4 cell types (ISCs, EBs, ECs and EEs) atleast 2 folds with 95% confidence Results: 159 genes that were specifically enriched in ISCs, 509 genes were specifically repressed in ISCs Conclusions: Our study represents the first detailed analysis of Drosophila intestinal cell transcriptomes, with biologic replicates, generated by RNA-seq technology.Our data facilitates comparative investigations of expression profiles of cells and reveals novel stem cell genes. Further region specific profiling adds precision to the analysis of variances in the midgut regions. We identify transcriptional regulators and regional transcription factors which modulate the midgut physiology. The dataset will be a great resource for hypothesis generation, tool building and fine tuned studies on the Drosophila midgut.
2015-05-23 | GSE61361 | GEO
Project description:Human utilization of the mulberry-silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species (Morus notabilis C. K. Schneider). In the 330 Mb genome assembly of M. notabilis, we identified 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which were supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating its spread to Europe, Africa, and America. It is among few eudicots but several Rosales not preserving genome duplications in more than 100 million years – however neopolyploid series in mulberry and several others suggest that new duplications may confer benefits. Strikingly, five predicted mulberry miRNAs were found in the hemolymph and silkglands of silkworm, suggesting profound molecular level interactions that promise to expand knowledge of plant-herbivore relationship which constitute key elements of most terrestrial habitats. In addition, we investigated the characters of hemolymph small RNA. small mRNA profiles of silkworm hemolymph in the fifth instar day-5 silkworm were generated by deep sequencing, in twice, using Illumina Hiseq 2000.
2013-09-12 | E-GEOD-48168 | biostudies-arrayexpress
Project description:To investigate effects of intake of mulberry leaves on hyperlipidemia, we performed gene expression profiling on rat liver by microarray analysis. Microarray analysis revealed that mulberry leaves up-regulated the genes involved in alpha-, beta-, and omega-oxidation of fatty acids, mainly relating to peroxisome proliferator-activated receptor signaling pathway, and down-regulated the gene expression involved in lipogenesis. Furthermore, the genes relating to response to oxidative stress were up-regulated in rats administrated mulberry leaves.
2011-01-01 | GSE21075 | GEO