Ontology highlight
ABSTRACT:
PROVIDER: PRJNA925024 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE16536: Using pooled earthworm RNA to test 244K probes on TA-1 test array design 2520022 sense 1 GSE16548: Using pooled earthworm RNA to test 244K probes on TA-2 test array design 2520023 antisense 1 GSE16549: Using pooled earthworm RNA to test 244K probes on TA-3 test array design 2520024 sense 2 GSE16550: Using pooled earthworm RNA to test 244K probes on TA-4 test array design 2520025 antisense 2 Refer to individual Series
2010-05-18 | E-GEOD-16551 | biostudies-arrayexpress
Project description:earthworm tissue, Lumbricus rubellus, 3D model building
2022-03-01 | PXD004399 | Pride
Project description:Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio), fruit fly (Drosophila melanogaster) and earthworm (Eisenia andrei) are still lacking. Here, we construct the zebrafish, Drosophila and earthworm cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish, Drosophila and earthworm, and studying difference between vertebrates and Invertebrates at single cell level.
2022-07-08 | GSE181511 | GEO
Project description:The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.
2020-04-25 | GSE149314 | GEO
Project description:Purpose:In order to elucidate the molecular mechanism of the effects of different diets on the antioxidant capacity of fish, three groups of adult common carp (Cyprinus carpio) (initial weight 517.8 ±50 g) were fed with earthworm, earthworm + duckweed and duckweed, respectively, which were performed by miRNA sequencing. Methods:MiRNA profiles of common carp fed with earthworm, earthworm + duckweed and duckweed were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500 platform. qRT–PCR validation was performed using SYBR Green assays Results: We built microRNA libraries by using total RNA and contained filtered 20,868,000, 18,984,242, 22,300,487, 19,538,683, 17,110,676 and 14,747,090 high-quality reads that were obtained from sample A1, A2, M1, M2, P1 and P2 respectively.In total, we discovered 236 known carp miRNAs (225, 225, 222, 227, 228 and 219 in A1, A2, M1, M2, P1and P2, respectively).For the known miRNA, 9 differentially expressed miRNAs (DEM) were found between A and M and 8 known miRNAs differentially expressed between P and M, and 11 of these were validated with qRT–PCR. The expression level of 11 known microRNAs via miRNA-seq had highly similar with the relative expression level of 11 known microRNAs via qRT-PCR. Conclusions: In present study, we demonstrated the transcriptional profiles, identification of 5 differentially expressed miRNAs be reported related to oxidative stress, including miR-137-3p, miR-143-3p, miR-146a-5p, miR-21-5p and miR-125b-5p. For omnivorous fish, feed a single bait may might cause oxidative stress inordinately.
2018-07-14 | GSE117059 | GEO
Project description:Motivation: Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT, RDX and HMX. One important goal of microarray experiments is to discover novel biomarker genes for quantitative phenotypic prediction. We have developed an earthworm microarray containing 15,208 unique oligo probes. Our objective was to identify biomarker genes that can be used to quantitatively predict earthworm tissue residues of the explosives compounds that they were exposed to and took in from the HMX-spiked soil. Results: We collected a large microarray gene expression and earthworm tissue residue dataset. First, differentially expressed genes were identified for each exposure duration (4, 14 and 28 days). These genes were used in multivariate regression modeling for HMX residue prediction. Eighteen different regression models were tested and compared. The best performing model was able to achieve very high prediction accuracies with R2 values of 0.715, 0.728 and 0.822 for 4 days, 14 days and 28 days exposures, separately. Conclusions: This study demonstrated that multivariate regression coupled with high throughput microarray gene expression was a promising approach to quantitative phenotypic prediction.
2013-08-10 | GSE42866 | GEO
Project description:To understand molecular mechanisms of the joint effects of 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), both widely used ordnance compounds, we constructed a microarray consisting of 4,032 cDNA isolated from the earthworm Eisenia fetida using the suppressive subtractive hybridization technique. Worms were exposed to TNT-, RDX-, or TNT+RDX-spiked soil for 28 days (TNT 50 mg/kg, RDX 30 mg/kg). Keywords: Combined toxicity of TNT and RDX to earthworm (Eisenia fetida)
2008-08-28 | GSE8909 | GEO
Project description:Prokaryotic microbiomes associated with tea litter decay - associated soil microbiomes
| PRJEB44019 | ENA
Project description:To understand molecular mechanisms of the chronic, sublethal toxicity of 2,4,6-trinitrotoluene (TNT), a widely used ordnance compound of public concerns, we constructed a microarray consisting of 4,032 cDNA isolated from the earthworm Eisenia fetida using the suppressive subtractive hybridization technique. Worms were exposed to a gradient of TNT-spiked soil for 28 days. Based on the reproduction response to TNT, four treatments, i.e., control, 7, 35 and 139 ppm, were selected for gene expression studies. Keywords: Sublethal toxicity of TNT (dose-response) to earthworm (Eisenia fetida)
2007-10-15 | GSE7024 | GEO