GEO DataSets

(Submitter supplied) The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. more...

Organism:

Eisenia andrei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30479

2 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio; Drosophila melanogaster; Eisenia andrei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30479 GPL30277 GPL32518

13 Samples

Download data: BED

(Submitter supplied) The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. more...

Organism:

Eisenia andrei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30479

1 Sample

Download data: BED

(Submitter supplied) 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.

Organism:

Eisenia andrei

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30479 GPL30478

28 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio; Drosophila melanogaster; Eisenia andrei

Type:

Expression profiling by high throughput sequencing

5 related Platforms

151 Samples

Download data: TXT

(Submitter supplied) Purpose: We studied the potential effects of lindane aging in soil on model earthworm Eisenia fetida at the transcriptomic level. Methods: transcriptomes of earthworms were generated by RNA sequencing using Illumina Hiseq Xten platform. Results: There were 1325 DE unigenes in G2 (1074 up and 251 down), 784 DE unigenes in G3 (457 up and 327 down), 3658 DE unigenes in G4 (2294 up and 1364 down), and 1511 DE unigenes in G5 (929 up and 582 down) compared with G1. more...

Organism:

Eisenia fetida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25459

15 Samples

Download data: FA, TXT

(Submitter supplied) Purpose: The objective of this study was to investigate the TnBP-induced intestinal toxicity mechanism on earthworm Eisenia fetida. Methods: The intestinal tissues of nine earthworms under control and 10 mg/kg TnBP treatments were separately pooled into three replicates (three earthworms per replication) to obtain sufficient amounts of RNA for transcriptomic assessments, using BGISEQ-500. qRT–PCR validation was performed using SYBR Green assays. more...

Organism:

Eisenia fetida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28333

6 Samples

Download data: FA, TXT

(Submitter supplied) Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida, a terrestrial redworm, capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum annelida, in which the genomes of the marine oligochaete Capitella telata, and the freshwater leech Helobdella robusta have been sequenced and studied. more...

Organism:

Eisenia fetida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23700

26 Samples

Download data: FASTA, TXT

(Submitter supplied) Background: Earthworms are essential for a healthy soil ecosystem, performing key functions such as bioturbation. The soil ecosystem can be challenged by natural toxins such as isothiocyanates (ITC), secondary metabolites produced by many commercial crops. This study investigated the effects of the natural toxin, 2-phenylethyl isothiocyanate on the earthworm Eisenia andrei using an ecotoxicogenomics approach that combined standardised ecotoxicological testing with gene expression analyses. more...

Organism:

Eisenia andrei; Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL16366

12 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL9420

120 Samples

Download data: TXT

(Submitter supplied) 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 and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes. more...

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL9420

248 Samples

Download data: TXT

(Submitter supplied) The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understand toxicological modes of action and to facilitate the development of molecular biomarkers, we have obtained 30,245 unique EST sequences from E. more...

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL9416

48 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Eisenia fetida

Type:

Expression profiling by array

4 related Platforms

16 Samples

Download data: TXT

(Submitter supplied) To validate the 244K 60-mer or 40-mer probes using a custom-designed Agilent oligo array and assuming antisense orientation of all target sequences.

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL8683

4 Samples

Download data: TXT

(Submitter supplied) To validate the 244K 60-mer or 40-mer probes using a custom-designed Agilent oligo array and assuming sense orientation of all target sequences.

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL8681

4 Samples

Download data: TXT

(Submitter supplied) To validate the 244K 60-mer probes using a custom-designed Agilent oligo array and assuming antisense orientation of all target sequences.

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL8682

4 Samples

Download data: TXT

(Submitter supplied) To validate the 244K 60-mer probes using a custom-designed Agilent oligo array and assuming sense orientation of all target sequences.

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL8680

4 Samples

Download data: TXT

(Submitter supplied) 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). more...

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL5776

40 Samples

Download data: TIFF

(Submitter supplied) 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. more...

Organism:

Eisenia fetida

Type:

Expression profiling by array

Platform:

GPL4859

40 Samples

Download data: TIFF