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:Using pooled earthworm RNA to test 244K probes on TA-1, TA-2, TA-3, TA-4 test arrays

| PRJNA116177 | ENA

Eisenia fetida

Project description:Design, validation and annotation of transcriptome-wide oligonucleotide probes for the annelid Eisenia fetida

| PRJNA79469 | ENA

Using pooled earthworm RNA to test 244K probes on TA-2 test array design 2520023 antisense 1

Project description:To validate the 244K 60-mer probes using a custom-designed Agilent oligo array and assuming antisense orientation of all target sequences. A total of four test arrays were designed assuming both sense and antisense orientations. A sole pooled RNA was used for testing all 4 designs. Two arrays were hybridized for each design. This series contains test results for design 2520023.

2010-05-18 | E-GEOD-16548 | biostudies-arrayexpress

Using pooled earthworm RNA to test 244K probes on TA-4 test array design 2520025 antisense 2

Project description: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. A total of four test arrays were designed assuming both sense and antisense orientations. A sole pooled RNA was used for testing all 4 designs. Two arrays were hybridized for each design. This series contains test results for design 2520025.

2010-05-18 | E-GEOD-16550 | biostudies-arrayexpress

Microarray analysis of CL-20 reversible neurotoxicity in the earthworm Eisenia fetida

Project description: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. fetida and have designed a novel microarray with 15,119 60-mer oligonucleotide probes. These probes target the unique non-redundant EST sequences identified in E. fetida. Using this array we have profiled gene expression of E. fetida after exposure to CL-20, a cage cyclic nitramine previously found exhibiting reversible neurotoxicity to worms. Worms were exposed for 6 days to CL-20. Half of the exposed worms were allowed to recover in a clean environment for 7 days. Electrophysiological analysis showed that the conduction velocity of worm medial giant nerve fiber was significantly decreased after 6-d exposure to CL-20, and that giant nerve fiber function was restored at the end of the 7-d recovery period. Total RNA samples isolated from four treatment groups (6 replicates per group), i.e., 6-d control, 6-d exposed, 13-d control and 6-d exposed with 7-d recovery, were analyzed using the new 15K oligo array. Bioinformatics and statistical analyses have identified specific neurological pathways affected by CL-20 and recovery of these pathways after CL-20 removal. These results provide significant insights on the CL-20 toxic mode of action and how earthworms can recover from chemical stressors.

2009-10-14 | GSE18536 | GEO

Eisenia fetida

Project description:Discovery of biomarker genes form earthworm microarray data

| PRJNA120243 | ENA