Project description:We performed RNA-Seq across multiple time points of development (stages 13, 19, 21, 23) in Parhyale hawaiensis and generated an improved genome annotation.
2022-05-25 | GSE202252 | GEO
Project description:Time course RNA-Seq on Parhyale hawaiensis embryos
Project description:Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility.
Project description:Examination of temporal small RNA expression during the embryonic development, larval and adult stages of Drosophila virilis Small RNA sequencing of samples representing different stages of D. virilis development, including eight 2-hour intervals during the first 16 hours of development (0-2h, 2-4h, etc.), late embryos until hatching (16-30h), 3rd instar larvae and adults
