{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE197nnn/GSE197886/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"species":["Parhyale hawaiensis"],"gds_type":["Genome binding/occupancy profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197886"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis","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.","dates":{"publication":"2022/05/25"},"accession":"GSE197886","cross_references":{"GSM":["GSM5931712","GSM5931711","GSM5931697","GSM5931696","GSM5931710","GSM5931699","GSM5931698","GSM5931693","GSM5931692","GSM5931695","GSM5931694","GSM5931691","GSM5931690","GSM5931709","GSM5931708","GSM5931705","GSM5931704","GSM5931707","GSM5931706","GSM5931701","GSM5931689","GSM5931700","GSM5931703","GSM5931702","GSM5931686","GSM5931685","GSM5931688","GSM5931687","GSM5931684","GSM5931683"],"GPL":["32017"],"GSE":["197886"],"taxon":["Parhyale hawaiensis"]}}