Compressed directory of scripts and data files associated with the assembly of the strain AEP H. vulgaris genome assembly. Detailed file descriptions, along with a step-by-step description of the assembly process, can be found in the markdown file 01_aepGenomeAssembly.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the repeat annotation and masking of the H. oligactis and strain AEP H. vulgaris genome assemblies. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 02_repeatMasking.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the annotation of the strain AEP, H. vulgaris genome assembly. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 03_aepGenomeAnnotation.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the assembly and annotation of the H. oligactis genome assembly. Detailed file descriptions, along with a step-by-step description of the assembly process, can be found in the markdown file 04_oligactisDraftGenome.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the generation of the updated version of the Hydra single-cell RNA-seq atlas mapped to the strain AEP H. vulgaris genome assembly. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 05_hydraAtlasReMap.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the phylostratigraphic analysis to assign ages to gene models in the strain AEP H. vulgaris genome assembly. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 06_geneAge.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the generation of a cross-species whole-genome alignment using five hydrozoan genomes along with the subsequent analysis of sequence conservation in the strain AEP H. vulgaris genome assembly. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 07_genomeConservation.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the annotation of cis-regulatory elements in the strain AEP H. vulgaris genome assembly using ATAC-seq and CUT&Tag. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 08_creIdentification.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the characterization of 3D chromatin organization in the strain AEP H. vulgaris genome assembly using Hi-C. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 09_3dChromatin.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the analysis identifying candidate regulators of cell-type-specific transcription in Hydra using the Hydra single-cell atlas, cis-regulatory element annotations, and phylogenetic footprinting. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 10_hydraRegulators.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the generation of an updated version of the Clytia medusa single-cell RNA-seq atlas mapped to updated gene models for the v2 Clytia hemisphaerica genome assembly. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 11_clytiaAtlasReMap.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the generation of a cross-species single-cell RNA-seq atlas that aligns the Hydra atlas with the Clytia medusa atlas. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 12_crossSpeciesAtlasAlignment.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory of scripts and data files associated with the analysis identifying candidate regulators of cell-type-specific transcription that are conserved in Clytia medusae and Hydra polyps. Detailed file descriptions, along with a step-by-step description of the analysis, can be found in the markdown file 13_conservedRegulators.md available at github.com/cejuliano/brown_hydra_genomes.

Compressed directory containing the raw fastq-formatted 10X chromium linked-read sequencing data used for generating the strain AEP H. vulgaris genome assembly.

Compressed directory containing the raw fastq-formatted whole-animal ATAC-seq data used for annotating cis-regulatory elements in the strain AEP H. vulgaris genome assembly.

Binary R data file containing the Seurat-formatted (v4) Hydra single-cell RNA-seq atlas mapped to the strain AEP H. vulgaris genome gene models. This version of the atlas retains doublets, including battery cells.

Binary R data file containing the Seurat-formatted (v4) Hydra single cell RNA-seq atlas mapped to the strain AEP H. vulgaris genome gene models. This version of the atlas has had doublets removed. The metadata slots of this Seurat object include single-cell motif enrichment scores, non-negative matrix factorization cell scores, and transcriptome age index scores.

Binary R data file containing the Seurat-formatted (v4) cross-species single-cell RNA-seq atlas that aligns the Clytia medusa and Hydra atlases.

Compressed directory containing the raw fastq-formatted whole-animal histone modification CUT&Tag sequencing data used for annotating cis-regulatory elements in the strain AEP H. vulgaris genome assembly.

Compressed directory containing the raw fastq-formatted Hi-C sequencing data used for generating the strain AEP H. vulgaris genome assembly.

Compressed directory containing the raw fastq-formatted whole-animal paired-end RNA-seq data used for annotating the strain AEP H. vulgaris genome assembly.

Compressed directory containing the raw fast5-formatted Oxford Nanopore PromethION sequencing data used for generating the strain AEP H. vulgaris genome assembly.

Compressed directory containing the raw fastq-formatted whole-animal single-end RNA-seq data used for benchmarking mapping efficiency for the strain AEP H. vulgaris genome assembly as compared to the strain 105 H. vulgaris genome assembly.

Compressed directory containing the error-corrected reads from the Oxford Nanopore and PacBio sequencing data used for generating the strain AEP H. vulgaris genome assembly.

Compressed directory containing the raw fast5-formatted Oxford Nanopore MinION sequencing data used for generating the H. oligactis genome assembly.

File containing the basecalled fastq-formatted Oxford Nanopore MinION sequencing data used for generating the H. oligactis genome assembly.

File containing the basecalled fastq-formatted Oxford Nanopore PromethION sequencing data used for generating the strain AEP H. vulgaris genome assembly.

File containing the unmapped BAM-formatted PacBio Sequel II reads used for generating the strain AEP H. vulgaris genome assembly.