| Aligned ATAC-seq tracks | Aligned ATAC-seq reads as quantitative data in an x/y plot. ATAC-seq reads (replicate 1, 2, and 3) were generated for whole homeostatic Hydra. The Juliano_whole_peaks track is a consensus peak track consisting of all peaks that passed an IDR threshold of 0.1 for at least one pairwise comparison among the three biological replicates (Juliano_whole_rep1-3). |
| Aligned ATAC-seq reads from Murad et al. 2019 from adult tissues and regeneration time points 0-48h. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2. |
| Aligned ChIP-seq | Aligned ChIP-seq reads from Murad et al. 2019 from whole Hydra, Hydra head and regeneration time points 0-24h. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2. |
| Aligned RNA-seq tracks | RNA-seq reads from Petersen et al. 2015 (Molecular Biology and Evolution) from time points 0-48h were aligned to the Hydra 2.0 genome using HISAT2. Aligned reads tracks display all aligned RNA-seq reads. BigWig XY tracks display the aligned RNA-seq reads as quantitative data in an x/y plot. |
| Aligned RNA-seq reads from Murad et al. 2019 from adult Hydra hypostome, tentacles, body column, budding zone and foot, also from regeneration time points 0-48h and budding stages 1-10. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2. |
| Juliano_Trinity | RNA-seq reads from Juliano et al. 2014 (PNAS) were assembled into Trinity transcripts. The Trinity assembled transcripts were aligned to the Hydra 2.0 genome using Splign. |
| Juliano_aepLRv2 | Transcripts from a transcriptome assembly for Hydra vulgaris AEP (38,749 transcripts) were aligned to the Hydra 2.0 genome using Splign. |
| Petersen_Trinity | RNA-seq reads from Petersen et al. 2015 (Molecular Biology and Evolution) from time points 0–12 h were used to assemble a de novo transcriptome, which consists of 36,338 high quality transcripts. The Trinity assembled transcripts were aligned to the Hydra (2.0) genome using Splign. |
| AUGUSTUS | Hydra 2.0 gene models predicted using AUGUSTUS. |
| AUGUSTUS_unmasked | Hydra 2.0 gene models predicted using AUGUSTUS with the unmasked genome. |
| FGENESH | Hydra 2.0 gene models predicted using FGENESH. |
| PASA | RNA-seq reads from Juliano et al. 2014 (PNAS) were assembled into Trinity transcripts. Transcripts were used to create gene structures based on spliced alignments with PASA. |
| Hydra1.0_JGI | Hydra 1.0 gene models (from JGI) aligned to the Hydra 2.0 genome assembly using Splign. |
| Hydra1.0_NCBI | Hydra 1.0 gene models (from NCBI) aligned to the Hydra 2.0 genome assembly using Splign. |
| BLASTP_augustus_vs_NCBI_nr | BLASTP results from using AUGUSTUS protein models as queries against the NCBI nr protein database with an e-value cutoff of 1e-5. |
| BLASTP_augustus_vs_UniProt | BLASTP results from using AUGUSTUS protein models as queries against the UniProt protein database with an e-value cutoff of 1e-5. |
| PASA_coding_regions | Candidate coding regions identified from PASA gene structures by TransDecoder. |
| AUGUSTUS_PFAM | Hydra 2.0 protein domains derived from PFAM HMMscans with an e-value cutoff of 1e-6 using the AUGUSTUS datasets. |
| 6FRAMES_PFAM | Hydra 2.0 protein domains derived from PFAM HMMscans with an e-value cutoff of 1e-6 using the six-frame translations of the Hydra 2.0 genome. |
| Reference Sequence | The Hydra 2.0 genomic sequence and corresponding six-frame translations depicted when fully zoomed-in. |
| MASK | Genomic regions that have been masked using RepeatMasker and RepeatModeler are highlighted in light blue. |
| SCF | Assembled genomic scaffolds (SCF) appear as solid black tracks with intermittent gaps shaded bright pink. |