Supplementary data for 'Genome-wide discovery of cis-regulatory elements in a large genome'

Supplementary data for 'Genome-wide discovery of cis-regulatory elements in a large genome'

Forbes, Skafida, Karapidaki, Moinet, Dandamudi, Çevrim, Momtazi, Anastasiadou, Lo Brutto, Averof and Paris (2025) Genome-wide discovery of cis-regulatory elements in a large genome. bioRxiv 2026.03.07.709930

The supplementary data include:

Suppl. Data 1. Genome browser tracks and peaks for bulk ATACseq data (.zip file).  Genome browser tracks are provided for the genome-wide ATACseq profiles detected in whole embryos (datasets E20, E23, E24), embryonic legs (datasets EL1, EL2, EL3), adult legs (datasets L1, L2, L3), and naked DNA, normalised as counts per million. The tracks are provided in bedgraph (.bdg) format; they refer to the Parhyale hawaiensis Phaw_5.0 genome assembly (GenBank GCA_001587735.2) updated by Almazán et al. 2022, available at https://zenodo.org/records/19051450/files/genome_mito.fa.zip; genome annotation can be found here https://zenodo.org/records/6420694/files/Dataset_S1_Annotation_Reg_Embryo_500_cleanOverlap0.5_3.gtf.zip. The ATACseq peaks detected in each dataset (used to generate Table 1 and figures 1 & 3) are provided as .narrowpeak files in BED6+4 format.

Suppl. Data 2. Genome browser tracks for single-nuclei ATACseq data (.zip file).  Genome browser tracks are provided for the genome-wide ATACseq profiles detected in selected cell types (epidermis, muscles, neurons and hemocytes), from the integrated SN1 and SN2 datasets, normalised as counts per million. The tracks are provided in bedgraph (.bdg) format; they refer to the Parhyale hawaiensis Phaw_5.0 genome assembly (GenBank GCA_001587735.2) updated by Almazán et al. 2022, available at https://zenodo.org/records/19051450/files/genome_mito.fa.zip; genome annotation can be found here https://zenodo.org/records/6420694/files/Dataset_S1_Annotation_Reg_Embryo_500_cleanOverlap0.5_3.gtf.zip.

Suppl. Data 3. Genome browser tracks and peaks for sequence conservation (.zip file).  Genome browser tracks are provided for genome-wide profiles of sequence conservation determined by mapping sequencing reads from Parhyale aquilina, Parhyale darvishi and Parhyale plumicornis onto the genome Parhyale hawaiensis, normalised as counts per million. The tracks are provided in bedgraph (.bdg) format; they refer to the Parhyale hawaiensis Phaw_5.0 genome assembly (GenBank GCA_001587735.2) updated by Almazán et al. 2022, available at https://zenodo.org/records/19051450/files/genome_mito.fa.zip; genome annotation can be found here https://zenodo.org/records/6420694/files/Dataset_S1_Annotation_Reg_Embryo_500_cleanOverlap0.5_3.gtf.zip. The peaks of sequence conservation detected in each dataset (used to generate figure 3) are provided as .bed files.

Suppl. Data 4. Sequence alignment for phylogeny (.fasta text file).  The alignment is a concatenation of all the BUSCO gene sequences that could be found in all four Parhyale species (Parhyale hawaiensis, Parhyale aquilina, Parhyale darvishi, Parhyale plumicornis) and in the ourgroup Hyalella azteca. Only sites that are found in the four Parhyale species were included in the alignment.

Suppl. Data 5. DNA sequences and genome coordinates of all the tested CREs (.zip file).  Annotated DNA sequences of the tested CREs in genbank (.gb) format, and genome coordinates for each CRE (.txt). The genome coordinates refer to the Parhyale hawaiensis Phaw_5.0 genome assembly (GenBank GCA_001587735.2) updated by Almazán et al. 2022, available at https://zenodo.org/records/19051450/files/genome_mito.fa.zip.

Suppl. Data 6. Microscopy data (.zip file).  Raw and processed image data from embryos, hatchlings and juveniles carrying the reporters ubi1 and ubi2 (figure 4), neuro5, neuro6 and mhc (figure 5), and combined neuro5+neuro6 (suppl. figure 5), in TIFF format. Read_me file (.txt) provides additional information on the images and image processing.