Western swamp tortoise, Reference genome, PacBio-HiFi, Heart
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Data and Resources
This data is made available openly under a Creative Commons Attribution license.
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Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:tsi-consortium-members |
| Access Control Date | 2026-04-03 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| access_rights | Location information restricted |
| ala_specimen_url | https://bie.ala.org.au/species/https://biodiversity.org.au/afd/taxa/8308a376-50a5-483b-ac9f-39d702b817ec |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 13.3.0.253824 |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-1771/20250403_TSI_AGRF_CAGRF25020127_m84073_250327_060234_s3/ |
| bioplatforms_project | Threatened Species Initiative |
| birth_date | 2024-06-04 |
| cell_postion | C01 |
| certainty | not determined |
| class | Reptilia |
| collection_date | 2024-08-08 |
| collection_method | Dissection |
| collector | Perth Zoo |
| common_name | Western swamp tortoise |
| country | Australia |
| data_context | Reference genome |
| data_custodian | Kym Ottewell | DBCA |
| data_type | PacBio-HiFi |
| dataset_id | 102.100.100/419499 |
| date_of_transfer | 2025-04-03 |
| date_of_transfer_to_archive | 2025-04-04 |
| death_date | 2024-08-08 |
| dna_treatment | SHEARING |
| experimental_design | NA |
| facility_project_code | CAGRF25020127 |
| facility_sample_id | 417576_1 |
| family | Chelidae |
| fast5_compression | NA |
| file_type | BAM |
| flowcell_id | m84073_250327_060234_s3 |
| flowcell_type | SMRT Cell 25M |
| folder_name | 20250403_TSI_AGRF_CAGRF25020127_m84073_250327_060234_s3 |
| genus | Pseudemydura |
| insert_size_range | 13000.0 |
| institution_name | Department of Biodiversity, Conservation and Attractions |
| library_comments | NA |
| library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 |
| library_id | 102.100.100/417576 |
| library_index_id | NA |
| library_index_id_dual | NA |
| library_index_seq_dual | NA |
| library_index_sequence | NA |
| library_layout | NA |
| library_location | AGRF |
| library_ng_ul | 300pM |
| library_oligo_sequence | NA |
| library_oligo_sequence_dual | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2025-03-02 |
| library_prepared_by | Trent Peters |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| lifestage | juvenile stage |
| location_text | Perth Zoo |
| material_conc_ng_ul | 370.0 |
| material_extracted_by | Elspeth McLennan |
| material_extraction_date | 2025-02-10 |
| material_extraction_method | PacBio Nanobind Tissue |
| material_extraction_type | HMW DNA |
| metadata_revision_date | 2025-08-26 |
| metadata_revision_filename | 20250826_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| method_of_determination | not determined |
| model_base_caller | NA |
| movie_length | 30Hrs |
| n_libraries_pooled | 1.0 |
| order | Testudines |
| phenotypic_sex | not determined |
| phylum | Chordata |
| prior_genetics | None |
| sample_custodian | Kym Ottewell | DBCA |
| sample_id | 102.100.100/415570 |
| sample_quality | good |
| sample_type | Tissue |
| scientific_name | Pseudemydura umbrina |
| scientific_name_authorship | Siebenrock, 1901 |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Revio SPRQ sequencing plate |
| sequencing_model | PacBio Revio |
| sequencing_platform | PACBIO_SMRT |
| source_population | Sire captive bred, dam wild caugh Elllenbrook Nature Reserve |
| species | umbrina |
| specimen_id | C40075 |
| specimen_id_description | Perth Zoo sample |
| state_or_region | Western Australia |
| taxon_id | 44510 |
| taxonomic_group | Reptile |
| ticket | BPAOPS-1771 |
| tissue_collection | DBCA |
| tissue_collection_type | Zoo living collection |
| tissue_number | C40075_heart1 |
| tissue_preservation | flash frozen |
| tissue_preservation_temperature | -80.0 |
| tissue_type | Heart |
| wild_captive | captive |
| work_order | 14085 |