Regent Honeyeater, Genome Assembly, Pooled sample of kidney and heart
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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 | 2023-04-14 |
| Access Control Mode | date |
| Sequence Data Type | genome-assembly |
| analysis_description | The sample was obtained from a single animal. The sequencing was completed using multiple platforms and assembly was done using HiFikb Frag library prep and PacBio Sequel II sequencing SMRT cell 8M |
| assembly_date | 2021-07-14 |
| assembly_method | hifiasm, purge_dups |
| assembly_method_version | https://workflowhub.eu/workflows/221, https://workflowhub.eu/workflows/237 |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/assembly/BPAOPS-1222/regent_honeyeater/ |
| bioplatforms_project | Threatened Species Initiative (TSI) |
| bioplatforms_secondarydata_id | 102.100.100/359774 |
| birth_date | 2020-09-20 |
| bpa_library_id | 102.100.100/357464 |
| bpa_sample_id | 102.100.100/355453 |
| certainty | Certain |
| class | Aves |
| collection_date | 2020-10-28 |
| collection_method | Medical euthanasia due to poor prognosis |
| collector | Lydia Tong, Taronga |
| collector_sample_id | TARZ-13825.1 |
| common_name | Regent Honeyeater |
| completion_score | 0.95 |
| completion_score_method | BUSCO |
| computational_infrastructure | Galaxy Australia |
| contact_person | Jo Day |
| country | Australia |
| data_type | Genome Assembly |
| dataset_id | 358730 |
| date_of_transfer | 2022-04-14 |
| date_of_transfer_to_archive | 2022-04-14 |
| death_date | 2020-10-28 |
| decimal_latitude_public | -33.84 |
| decimal_longitude_public | 151.24 |
| description | Regent Honeyeater genome assembly |
| family | Meliphagidae |
| folder_name | regent_honeyeater |
| genome_size | 1.1GB |
| genus | Anthochaera |
| hybrid | No |
| hybrid_details | NA |
| institution_name | Taronga Conservation Society Australia |
| latitude | -33.84 |
| library_id | 357464 |
| lifestage | juvenile |
| location_text | Taronga Zoo, Bradleys Head Road, Mosman, NSW 2088 |
| longitude | 151.24 |
| material_conc_ng_ul | 105.0 |
| material_extracted_by | Jo Day (Taronga), Elspeth McLennan (USYD) |
| material_extraction_date | 2020-12-03 |
| material_extraction_method | Circulomics Kit ("Nanobind Tissue Big DNA Kit v1.0 11/19") |
| material_extraction_type | DNA |
| metadata_revision_date | 2023-11-30 |
| metadata_revision_filename | 20231130_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| method_of_determination | Dissection |
| n50 | 2 Mb |
| n_scaffolds | 2344 contigs |
| order | Passeriformes |
| phenotypic_sex | male |
| phylum | Chordata |
| polishing_scaffolding_data | NA |
| polishing_scaffolding_method | NA |
| reference_genome | de novo |
| sample_custodian | Jo Day |
| sample_id | 355453 |
| sample_quality | Good |
| scientific_name | Anthochaera phrygia |
| sequencing_facility | TCSA |
| sequencing_technology | PacBio Sequel II HiFi |
| source_population | Taronga Zoo |
| species | phrygia |
| specimen_id | WYR20-16179 |
| specimen_id_description | Species360 (GAN) number |
| state_or_region | New South Wales |
| system_used | Galaxy Australia |
| taxon_id | 2020318.0 |
| taxonomic_group | Bird |
| ticket | BPAOPS-1222 |
| tissue_number | WYR20-16179_pooled_kidney_heart |
| tissue_preservation | Flash frozen at -80C |
| tissue_type | Pooled sample of kidney and heart |
| wild_captive | captive |