Australian zebra finch, Reference genome, PacBio-HiFi, blood
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Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:aus-avian-consortium-members |
| Access Control Date | 2026-04-10 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| analysis_software | SMRT Link Analysis 13.3.0.253824 |
| ancillary_notes | This bird is taken from a captive population of zebra finches housed at Macquarie University Fauna Park, established from wild birds from Fowler's Gap in western NSW in 2009. She has previously been sequenced with short read data and is known to have the inversion haplotypes chr5:AA, chr11: AB, chr13: AB, chrZ: B. |
| associated_media | photos |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/avian_staging/pacbio-hifi/BPAOPS-1773/20250409_AVIAN_AGRF_CAGRF24110452_m84073_250214_024215_s4/ |
| bioplatforms_dataset_id | 102.100.100/613514 |
| bioplatforms_library_id | 102.100.100/611514 |
| bioplatforms_project | Australian Avian Genomics Initiative (AVIAN) |
| bioplatforms_sample_id | 102.100.100/609514 |
| birth_date | 2021-03-26 |
| cell_postion | B01 |
| class | Aves |
| collection_date | 2024-11-26 |
| collection_method | hand capture (from captivity) |
| collection_permit | MQ AEC 2024/007 |
| collector | Simon Griffith, Rhiannon Schembri, Muhammad Fakher Ud Din |
| collector_sample_id | B1035 |
| common_name | Australian zebra finch |
| country | Australia |
| data_context | Reference genome |
| data_type | PacBio-HiFi |
| date_of_transfer | 2025-04-10 |
| date_of_transfer_to_archive | 2025-04-11 |
| death_date | 2024-11-26 |
| dna_treatment | SHEARING |
| experimental_design | PacBio HiFi, long reads |
| facility_project_code | CAGRF24110452 |
| facility_sample_id | 611514.0 |
| family | Estrildidae |
| fast5_compression | NA |
| flowcell_id | m84073_250214_024215_s4 |
| flowcell_type | SMRT Cell 25M |
| folder_name | 20250409_AVIAN_AGRF_CAGRF24110452_m84073_250214_024215_s4 |
| genotypic_sex | female |
| genus | Taeniopygia |
| health_state | healthy |
| identified_by | Simon Griffith |
| indigenous_location | Wallamattagul |
| insert_size_range | 17000.0 |
| library_comments | NA |
| library_construction_protocol | Preparing HiFi SMRTbell Libraries using SMRTbell Express Template Prep Kit 3.0 |
| 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 | 285pM |
| library_oligo_sequence | NA |
| library_oligo_sequence_dual | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2025-02-02 |
| library_prepared_by | Trent Peters |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| lifestage | adult organism |
| location_text | Macquarie University |
| material_conc_ng_ul | 250.0 |
| material_extracted_by | Rhiannon Schembri |
| material_extraction_date | 2024-11-26 |
| material_extraction_method | PacBio Nanobind CBB HMW extraction kit |
| material_extraction_type | DNA |
| metadata_revision_date | 2025-07-22 |
| metadata_revision_filename | 20250722_AVIAN_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| method_sex_determination | visual, dissection |
| model_base_caller | NA |
| movie_length | 30Hrs |
| n_libraries_pooled | 1.0 |
| order | Passeriformes |
| phenotypic_sex | female |
| phylum | Chordata |
| project_collaborators | Rhiannon Schembri |
| project_lead | Simon Griffith |
| sample_collection_type | private |
| sample_custodian | Simon Griffith |
| sample_id | ZBF_B1035.01 |
| sample_id_description | Species code + Macquarie University Fauna Park band number + tissue sample code |
| sample_quality | Extractions performed immediately after sample collection |
| sample_type | tissue sample |
| scientific_name | Taeniopygia castanotis |
| scientific_name_authorship | Gould, 1837 |
| scientific_name_note | Taeniopygia castanotis was elevated to full species status by the International Ornithological Congress in 2022 (formerly subspecies T. guttata castanotis). NCBI database lists common name as "Chestnut-eared finch", but this name is not widely recognised. |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Revio SPRQ sequencing plate |
| sequencing_model | PacBio Revio |
| sequencing_platform | PACBIO_SMRT |
| sex_certainty | certain |
| source_population | Fowler's Gap |
| species | castanotis |
| specimen_custodian | Simon Griffith |
| specimen_id | ZBF_B1035 |
| specimen_id_description | Species code + Macquarie University Fauna Park band number |
| state_or_region | New South Wales |
| taxon_id | 644770 |
| taxonomic_group | Bird |
| ticket | BPAOPS-1773 |
| tissue | blood |
| tissue_preservation | EDTA; fresh |
| tissue_preservation_temperature | room temperature |
| type_status | NA |
| wild_captive | captive bred from wild stock |
| work_order | 26002 |