Orange-bellied parrot, Reference genome, Pacbio HiFi, Pooled sample of heart, kidney and pectoral muscle
Dataset size is: 839.97 GiB
Data and Resources
This data is made available openly under a Creative Commons Attribution license.
Please see the initiative
Data Policy
for attribution information.
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 | 2021-12-09 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| access_rights | Open Access |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 9.0.0.92188 |
| ancillary_notes | Medical euthanasia for welfare purposes |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-1001/TSI_AGRF_PacBio_C20104110/357367_TSI_AGRF_PacBio_DA052917_HiFi_metadata/ |
| birth_date | 2014-12-27 |
| cell_postion | D01 |
| certainty | Certain |
| class | Aves |
| collection_date | 2020-08-20 |
| collection_method | Medical euthanasia for welfare purposes |
| collector | Carolyn Hogg, USYD |
| collector_sample_id | 1.0 |
| common_name | Orange-bellied parrot |
| country | Australia |
| data_context | Reference genome |
| data_custodian | Carolyn Hogg (USYD) |
| data_type | Pacbio HiFi |
| dataset_id | 102.100.100/358725 |
| date_of_transfer | 2020-12-09 |
| date_of_transfer_to_archive | 2020-12-09 |
| death_date | 2020-08-20 |
| dna_treatment | Shearing |
| facility_sample_id | 357367.0 |
| family | Psittacidae |
| file_name | 357367_TSI_AGRF_PacBio_DA052917.ccs.bam; 357367_TSI_AGRF_PacBio_DA052917.subreads.bam |
| flowcell_id | DA052917 |
| flowcell_type | SMRT Cell 8M |
| folder_name | TSI_AGRF_PacBio_C20104110 |
| genus | Neophema |
| insert_size_range | 15976.0 |
| institution_name | University of Sydney |
| library_comments | NA |
| library_construction_protocol | Preparing HiFi SMRTbell® Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_id | 102.100.100/357367 |
| library_index_id | NA |
| library_index_sequence | NA |
| library_layout | NA |
| library_location | AGRF |
| library_ng_ul | 154.0 |
| library_oligo_sequence | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2020-11-10 |
| library_prepared_by | Trent Peters |
| library_selection | RANDOM |
| library_source | GENOMIC |
| library_status | Data available |
| library_strategy | Preparing HiFi SMRTbell® Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_type | WGS |
| lifestage | adult |
| location_text | Priam Psitticulture Centre; 2 Australis Place, Queanbeyan, NSW 2621 |
| material_conc_ng_ul | 87.0 |
| material_extracted_by | Emma Peel, Kate Farquharson, Elspeth McLennan (USYD) |
| material_extraction_date | 2020-09-30 |
| 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 |
| movie_length | 30hrs |
| n_libraries_pooled | NA |
| order | Psittaciformes |
| phenotypic_sex | male |
| phylum | Chordata |
| sample_custodian | Carolyn Hogg |
| sample_id | 102.100.100/355357 |
| sample_quality | Good |
| scientific_name | Neophema chrysogaster |
| sequencing_facility | AGRF |
| sequencing_model | PacBio Sequel II |
| sequencing_platform | PACBIO_SMRT |
| species | chrysogaster |
| specimen_id | 2035.0 |
| specimen_id_description | Studbook |
| state_or_region | New South Wales |
| taxon_id | 678581.0 |
| taxonomic_group | Bird |
| ticket | BPAOPS-1001 |
| tissue_collection_type | University |
| tissue_number | 2035_pooled_heart_kidney_pectoralmuscle |
| tissue_preservation | Flash frozen at -80C |
| tissue_type | Pooled sample of heart, kidney and pectoral muscle |
| wild_captive | captive |
| work_order | 14003 |