Brolga, Reference genome, PacBio-HiFi, blood

Gruidae, Antigone rubicunda, 350-03392, bird, Project Lead: Lauren White, Arthur Rylah Institute

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Geospatial Coverage

Dataset extent

Map tiles & Data by OpenStreetMap, under CC BY SA.
Resource Permissions organization_member
Access Control Date 2025-12-24
Access Control Mode date
Sequence Data Type pacbio-hifi
altitude NA
analysis_software SMRT Link Analysis 13.0.0.207600
ancillary_notes NA
associated_media NA
bait_set_name NA
bait_set_reference NA
base_url https://downloads-qcif.bioplatforms.com/bpa/avian_staging/pacbio-hifi/BPAOPS-1735/20241223_AVIAN_AGRF_CAGRF24080145_m84073_241220_104627_s4/
bioplatforms_dataset_id 102.100.100/613513
bioplatforms_library_id 102.100.100/611513
bioplatforms_project Australian Avian Genomics Initiative (AVIAN)
bioplatforms_sample_id 102.100.100/609513
cell_postion D01
class Aves
collection_date 2024-03-21
collection_method Australian noose trap with call playback and taxidermy decoy (description in Veltheim et al. 2015 https://doi.org/10.1071/WR14238)
collection_permit Research under Wildlife Act permit 10010774, with ethics approval from Victorian Department of Energy, Environment and Climate Action Animal Ethics Committee under application 23-001.
collector Danny Rogers, Nyil Kwaja, Inka Veltheim, Neville Amos, Arthur Rylah Institute
collector_sample_id 350-03392
common_name Brolga
country Australia
data_context Reference genome
data_type PacBio-HiFi
date_of_transfer 2024-12-24
date_of_transfer_to_archive 2025-01-06
decimal_latitude_public -36.5162
decimal_longitude_public 144.842
dna_treatment SHEARING
env_broad_scale cropland biome [ENVO_01000245]
env_local_scale freshwater biome [ENVO_00000873]
env_medium NA
experimental_design PacBio HiFi, long reads
facility_project_code CAGRF24080145
facility_sample_id 611513.0
family Gruidae
fast5_compression NA
flowcell_id m84073_241220_104627_s4
flowcell_type SMRT Cell 25M
folder_name 20241223_AVIAN_AGRF_CAGRF24080145_m84073_241220_104627_s4
genotypic_sex NA
genus Antigone
habitat cropland biome [ENVO_01000245]
health_state unknown
identified_by Danny Rogers, Nyil Kwaja, Inka Veltheim, Neville Amos, Arthur Rylah Institute
indigenous_location Taungurung
insert_size_range 17000.0
latitude -36.5162
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_prepared_by Trent Peters
library_selection size fractionation
library_source GENOMIC
library_strategy WGS
library_type PacBio-HiFi
lifestage adult
location_info_restricted No
location_text Private property, Burramboot, Between Gaynor Swamp and Lake Stewart
longitude 144.842
material_conc_ng_ul 412.64
material_extracted_by Lauren White
material_extraction_date 2024-10-08
material_extraction_method PacBio NanoBind HMW PanDNA kit
material_extraction_type DNA
metadata_revision_date 2025-01-06
metadata_revision_filename 20250106_AVIAN_Sample_metadata_COMBINED-FOR-PORTAL_NOPRIVLATLON.xlsx
method_sex_determination observation, behaviour
model_base_caller NA
movie_length 30Hrs
n_libraries_pooled 1.0
order Gruiformes
phenotypic_sex female
phylum Chordata
project_lead Lauren White, Arthur Rylah Institute
sample_collection_type other (Research Institute - government)
sample_custodian Lauren White, Arthur Rylah Institute
sample_id 350-03392
sample_id_description Arthur Rylah Institute
sample_quality NA
sample_type tissue
scientific_name Antigone rubicunda
scientific_name_authorship NA
scientific_name_note NA
sequencing_facility AGRF
sequencing_kit_chemistry_version Revio sequencing plate
sequencing_model PacBio Revio
sequencing_platform PACBIO_SMRT
sex_certainty unsure
source_population North-Victoria
species rubicunda
specimen_custodian Lauren White, Arthur Rylah Institute
specimen_id 350-03392
specimen_id_description Arthur Rylah Institute
state_or_region Victoria
sub_species NA
taxon_id 2717061.0
taxonomic_group bird
temperature NA
ticket BPAOPS-1735
tissue blood
tissue_preservation frozen
tissue_preservation_temperature -20.0
type_status NA
wild_captive wild
work_order 26001