Hooded Plover, Reference genome, PacBio-HiFi, heart
Dataset size is: 21.14 GiB
This dataset is currently under a short embargo period until July 26, 2024 to enable primary access by research partners.
If you would like access during this period please contact us here or contact the project lead directly (see details in the table below) for collaboration opportunities.
Data and Resources
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 | 2024-07-26 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| access_rights | No restrictions |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 12.0.0.172289 |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-1445/20230726_TSI_AGRF_CAGRF230414583_m84073_230713_055821_s2/ |
| bioplatforms_project | Threatened Species Initiative |
| cell_postion | B01 |
| class | Aves |
| collection_date | 1985-03-18 |
| collector_sample_id | B771 |
| common_name | Hooded Plover |
| country | Australia |
| data_context | Reference genome |
| data_custodian | Jo Sumner |
| data_type | PacBio-HiFi |
| dataset_id | 102.100.100/358818 |
| date_of_transfer | 2023-07-27 |
| date_of_transfer_to_archive | 2023-07-28 |
| death_date | 1985-03-18 |
| description | Black-eared miner (HiFi Revio) |
| dna_treatment | SHEARING |
| experimental_design | NA |
| facility_project_code | CAGRF230414583 |
| facility_sample_id | 462067.0 |
| family | Charadriidae |
| fast5_compression | NA |
| file_type | BAM |
| flowcell_id | m84073_230713_055821_s2 |
| flowcell_type | SMRT Cell 25M |
| folder_name | 20230726_TSI_AGRF_CAGRF230414583_m84073_230713_055821_s2 |
| genus | Thinornis |
| insert_size_range | 13500.0 |
| institution_name | Museums Victoria |
| library_comments | NA |
| library_construction_protocol | Preparing HiFi SMRTbell Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_id | 102.100.100/462067 |
| 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 | 250pM |
| library_oligo_sequence | NA |
| library_oligo_sequence_dual | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2023-06-07 |
| library_prepared_by | Jack Royle |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| location_text | Greens Beach |
| material_extracted_by | Joanna Sumner |
| material_extraction_date | 2023-06-02 |
| material_extraction_type | DNA |
| metadata_revision_date | 2023-11-30 |
| metadata_revision_filename | 20231130_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| model_base_caller | NA |
| movie_length | 24Hrs |
| n_libraries_pooled | 1.0 |
| order | Charadriiformes |
| phenotypic_sex | female |
| phylum | Chordata |
| prior_genetics | https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2699.1999.00269.x, https://www.ncbi.nlm.nih.gov/nuccore/U62698.1/, https://www.ncbi.nlm.nih.gov/nuccore/U62699.1/ |
| sample_custodian | Museums Victoria |
| sample_id | 102.100.100/460030 |
| sample_quality | collected 1995, potentially some degredation |
| sample_type | tissue sample |
| scientific_name_authorship | J.F. Gmelin 1789 |
| scientific_name_note | homotypic synonym:Charadrius rubricollis |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Revio sequencing plate |
| sequencing_model | PacBio Revio |
| sequencing_platform | PACBIO_SMRT |
| species | rubricollis |
| specimen_id | NMVZ48771 |
| specimen_id_description | Museums Victoria tissue registration number |
| state_or_region | Tasmania |
| taxon_id | 50410.0 |
| taxonomic_group | Bird |
| ticket | BPAOPS-1445 |
| tissue_collection | Ian Potter Australian Wildlife BioBank |
| tissue_collection_type | museum |
| tissue_number | NMVZ48771 |
| tissue_preservation | frozen, -20, -80, -196 |
| tissue_preservation_temperature | -20, -80, -196 |
| tissue_type | heart |
| work_order | 14052 |