Hooded Plover, Reference genome, PacBio-HiFi, heart
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Data and Resources
This data is made available openly under a Creative Commons Attribution license.
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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 | 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 | 2024-07-11 |
| metadata_revision_filename | 20240711_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 |