Maugean skate, Reference Genome, PacBio-HiFi, Blood
Dataset size is: 19.46 GiB
This dataset is currently under a short embargo period until June 15, 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 |
|---|---|
| Geospatial Coverage |
Dataset extentMap tiles & Data by OpenStreetMap, under CC BY SA.
|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:tsi-consortium-members |
| Access Control Date | 2024-06-15 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| access_rights | On request |
| ala_specimen_url | https://bie.ala.org.au/species/https://biodiversity.org.au/afd/taxa/0d9d194f-ab8d-46da-a835-bb9c9fbda130 |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 12.0.0.172289 |
| bait_set_name | NA |
| bait_set_reference | NA |
| barcode_id | FOAE223-06, FOAE224-06, GBMNA14226-19 , GBMNA18546-19, GBMNA18588-19 |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-1418/20230615_TSI_AGRF_CAGRF230314042_m84073_230605_044025_s1/ |
| bioplatforms_project | Threatened Species Initiative |
| cell_postion | A01 |
| certainty | >99% |
| class | Chondrichthyes |
| collection_method | Gill net |
| collector | D Moreno |
| collector_sample_id | MS19 |
| common_name | Maugean skate |
| country | Australia |
| data_context | Reference Genome |
| data_custodian | Jawahar Patil |
| data_type | PacBio-HiFi |
| dataset_id | 102.100.100/358814 |
| date_of_transfer | 2023-06-16 |
| date_of_transfer_to_archive | 2023-06-16 |
| decimal_latitude_public | -42.15 |
| decimal_longitude_public | 145.31 |
| description | Zearaja maugeana |
| dna_treatment | SHEARING |
| experimental_design | NA |
| facility_project_code | QAGRF230314042 |
| facility_sample_id | 460864.0 |
| family | Rajidae |
| fast5_compression | NA |
| file_type | BAM |
| flowcell_id | m84073_230605_044025_s1 |
| flowcell_type | SMRT Cell 25M |
| folder_name | 20230615_TSI_AGRF_CAGRF230314042_m84073_230605_044025_s1 |
| genotypic_sex | Not determined |
| genus | Zearaja |
| habitat | Estuarine |
| health_state | Good |
| insert_size_range | 13000.0 |
| institution_name | IMAS, UTAS |
| latitude | -42.15 |
| library_comments | NA |
| library_construction_protocol | Preparing HiFi SMRTbell Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_id | 102.100.100/460864 |
| 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 | 225pM |
| library_oligo_sequence | NA |
| library_oligo_sequence_dual | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2023-05-26 |
| library_prepared_by | Jack Royle |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| lifestage | adult |
| location_text | Long Bay |
| longitude | 145.31 |
| material_conc_ng_ul | 250.0 |
| material_extracted_by | JPatil/TKwan |
| material_extraction_date | 2023-03-23 |
| material_extraction_method | Phenol chloroform |
| material_extraction_type | DNA |
| metadata_revision_date | 2023-11-30 |
| metadata_revision_filename | 20231130_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| method_of_determination | Secondary sexual characters |
| model_base_caller | NA |
| movie_length | 24Hrs |
| n_libraries_pooled | 1.0 |
| order | Rajiformes |
| phenotypic_sex | Female |
| phylum | Chordata |
| prior_genetics | Weltz, K., Lyle, J.M., Semmens, J.M. et al. Population genetics of the endangered Maugean skate (Zearaja maugeana) in Macquarie Harbour, Tasmania. Conserv Genet 19, 1505–1512 (2018). https://doi.org/10.1007/s10592-018-1117-0 |
| sample_custodian | J Semmens, D Moreno, J Patil |
| sample_id | 102.100.100/458827 |
| sample_quality | Good |
| sample_type | Tissue sample |
| scientific_name | Zearaja maugeana |
| scientific_name_authorship | Last & Gledhill, 2007 |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Revio sequencing plate |
| sequencing_model | PacBio Revio |
| sequencing_platform | PACBIO_SMRT |
| source_population | Macquarie Harbour |
| species | maugeana |
| specimen_id | ZM F MS19 |
| specimen_id_description | IMAS, UTAS internal identifier |
| state_or_region | Tasmania |
| subspecies | NA |
| taxon_id | 496415.0 |
| taxonomic_group | Fish |
| ticket | BPAOPS-1418 |
| tissue_collection | MS19 |
| tissue_collection_type | IMAS Collection |
| tissue_number | ZM F MS19_Blood |
| tissue_preservation | Frozen |
| tissue_preservation_temperature | -80.0 |
| tissue_type | Blood |
| type_status | wild |
| wild_captive | wild |
| work_order | 14049 |