Yarra pygmy perch, Reference genome, PacBio-HiFi, muscle
Dataset size is: 13.10 GiB
This dataset is currently under a short embargo period until November 1, 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 | 2024-11-01 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| access_rights | No restrictions |
| ala_specimen_url | NA |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 12.0.0.172289 |
| ancillary_notes | captive breeding program |
| associated_media | NA |
| bait_set_name | NA |
| bait_set_reference | NA |
| barcode_id | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-1510/20231031_TSI_AGRF_CAGRF230414583_m84073_231020_062031_s1/ |
| bioplatforms_project | Threatened Species Initiative |
| cell_postion | A01 |
| certainty | moderated |
| class | Actinopterygii |
| collection_date | 2023-04-12 |
| collection_method | Hand net |
| collector | Prof Luciano Beheregaray, Dr Chris Brauer, Dr Jonathan Sandoval |
| collector_sample_id | TSIYPP03 |
| common_name | Yarra pygmy perch |
| country | Australia |
| data_context | Reference genome |
| data_custodian | Prof Luciano Beheregaray |
| data_type | PacBio-HiFi |
| dataset_id | 102.100.100/358820 |
| date_of_transfer | 2023-11-02 |
| date_of_transfer_to_archive | 2023-11-03 |
| death_date | 2023-04-12 |
| decimal_latitude_public | -35.5 |
| decimal_longitude_public | 138.9 |
| description | Howard River toadlet, Yarra Pygmy Perch (HiFi Revio) |
| dna_treatment | SHEARING |
| experimental_design | NA |
| facility_project_code | CAGRF230414583 |
| facility_sample_id | 462070.0 |
| family | Percichthyidae |
| fast5_compression | NA |
| file_type | BAM |
| flowcell_id | m84073_231020_062031_s1 |
| flowcell_type | SMRT Cell 25M |
| folder_name | 20231031_TSI_AGRF_CAGRF230414583_m84073_231020_062031_s1 |
| genotypic_sex | not determined |
| genus | Nannoperca |
| habitat | Water channel |
| health_state | Diseased but healthy at the time of death |
| insert_size_range | 7200.0 |
| institution_name | Flinders University |
| latitude | -35.5 |
| library_comments | NA |
| library_construction_protocol | Preparing HiFi SMRTbell Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_id | 102.100.100/462070 |
| 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 | 2023-09-26 |
| library_prepared_by | Trent Peters |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| lifestage | adult |
| location_text | Mundoo Channel, Hindmarsh Island |
| longitude | 138.9 |
| material_conc_ng_ul | 150.0 |
| material_extracted_by | Diana Vornicu |
| material_extraction_date | 2023-04-01 |
| material_extraction_method | Salting-out (https://doi.org/10.1093/oxfordjournals.molbev.a025612) |
| material_extraction_type | DNA,RNA |
| metadata_revision_date | 2023-11-30 |
| metadata_revision_filename | 20231130_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| method_of_determination | dissection |
| model_base_caller | NA |
| movie_length | 24Hrs |
| n_libraries_pooled | 1.0 |
| order | Perciformes |
| phenotypic_sex | male |
| phylum | Chordata |
| prior_genetics | NA |
| sample_custodian | Prof Luciano Beheregaray |
| sample_id | 102.100.100/460033 |
| sample_quality | High quality |
| sample_type | Muscle tissue sample |
| scientific_name | Nannoperca obscura |
| scientific_name_authorship | Klunzinger 1872 |
| scientific_name_note | NA |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Revio sequencing plate |
| sequencing_model | PacBio Revio |
| sequencing_platform | PACBIO_SMRT |
| source_population | Murray-Darling Basin |
| species | obscura |
| specimen_id | TSIYPP03 |
| specimen_id_description | Molecular Ecology Lab Flinders University |
| state_or_region | South Australia |
| subspecies | NA |
| taxon_id | 135771.0 |
| taxonomic_group | Fish |
| ticket | BPAOPS-1510 |
| tissue_collection | YPPMELFU |
| tissue_collection_type | University |
| tissue_number | TSIYPP03Mus |
| tissue_preservation | frozen, ethanol |
| tissue_preservation_temperature | -80.0 |
| tissue_type | muscle |
| type_status | NA |
| wild_captive | captive |
| work_order | 14052 |