Yarra pygmy perch, Reference genome, PacBio-HiFi, muscle
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Data and Resources
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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 | 2024-07-11 |
| metadata_revision_filename | 20240711_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 |