Koala, Pangenome, PacBio-HiFi
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Data and Resources
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Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:cipps001 |
| Access Control Date | 2024-12-17 |
| Access Control Mode | date |
| Sequence Data Type | PacBio-HiFi |
| access_rights | open |
| ala_specimen_url | https://bie.ala.org.au/species/https://biodiversity.org.au/afd/taxa/e9d6fbbd-1505-4073-990a-dc66c930dad10 |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 12.0.0.172289 |
| ancillary_notes | NA |
| associated_media | NA |
| barcode_id | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/cipps_staging/pacbio-hifi/BPAOPS-1535/20231218_CIPPS_AGRF_CAGRF23101336_m84073_231129_043559_s4/ |
| bioplatforms_dataset_id | 102.100.100/419487 |
| bioplatforms_library_id | 102.100.100/417513 |
| bioplatforms_project_code | CIPPS_koala |
| bioplatforms_sample_id | 102.100.100/415511 |
| cell_postion | C01 |
| class | Mammalia |
| collection_date | 2020-07-24 |
| collection_method | Wild capture |
| collector_sample_id | Bronwen |
| common_name | Koala |
| country | Australia |
| data_context | Pangenome |
| data_custodian | Carolyn Hogg |
| date_of_transfer | 2023-12-18 |
| date_of_transfer_to_archive | 2023-12-19 |
| dna_treatment | SHEARING |
| experimental_design | NA |
| facility_sample_id | 417513.0 |
| family | Phascolarctidae |
| file_type | BAM |
| flowcell_id | m84073_231129_043559_s4 |
| flowcell_type | SMRT Cell 25M |
| genotypic_sex | Female |
| genus | Phascolarctos |
| habitat | Alpine forest |
| health_state | unknown |
| insert_size_range | 13909.0 |
| institution_name | University of Sydney |
| library_comments | NA |
| library_construction_protocol | Preparing HiFi SMRTbell Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_index_id | NA |
| library_index_sequence | NA |
| library_layout | NA |
| library_location | AGRF |
| library_ng_ul | 250pM |
| library_oligo_sequence | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2023-11-17 |
| library_prepared_by | Jack Royle |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| lifestage | Adult |
| material_conc_ng_ul | 49.2 |
| material_extracted_by | Elspeth McLennan |
| material_extraction_date | 2023-10-09 |
| material_extraction_method | Circulomics |
| material_extraction_type | DNA |
| metadata_revision_date | 2023-12-19 |
| metadata_revision_filename | 20231219_CIPPS_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| method_sex_determination | Physical examination |
| movie_length | 24Hrs |
| n_libraries_pooled | 1.0 |
| order | Diprotodontia |
| phenotypic_sex | Female |
| phylum | Chordata |
| sample_custodian | Carolyn Hogg |
| sample_quality | Moderate |
| sample_type | Blood |
| scientific_name | Phascolarctos cinereus |
| scientific_name_authorship | NA |
| scientific_name_note | NA |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Revio sequencing plate |
| sequencing_model | PacBio Revio |
| sequencing_platform | PACBIO_SMRT |
| sex_certainty | High |
| source_population | Monaro |
| species | cinereus |
| specimen_id | Bronwen |
| specimen_id_description | Australian National University ID |
| state_or_region | New South Wales |
| subspecies | NA |
| taxon_id | 38625.0 |
| taxonomic_group | Mammal |
| ticket | BPAOPS-1535 |
| tissue_collection | Research archive |
| tissue_collection_type | Wild capture |
| tissue_number | USYD_Bronwen_1 |
| tissue_preservation | Freezer |
| tissue_preservation_temperature | -20.0 |
| wild_captive | Wild |
| work_order | 14057 |