Koala, Pangenome, PacBio-HiFi
Dataset size is: 29.86 GiB
This dataset is currently under a short embargo period until December 17, 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 |
|---|---|
| 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-dc66c930dad11 |
| 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-1537/20231218_CIPPS_AGRF_CAGRF23101336_m84073_231212_101727_s3/ |
| bioplatforms_dataset_id | 102.100.100/419487 |
| bioplatforms_library_id | 102.100.100/417514 |
| bioplatforms_project_code | CIPPS_koala |
| bioplatforms_sample_id | 102.100.100/415512 |
| cell_postion | D01 |
| class | Mammalia |
| collection_date | 2022-05-05 |
| collection_method | Wild capture |
| collector_sample_id | MR005 |
| 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 | 417514.0 |
| family | Phascolarctidae |
| file_type | BAM |
| flowcell_id | m84073_231212_101727_s3 |
| flowcell_type | SMRT Cell 25M |
| genotypic_sex | Male |
| genus | Phascolarctos |
| habitat | Alpine forest |
| health_state | unknown |
| insert_size_range | 16696.0 |
| 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 | 40.3 |
| 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 | Male |
| 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 | Cobram |
| species | cinereus |
| specimen_id | MR005 |
| specimen_id_description | University of Queensland ID |
| state_or_region | Victoria |
| subspecies | NA |
| taxon_id | 38625.0 |
| taxonomic_group | Mammal |
| ticket | BPAOPS-1537 |
| tissue_collection | Research archive |
| tissue_collection_type | Wild capture |
| tissue_number | USYD_MR005_1 |
| tissue_preservation | Freezer |
| tissue_preservation_temperature | -20.0 |
| wild_captive | Wild |
| work_order | 14057 |