GAP PacBio-HiFi, Reference genomes, 378160
Dataset size is: 770.11 GiB
This dataset is currently under a short embargo period until June 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
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378160_GAP_GWA_DA180995-SeqQC.pdf Metadata Only PDF
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378160_GAP_GWA_DA180995.subreads.bam Metadata Only BAM
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378160_GAP_GWA_DA180995.pdf Metadata Only PDF
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378160_GAP_GWA_DA180995.xlsx Metadata Only XLSX
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378160_GAP_GWA_DA180995_ccs_stat... Metadata Only CSV
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378160_GAP_GWA_DA180995.ccs.bam Metadata Only BAM
Please see the initiative
Data Policy
for attribution information.
Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member |
| Access Control Date | 2024-06-01 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| analysis_software | SMRT Link |
| analysis_software_version | 11.1.0.166339 |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/plants_staging/pacbio-hifi/BPAOPS-1403/20230325_GAP_GWA_GWA-AJ-774_DA180995/ |
| cell_postion | B01 |
| country | Australia |
| data_type | Main dataset |
| dataset_id | 102.100.100/83747 |
| dataset_url | https://data.bioplatforms.com/dataset/?ext_search_by=&q=ticket%3ABPAOPS-1403 |
| date_data_published | 07/06/2023 |
| date_of_transfer | 2023-06-02 |
| date_of_transfer_to_archive | 2023-06-05 |
| description | PacBio-HiFi |
| dna_treatment | Shearing on Diagenode megaruptor-3, FFPE repair with NEB kit, Blue Pippin Size selection > 15kB before library preparation |
| facility | GWA |
| facility_sample_id | iLab ID GWA-AJ-774 BERB RAW L249 PBS031 |
| family | Berberidopsidaceae |
| flowcell_id | DA180995 |
| flowcell_type | 8M SMRT cell |
| folder_name | 20230325_GAP_GWA_GWA-AJ-774_DA180995 |
| genomic_material_associated_references | Jones et al (2021) PLOS ONE https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253830 |
| genomic_material_preparation_date | 2022-02-01 |
| genomic_material_preparation_materials | In the protocol |
| genomic_material_preparation_process | Jones et al (2021) PLOS ONE https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253830 |
| genomic_material_preparation_type | Leaf gDNA |
| genomic_material_prepared_by | Ashley Jones |
| herbarium_code | NE |
| insert_size_range | 20760.0 |
| library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 PN 102-166-600 APR2022 |
| library_id | 102.100.100/383121 |
| library_layout | NA |
| library_location | GWA FRIDGE 7 |
| library_ng_ul | 138.0 |
| library_prep_date | 2023-03-14 |
| library_prepared_by | Ali Sadiq Cheema |
| library_selection | RANDOM |
| library_source | GENOMIC |
| library_status | Library Sequenced |
| library_strategy | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 PN 102-166-600 APR2022 with custom steps |
| library_type | Long read Hi Fi library with custom steps |
| living_collections_catalog_number | 110681.0 |
| living_collections_event_date | 2022-10-16 |
| living_collections_material_sample_rna | N/A |
| living_collections_record_number | JJB3787 |
| living_collections_recorded_by | J.J. Bruhl |
| location_id | Northern Tablelands: New England National Park, 1.3 km along Robinsons Knob Trail from Point Lookout Rd, c. 50 m S of fire trail. |
| metadata_revision_date | 2024-02-28 |
| metadata_revision_filename | 2024-02-28_Combined_plant_sample_metadata_forQCIF.xlsx |
| movie_length | 30 hours |
| nagoya_protocol_compliance | Yes |
| nagoya_protocol_permit_number | SL100305 |
| preservation_date_begin | 2022-11-01 |
| preservation_temperature | Leaf −80°C (2022-11), DNA 4°C (2023-02) |
| preservation_type | Freezing, fridge |
| project_aim | Reference genomes |
| sample_id | 102.100.100/378160 |
| sample_submission_date | 2022-10-17 |
| sample_submitter_email | jbruhl@une.edu.au |
| sample_submitter_name | J.J. Bruhl |
| scientific_name | Berberidopsis beckleri |
| scientific_name_authorship | (F.Muell.) Veldkamp |
| sequencing_facility | Genomics WA |
| sequencing_model | PacBio Sequel II |
| sequencing_platform | PACBIO_SMRT |
| state_or_territory | NSW |
| ticket | BPAOPS-1403 |
| voucher_herbarium_catalog_number | NE 113249 |
| voucher_herbarium_collector_id | J.J. Bruhl |
| voucher_herbarium_event_date | 2022-10-16 |
| voucher_herbarium_record_number | JJB3787 |
| voucher_herbarium_recorded_by | J.J. Bruhl |