GAP PacBio-HiFi, Reference genomes, 378174
Dataset size is: 1.10 TiB
This dataset is currently under a short embargo period until August 10, 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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378174_GAP_GWA_DA266090.pdf Metadata Only PDF
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378174_GAP_GWA_DA266090.subreads.bam Metadata Only BAM
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378174_GAP_GWA_DA266090-SeqQC.pdf Metadata Only PDF
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378174_GAP_GWA_DA266090.ccs.bam Metadata Only BAM
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378174_GAP_GWA_DA266090.xlsx Metadata Only XLSX
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378174_GAP_GWA_DA266090_ccs_stat... Metadata Only CSV
Please see the initiative
Data Policy
for attribution information.
Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member |
| Access Control Date | 2024-08-10 |
| 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-1457/20230803_GAP_GWA_GWA-AJ-853_DA266090/ |
| cell_postion | C01 |
| country | Australia |
| data_type | Main dataset |
| dataset_id | 102.100.100/83825 |
| dataset_url | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1457 |
| date_data_published | 21/06/2023 |
| date_of_transfer | 2023-08-11 |
| date_of_transfer_to_archive | 2023-08-17 |
| 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-853 Phyllanthus gunnii L290 PBS036 |
| family | Phyllanthaceae |
| flowcell_id | DA266090 |
| flowcell_type | 8M SMRT cell |
| folder_name | 20230803_GAP_GWA_GWA-AJ-853_DA266090 |
| 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 | 2023-06-01 |
| 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 | MEL |
| id_vetting_by | Gareth Holmes |
| id_vetting_date | 2023-04-03 |
| insert_size_range | 20303.0 |
| library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 PN 102-166-600 APR2022 |
| library_id | 102.100.100/384047 |
| library_layout | NA |
| library_location | GWA FRIDGE 10 |
| library_ng_ul | 158.5 |
| library_prep_date | 2023-07-18 |
| 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 | RBGM 170598.1 |
| living_collections_event_date | 2023-04-03 |
| living_collections_material_sample_rna | N/A |
| living_collections_record_number | DJC 2363 |
| living_collections_recorded_by | Gareth Holmes |
| location_id | Royal Botanic Gardens Victoria, Melbourne, Xanthorrhoea Bed |
| 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 | 10008918.0 |
| preservation_date_begin | 2023-04-01 |
| preservation_temperature | Leaf −80°C (2023-04), DNA 4°C (2023-06) |
| preservation_type | Freezing, fridge |
| project_aim | Reference genomes |
| sample_id | 102.100.100/378174 |
| sample_submitter_email | David.Cantrill@rbg.vic.gov.au |
| sample_submitter_name | David Cantrill |
| scientific_name | Phyllanthus gunnii |
| scientific_name_authorship | Hook.f. |
| sequencing_facility | Genomics WA |
| sequencing_model | PacBio Sequel II |
| sequencing_platform | PACBIO_SMRT |
| state_or_territory | Victoria |
| ticket | BPAOPS-1457 |
| voucher_herbarium_catalog_number | MEL 2529502A |
| voucher_herbarium_collector_id | David Cantrill |
| voucher_herbarium_event_date | 2023-04-03 |
| voucher_herbarium_record_number | DJC 2363 |
| voucher_herbarium_recorded_by | David Cantrill |