GAP PacBio-HiFi, Reference genomes, 378168
Dataset size is: 1.12 TiB
This dataset is currently under a short embargo period until November 14, 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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378168_GAP_GWA_DA267077.subreads.bam Metadata Only BAM
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378168_GAP_GWA_DA267077.pdf Metadata Only PDF
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378168_GAP_GWA_DA267077.ccs.bam Metadata Only BAM
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378168_GAP_GWA_DA267077-SeqQC.pdf Metadata Only PDF
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378168_GAP_GWA_DA267077.xlsx Metadata Only XLSX
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378168_GAP_GWA_DA267077_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 | 2024-11-14 |
| 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-1519/20231106_GAP_GWA_GWA-AJ-851_DA267077/ |
| cell_postion | D01 |
| country | Australia |
| data_type | Main dataset |
| dataset_id | 102.100.100/83824 |
| dataset_url | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1519 |
| date_data_published | 22/11/2023 |
| date_of_transfer | 2023-11-15 |
| date_of_transfer_to_archive | 2023-11-20 |
| description | PacBio-HiFi |
| dna_treatment | Shearing on Diagenode megaruptor-3, FFPE repair with NEB kit, Blue Pippin Size selection > 7kB before library preparation |
| facility | GWA |
| facility_sample_id | iLab ID GWA-AJ-851 Roepera similis L290 PBS039 |
| family | Zygophyllaceae |
| flowcell_id | DA267077 |
| flowcell_type | 8M SMRT cell |
| folder_name | 20231106_GAP_GWA_GWA-AJ-851_DA267077 |
| 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 | 2018-09-13 |
| insert_size_range | 18763.0 |
| library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 PN 102-166-600 APR2022 |
| library_id | 102.100.100/384046 |
| library_layout | NA |
| library_location | GWA FRIDGE 10 |
| library_ng_ul | 51.7 |
| library_prep_date | 2023-11-01 |
| 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 | RBGC 194032.1 |
| living_collections_event_date | 2023-04-03 |
| living_collections_material_sample_rna | N/A |
| living_collections_record_number | GDH 156 |
| living_collections_recorded_by | Gareth Holmes |
| location_id | Royal Botanic Gardens Victoria, Cranbourne, Nursery |
| 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 | 102.100.100/378168 |
| sample_submitter_email | David.Cantrill@rbg.vic.gov.au |
| sample_submitter_name | David Cantrill |
| scientific_name | Roepera simile |
| scientific_name_authorship | (H.Eichler) Beier & Thulin |
| sequencing_facility | Genomics WA |
| sequencing_model | PacBio Sequel II |
| sequencing_platform | PACBIO_SMRT |
| state_or_territory | Victoria |
| ticket | BPAOPS-1519 |
| voucher_herbarium_catalog_number | MEL 2478506A |
| voucher_herbarium_collector_id | Bronwyn Swartz |
| voucher_herbarium_event_date | 2018-09-13 |
| voucher_herbarium_record_number | Swartz, B.A. 15 |
| voucher_herbarium_recorded_by | Bronwyn Swartz |