GAP PacBio-HiFi, Reference genomes, 376316
Dataset size is: 721.06 GiB
Data and Resources
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376316_GAP_GWA_DA110355.pdf Metadata Only PDF
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376316_GAP_GWA_DA110355.ccs.bam Metadata Only BAM
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376316_GAP_GWA_DA110355_ccs_stat... Metadata Only CSV
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376316_GAP_GWA_DA110355.xlsx Metadata Only XLSX
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376316_GAP_GWA_DA110355_final.co... Metadata Only XML
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376316_GAP_GWA_DA110355.subreads.bam Metadata Only BAM
This data is made available openly under a Creative Commons Attribution license.
Please see the initiative
Data Policy
for attribution information.
Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member |
| Access Control Date | 2022-10-01 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| Related Data | Multiple datasets sample_id:376318 library_id:382897 |
| analysis_software | SMRT Link |
| analysis_software_version | 10.1.0.119588 |
| bait_set_reference | not applicable |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/plants_staging/pacbio-hifi/BPAOPS-1141/20210909_GAP_GWA_AJ-236_DA110355/ |
| cell_postion | Cell2 |
| country | Australia |
| data_type | Main dataset |
| dataset_id | 102.100.100/83686 |
| dataset_url | https://data.bioplatforms.com/dataset/bpa-gap-pacbio-hifi-380537-da110355 |
| date_data_published | 11/10/2021 |
| date_of_transfer | 2021-10-01 |
| date_of_transfer_to_archive | 2021-10-04 |
| description | PacBio-HiFi |
| dna_treatment | Shearing on Diagenode megaruptor-3, FFPE repair with NEB kit, Blue Pippin fize selection > 15kB before library preparation |
| facility | GWA |
| facility_sample_id | iLab ID GWA-AJ-236 PS L74&L91 PBS007 |
| family | Rutaceae |
| flowcell_id | DA110355 |
| flowcell_type | 8M SMRT cell |
| folder_name | 20210909_GAP_GWA_GWA-AJ-236_DA110355 |
| genomic_material_associated_references | In the protocol |
| genomic_material_preparation_date | 2020-12-11 |
| genomic_material_preparation_materials | In the protocol |
| genomic_material_preparation_process | HMW DNA Prep https://www.protocols.io/view/scalable-high-molecular-weight-dna-extraction-for-bnjhmcj6 |
| genomic_material_preparation_type | Leaf gDNA |
| genomic_material_prepared_by | Ashley Jones |
| herbarium_code | NE |
| id_vetting_by | Jeremy Bruhl |
| id_vetting_date | 2019-03-09 |
| insert_size_range | 21739 bp |
| library_construction_protocol | HiFi SMRTbell® Libraries using the SMRTbell Express Template Prep Kit 2.0 primer V5 PN 101-853-100 Version 04 (April 2021) |
| library_id | 102.100.100/380537 |
| library_layout | NA |
| library_location | TKI_Freezer09 |
| library_ng_ul | 81.3 |
| library_prep_date | 2021-09-03 |
| library_prepared_by | Hadi Shamaileh |
| library_selection | RANDOM |
| library_source | GENOMIC |
| library_status | Library Sequenced |
| library_strategy | WGS |
| library_type | Long read Hi Fi library with custom steps |
| living_collections_catalog_number | UNE20201105 |
| living_collections_event_date | 2020-11-05 |
| living_collections_material_sample_rna | not applicable |
| living_collections_record_number | SD354 |
| living_collections_recorded_by | S. Dema, J.J.Bruhl & I.Telford |
| location_notes | Wild Cattle Creek State Forest, N of Cascade, 2.3 km along Measuring Hut Road from junction with Moses Rock Road |
| 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 | 2020-12-01 |
| preservation_temperature | Leaf −4°C short-term UNE and postal (2020-11-05) |Leaf −80C long-term ANU (2020-11-17)| DNA 4°C (2020-12-11) |
| preservation_type | Freezing, fridge |
| project_aim | Reference genomes |
| sample_id | 102.100.100/376316 |
| sample_submission_date | 2021-06-18 |
| sample_submitter_email | randre20@une.edu.au | ashley.jones@anu.edu.au |
| sample_submitter_name | Rose Andrew | Ash Jones |
| scientific_name | Phebalium stellatum |
| scientific_name_authorship | I.Telford & J.J.Bruhl |
| scientific_name_notes | NA |
| sequencing_facility | Genomics WA |
| sequencing_model | PacBio Sequel II |
| sequencing_platform | PACBIO_SMRT |
| silica_gel | no |
| state_or_territory | NSW |
| ticket | BPAOPS-1141 |
| voucher_herbarium_catalog_number | 109286 |
| voucher_herbarium_collector_id | S.Dema |
| voucher_herbarium_event_date | 2019-09-03 |
| voucher_herbarium_record_number | S.Dema 354 |
| voucher_herbarium_recorded_by | Sangay Dema | Jeremy Bruhl | Ian Telford | University of New England |