Plant Pathogen, Genomics, PacBio HiFi, Sample ID 395840
Dataset size is: 7.51 GiB
This dataset is currently under a short embargo period until July 4, 2025 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:pp-prj045 |
| Access Control Date | 2025-07-04 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| analysis_software | SMRT Link Analysis |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/pp_staging/pacbio-hifi/BPAOPS-1606/20240703_PP_AGRF_CAGRF24040395_m84073_240628_102757_s3/ |
| bioplatforms_dataset_id | 102.100.100/399054 |
| bioplatforms_library_id | 102.100.100/398101 |
| bioplatforms_project | Plant Pathogen Initiative |
| bioplatforms_project_code | PP045_P_brassicae |
| bioplatforms_sample_id | 102.100.100/395840 |
| ccg_jira_ticket | BPAOPS-1606 |
| cell_postion | C01 |
| class | Phytomyxea |
| collection_date | 2023-12-12 |
| collector | Alexandra Keith |
| common_name | Clubroot |
| country | Australia |
| data_context | Genomics |
| data_type | PacBio-HiFi |
| date_data_published | 05/07/2024 |
| date_of_transfer | 2024-07-04 |
| date_of_transfer_to_archive | 2024-07-05 |
| description | PacBio-HiFi |
| dna_treatment | SHEARING |
| download | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1606 |
| experimental_design | 13.1.0.221970 |
| facility | AGRF |
| facility_project_code | CAGRF24040395 |
| facility_sample_id | 395840 |
| family | Plasmodiophoridae |
| fast5_compression | NA |
| flowcell_id | m84073_240628_102757_s3 |
| flowcell_type | SMRT Cell 25M |
| folder_name | 20240703_PP_AGRF_CAGRF24040395_m84073_240628_102757_s3 |
| genus | Plasmodiophora |
| health_state | disease |
| host_common_name | Broccoli Pennybridge |
| host_family | Brassicaceae |
| host_organ | Roots |
| host_scientific_name | Brassica oleracea var. italica |
| host_status | Cultivated crop |
| host_symptom | Galling |
| insert_size_range | 9000.0 |
| library_comments | NA |
| library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 |
| library_id | 398101 |
| library_index_id | NA |
| library_index_id_dual | NA |
| library_index_seq_dual | NA |
| library_index_sequence | NA |
| library_layout | NA |
| library_location | AGRF |
| library_ng_ul | 250pM |
| library_oligo_sequence | NA |
| library_oligo_sequence_dual | NA |
| library_prep_date | 2024-06-10 |
| library_prepared_by | Trent Peters |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| life_stage | unknown |
| location_info_restricted | yes |
| location_text | Lindenow |
| material_conc_ng_ul | 580.0 |
| material_extracted_by | Maxim Prokchorchik | University of Sydney |
| material_extraction_date | 2024-04-22 |
| material_extraction_method | Spore purification / CTAB-extraction |
| material_extraction_type | gDNA |
| metadata_revision_date | 2024-12-05 |
| metadata_revision_filename | 2024-11-06_Combined_Plant_Pathogen_sample_metadata_forQCIF_removelatlong.xlsx |
| model_base_caller | NA |
| movie_length | 30Hrs |
| n_libraries_pooled | 3.0 |
| order | Plasmodiophorida |
| phylum | Endomyxa |
| project_lead | Maxim Prokchorchik | University of Sydney |
| sample_collection_type | University |
| sample_custodian | Maxim Prokchorchik | University of Sydney |
| sample_id | 395840 |
| sample_type | Field isolate |
| scientific_name | Plasmodiophora brassicae |
| scientific_name_authorship | Woronin (1877) |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Revio sequencing plate |
| sequencing_model | PacBio Revio |
| sequencing_platform | PACBIO_SMRT |
| species | brassicae |
| specimen_custodian | Maxim Prokchorchik | University of Sydney |
| specimen_id | VIC3 |
| specimen_id_description | Maxim Prokchorchik | University of Sydney |
| state_or_region | Victoria |
| taxon_id | 37360 |
| taxonomic_group | Protist |
| ticket | BPAOPS-1606 |
| type_status | unknown |