Plant Pathogen, Genomics, Illumina Shortread, Sample ID 395983
Dataset size is: 4.19 GiB
This dataset is currently under a short embargo period until August 1, 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 | 2025-08-01 |
| Access Control Mode | date |
| Sequence Data Type | illumina-shortread |
| analysis_software | NovaSeq X Control Software v1.2.2.48004; Real Time Analysis v4.6.7; Dragen BCL Convert v07.021.645.4.0.3 |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/pp_staging/illumina-shortread/BPAOPS-1632/20240801_PP_AGRF_CAGRF24050040_22N37VLT3/ |
| bioplatforms_dataset_id | 102.100.100/399062 |
| bioplatforms_library_id | 102.100.100/398245 |
| bioplatforms_project | Plant Pathogen Initiative |
| bioplatforms_project_code | PP045_P_brassicae |
| bioplatforms_sample_id | 102.100.100/395983 |
| ccg_jira_ticket | BPAOPS-1632 |
| class | Phytomyxea |
| collection_date | 1961-08-18 |
| collector | Conroy, Richard J |
| common_name | Clubroot |
| country | Australia |
| data_context | Genomics |
| data_type | Short read |
| date_data_published | 02/08/2024 |
| date_of_transfer | 2024-08-01 |
| date_of_transfer_to_archive | 2024-08-02 |
| description | Illumina Short Read - dataset 1 |
| download | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1632 |
| facility | AGRF |
| facility_project_code | CAGRF24050040 |
| facility_sample_id | 16527-6 |
| family | Plasmodiophoridae |
| flowcell_id | 22N37VLT3 |
| flowcell_type | 10B-300 |
| folder_name | 20240801_PP_AGRF_CAGRF24050040_22N37VLT3 |
| genus | Plasmodiophora |
| host_family | Brassicaceae |
| host_organ | Root |
| host_scientific_name | Brassica napus var. napobrassica |
| host_status | Cultivated crop |
| host_symptom | Galling |
| insert_size_range | 350 bp ± 75 bp |
| library_comments | No shearing |
| library_construction_protocol | IDT xGen cfDNA & FFPE Library Preperation |
| library_id | 398245 |
| library_index_seq_dual | 7-360 & 5-312 |
| library_layout | Paired-End |
| library_location | AGRF Melbourne |
| library_ng_ul | 21.5486041287 |
| library_oligo_sequence_dual | TGTCCAAA-ACAACCAA |
| library_pcr_cycles | 9 |
| library_prep_date | 2024-06-26 |
| library_prepared_by | BP |
| library_selection | PCR-based Ligation |
| library_source | DNA |
| library_strategy | Whole-genome Sequencing |
| library_type | WGS |
| location_text | Tamworth |
| material_conc_ng_ul | 84.0 |
| material_extracted_by | Maxim Prokchorchik | University of Sydney |
| material_extraction_date | 2024-05-02 |
| material_extraction_method | Spore isolation the CTAB gDNA extraction |
| material_extraction_type | gDNA |
| metadata_revision_date | 2025-02-27 |
| metadata_revision_filename | 2024-12-20_Combined_Plant_Pathogen_sample_metadata_forQCIF_removelatlong.xlsx |
| order | Plasmodiophorida |
| phylum | Endomyxa |
| project_lead | Maxim Prokchorchik | University of Sydney |
| sample_collection_type | Herbarium |
| sample_custodian | Maxim Prokchorchik | University of Sydney |
| sample_type | Dried diseased plants |
| scientific_name | Plasmodiophora brassicae |
| scientific_name_authorship | Woronin (1877) |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | XLEAP SBS |
| sequencing_model | X Plus |
| sequencing_platform | NovaSeq |
| species | brassicae |
| specimen_custodian | NSW Plant Pathology & Mycology Herbarium |
| specimen_id | DAR6254 |
| specimen_id_description | NSW Plant Pathology & Mycology Herbarium |
| state_or_region | New South Wales |
| taxon_id | 37360 |
| taxonomic_group | Protist |
| ticket | BPAOPS-1632 |
| work_order | WO20049 |