Plant Pathogen, Transcriptomics, Illumina Shortread, Sample ID 395839
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This dataset is currently under a short embargo period until December 13, 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 | 2025-12-13 |
| 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-1728/20241213_PP_AGRF_CAGRF24100180_22VH55LT3/ |
| bioplatforms_dataset_id | 102.100.100/399075 |
| bioplatforms_library_id | 102.100.100/398421 |
| bioplatforms_project | Plant Pathogen Initiative |
| bioplatforms_project_code | PP045_P_brassicae |
| bioplatforms_sample_id | 102.100.100/395839 |
| ccg_jira_ticket | BPAOPS-1728 |
| class | Phytomyxea |
| collection_date | 2023-11-28 |
| collector | Subhashini Marri |
| common_name | Clubroot |
| country | Australia |
| data_context | Transcriptomics |
| data_type | Short read |
| date_data_published | 19/12/2024 |
| date_of_transfer | 2024-12-13 |
| date_of_transfer_to_archive | 2024-12-13 |
| description | Illumina Short read - need to add _1, _2 on flowcell ID to get the data to ingest |
| download | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1728 |
| facility | AGRF |
| facility_project_code | CAGRF24100180 |
| facility_sample_id | 17932-1 |
| family | Plasmodiophoridae |
| flowcell_id | 22VH55LT31 |
| flowcell_type | 10B-300 |
| folder_name | 20241213_PP_AGRF_CAGRF24100180_22VH55LT3 |
| genus | Plasmodiophora |
| health_state | disease |
| host_common_name | Spider mustard |
| host_family | Brassicaceae |
| host_organ | Roots |
| host_scientific_name | Brassica juncea var. japonica |
| host_status | Cultivated crop |
| host_symptom | Galling |
| insert_size_range | 383.0 |
| library_construction_protocol | Illumina Stranded mRNA (RNA-Seq) |
| library_id | 398421 |
| library_index_seq_dual | UDP0281-F & UDP0281-R |
| library_layout | Paired-End |
| library_location | AGRF Melbourne |
| library_ng_ul | 10.6 |
| library_oligo_sequence_dual | TATCACTCTG-AACGTTACAT |
| library_pcr_cycles | 13 |
| library_prep_date | 2024-11-11 |
| library_prepared_by | JL |
| library_source | RNA |
| library_type | RNA |
| life_stage | unknown |
| location_info_restricted | yes |
| location_text | Maffra |
| material_conc_ng_ul | 143.0 |
| material_extracted_by | Maxim Prokchorchik | University of Sydney |
| material_extraction_date | 2024-05-06 |
| material_extraction_method | RNA extraction kit |
| material_extraction_type | RNA |
| metadata_revision_date | 2025-06-20 |
| metadata_revision_filename | 2025-04-08_Combined_Plant_Pathogen_sample_metadata_forQCIF_removelatlong.xlsx |
| order | Plasmodiophorida |
| phylum | Endomyxa |
| project_lead | Maxim Prokchorchik | University of Sydney |
| sample_collection_type | University |
| sample_custodian | Maxim Prokchorchik | University of Sydney |
| sample_type | Infected plant |
| 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 | Maxim Prokchorchik | University of Sydney |
| specimen_id | VIC2 |
| specimen_id_description | Maxim Prokchorchik | University of Sydney |
| state_or_region | Victoria |
| taxon_id | 37360 |
| taxonomic_group | Protist |
| ticket | BPAOPS-1728 |
| type_status | unknown |