Plant Pathogen, Transcriptomics, Illumina Shortread, Sample ID 395839
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Data and Resources
This data is made available openly under a Creative Commons Attribution license.
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Data Policy
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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 | 102.100.100/398425 |
| 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 | 17932-5 |
| family | Plasmodiophoridae |
| flowcell_id | 22VH55LT34 |
| 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 | 323.0 |
| library_construction_protocol | Illumina Stranded mRNA (RNA-Seq) |
| library_id | 398425 |
| library_index_seq_dual | UDP0285V3-F & UDP0285V3-R |
| library_layout | Paired-End |
| library_location | AGRF Melbourne |
| library_ng_ul | 0.58 |
| library_oligo_sequence_dual | CCTTGGCATC-GACCGATTCG |
| 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 | 236.0 |
| 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 | Resting spores |
| 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 |