Plant Pathogen, Transcriptomics, Illumina Shortread, Sample ID 395839

Plasmodiophora brassicae, Maxim Prokchorchik | University of Sydney

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Data and Resources

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_after_embargo:date_of_transfer_to_archive:365:pp-prj045
Access Control Date 2025-10-01
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 v07.021.645.4.0.7
base_url https://downloads-qcif.bioplatforms.com/bpa/pp_staging/illumina-shortread/BPAOPS-1697/20241004_PP_AGRF_CAGRF24050264_22NFMNLT3/
bioplatforms_dataset_id 102.100.100/399063
bioplatforms_library_id 102.100.100/398258
bioplatforms_project Plant Pathogen Initiative
bioplatforms_project_code PP045_P_brassicae
bioplatforms_sample_id 102.100.100/395839
ccg_jira_ticket BPAOPS-1697
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 09/10/2024
date_of_transfer 2024-10-01
date_of_transfer_to_archive 2024-10-08
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:BPAOPS-1697
facility AGRF
facility_project_code CAGRF24050264
facility_sample_id 16528-4
family Plasmodiophoridae
flowcell_id 22NFMNLT34
flowcell_type 10B-300
folder_name 20240930_PP_AGRF_CAGRF24050264_22NFMNLT3
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 333.0
library_construction_protocol TruSeq Stranded Total RNA w/ RiboZero Plant (WTS - Plant)
library_id 398258
library_index_seq_dual UDI0016-F & UDI0016-R
library_layout Paired-End
library_location AGRF Melbourne
library_ng_ul 21.1
library_oligo_sequence_dual TGACGAAT-CAGTAGGC
library_pcr_cycles 13
library_prepared_by JM
library_source RNA
library_strategy Total RNA
library_type RNA
life_stage unknown
location_info_restricted yes
location_text Maffra
material_conc_ng_ul 198.0
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-1697
type_status unknown