Plant Pathogen, Genomics, Illumina Shortread, Sample ID 394855
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Data and Resources
This data is made available openly under a Creative Commons Attribution license.
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Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:pp-prj043 |
| Access Control Date | 2024-05-18 |
| Access Control Mode | date |
| Sequence Data Type | illumina-shortread |
| analysis_software | Bcl2fastq2 |
| ancillary_notes | Syzygium luehmannii (F.Muell.) L.A.S.Johnson (host plant) vouchered at The National Herbarium of New South Wales. Voucher number: 1124137. |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/pp_staging/illumina-shortread/BPAOPS-1392/20230511_PP_UNSW_HCF2MDRX3_Q0010509_TOB11898/ |
| bioplatforms_dataset_id | 102.100.100/399021 |
| bioplatforms_library_id | 102.100.100/397106 |
| bioplatforms_project | Plant Pathogen Initiative |
| bioplatforms_project_code | PP043_A_psidii_host |
| bioplatforms_sample_id | 102.100.100/394855 |
| ccg_jira_ticket | BPAOPS-1392 |
| cell_postion | NA |
| class | Pucciniomycetes |
| collection_date | 2022-06-29 |
| collection_method | Sample taken at from controlled inoculation (14 June 2022) of plant. Diseased sample collected and stored in -80°C freezer 29th June 2022. |
| collector | Peri Tobias |
| common_name | Myrtle rust |
| country | Australia |
| data_context | Genomics |
| data_type | Hi-C |
| date_data_published | 22/05/2023 |
| date_of_transfer | 2023-05-19 |
| date_of_transfer_to_archive | 2023-05-22 |
| description | Illumina short read (Hi-C) |
| download | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1392 |
| experimental_design | NA |
| facility | UNSW |
| facility_project_code | UNSW |
| facility_sample_id | TOB11898A1 |
| family | Sphaerophragmiaceae |
| fast5_compression | NA |
| flowcell_id | HCF2MDRX3 |
| flowcell_type | NovaSeq SP |
| folder_name | 20230511_PP_UNSW_HCF2MDRX3_Q0010509_TOB11898 |
| genus | Austropuccinia |
| host_common_name | Riberry |
| host_family | Myrtaceae |
| host_organ | Leaves |
| host_scientific_name | Syzygium luehmannii (F.Muell.) L.A.S.Johnson |
| host_status | Cultivated from myrtle rust screened experimental plants. Specific individual plant is highly suscepyible to myrtle rust and given the specimen ID number 51 |
| host_symptom | Rust pustules |
| insert_size_range | 150 PE |
| library_construction_protocol | Proximo_Fungal_v4.5 |
| library_id | 397106 |
| library_index_id | F1 |
| library_index_id_dual | F1 |
| library_index_seq_dual | AGTACAGG |
| library_index_sequence | ACATTACC |
| library_layout | paired end |
| library_location | RAMAC |
| library_ng_ul | 7.34 |
| library_pcr_cycles | 12 |
| library_pcr_reps | 0 |
| library_prep_date | 2023-04-03 |
| library_prepared_by | RAMAC |
| library_selection | NA |
| library_source | cross-linked fungal material |
| library_strategy | Hi-C |
| library_type | Phase Genomics Proximo HiC |
| material_conc_ng_ul | 3-5 mg |
| material_extracted_by | Jacob Downs - University of Sydney |
| material_extraction_method | As per Ramiacottii instructions |
| material_extraction_type | Formaldehyde cross-linked leaf material ground in liqud nitrogen and transported frozen to Ramiacottii. |
| metadata_revision_date | 2024-01-16 |
| metadata_revision_filename | 2024-01-16_Combined_Plant_Pathogen_sample_metadata_forQCIF_removelatlong_v2.xlsx |
| model_base_caller | NA |
| movie_length | NA |
| n_libraries_pooled | 4.0 |
| order | Pucciniales |
| phylum | Basidiomycota |
| project_lead | Peri Tobias | University of Sydney |
| sample_collection_type | Infected Syzygium luehmannii plant |
| sample_custodian | University of Sydney, Plant Breeding Institute, Cobbitty, NSW |
| sample_type | Diseased plant |
| scientific_name | Austropuccinia psidii |
| scientific_name_authorship | (G. Winter) Beenken |
| sequencing_facility | UNSW |
| sequencing_kit_chemistry_version | NovaSeq v1.5 |
| sequencing_model | NovaSeq 6000 |
| sequencing_platform | Illumina |
| species | psidii |
| specimen_custodian | University of Sydney, Plant Breeding Institute, Cobbitty, NSW |
| specimen_id | Au_3, culture no. 622 and accession 115012 |
| specimen_id_description | Pandemic strain myrtle rust |
| state_or_region | NSW |
| taxon_id | 181123 |
| taxonomic_group | Fungi |
| ticket | BPAOPS-1392 |
| tissue | Leaf |
| tissue_preservation | Frozen |
| tissue_preservation_temperature | -80°C |
| work_order | 20017 |