Plant Pathogen, Genomics, Illumina Shortread, Sample ID 394568
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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-prj032 |
| Access Control Date | 2024-05-18 |
| Access Control Mode | date |
| Sequence Data Type | illumina-shortread |
| analysis_software | Bcl2fastq2 |
| associated_media | None |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/pp_staging/illumina-shortread/BPAOPS-1391/20230511_PP_UNSW_HCF2MDRX3_Q0010509_HEN11834/ |
| bioplatforms_dataset_id | 102.100.100/399016 |
| bioplatforms_library_id | 102.100.100/396818 |
| bioplatforms_project | Plant Pathogen Initiative |
| bioplatforms_project_code | PP032_P_coronata |
| bioplatforms_sample_id | 102.100.100/394568 |
| ccg_jira_ticket | BPAOPS-1391 |
| cell_postion | NA |
| class | Pucciniomycetes |
| collection_date | 2021-10-19 |
| collection_method | Infected leaves are removed from the plant and shipped to CSIRO in a paper envelope |
| collector | Figueroa, M. |
| common_name | Oat crown rust, leaf 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 |
| decimal_latitude_public | Part of community submission project - coordinates not provided |
| decimal_longitude_public | Part of community submission project - coordinates not provided |
| description | Illumina short read (Hi-C) |
| download | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1391 |
| experimental_design | NA |
| facility | UNSW |
| facility_project_code | UNSW |
| facility_sample_id | HEN11834A1 |
| family | Pucciniaceae |
| fast5_compression | NA |
| flowcell_id | HCF2MDRX3 |
| flowcell_type | NovaSeq SP |
| folder_name | 20230511_PP_UNSW_HCF2MDRX3_Q0010509_HEN11834 |
| genus | Puccinia |
| host_common_name | Oat |
| host_family | Poaceae |
| host_organ | Leaf |
| host_scientific_name | Avena spp. |
| host_status | Wild |
| host_symptom | Mild infection |
| insert_size_range | 150 PE |
| isolate | 21ACT116 |
| library_construction_protocol | Proximo_Fungal_v4.5 |
| library_id | 396818 |
| library_index_id | A1 |
| library_index_id_dual | A1 |
| library_index_seq_dual | TGACGTAG |
| library_index_sequence | TCAAGATC |
| library_layout | Paired end |
| library_location | RAMAC |
| library_ng_ul | 7.04 |
| library_pcr_cycles | 12 |
| library_pcr_reps | 0 |
| library_prep_date | 2023-03-13 |
| library_prepared_by | RAMAC |
| library_selection | NA |
| library_source | croslinked fungal material |
| library_strategy | Hi-C |
| library_type | Phase Genomics Proximo HiC |
| location_info_restricted | No |
| location_text | National Arboretum, Canberra |
| material_extracted_by | Eva Henningsen | CSIRO |
| material_extraction_method | Formaldehyde crosslinking |
| material_extraction_type | Cross-linked spores |
| 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 | Pucciniomycotina |
| project_lead | Melania Figueroa | CSIRO |
| sample_collection_type | Private |
| sample_custodian | David Lewis | CSIRO |
| sample_quality | Spores are viable |
| sample_type | Single pustule isolation |
| scientific_name | Puccinia coronata f. sp. avenae |
| scientific_name_authorship | Urban and Marková, 1993 |
| scientific_name_note | The full name assigned by Urban and Marková is Puccinia coronata var. avenae f. sp. avenae |
| sequencing_facility | UNSW |
| sequencing_kit_chemistry_version | NovaSeq v1.5 |
| sequencing_model | NovaSeq 6000 |
| sequencing_platform | Illumina |
| species | coronata |
| specimen_custodian | CSIRO |
| specimen_id | 21ACT116 |
| specimen_id_description | CSIRO |
| state_or_region | Australian Captial Territory |
| sub_species | f. sp. avenae |
| taxon_id | 200324 |
| taxonomic_group | Fungi |
| ticket | BPAOPS-1391 |
| tissue | Urediniospores |
| tissue_preservation | Frozen |
| tissue_preservation_temperature | -80°C |
| wild_captive | Wild |
| work_order | 20017 |