JSON
TSI Pacbio HiFi 102.100.100/357366
Data and Resources
Additional Info
| Field | Value |
|---|---|
| Geospatial Coverage | |
| Resource Permissions | organization_member |
| access_rights | |
| ala_specimen_url | |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 9.0.0.92188 |
| ancillary_notes | Tissue culture generated for the specimen (see Sommerville, K. D., Cuneo, P., Errington, G., Makinson, R. O., Pederson, S., Phillips, G., ... & Offord, C. A. Conservation in the wake of myrtle rust–a case study on two critically endangered Australian rainforest plants. Pacific Conservation Biology.) |
| archive_ingestion_date | 2020-12-01 |
| associated_media | |
| barcode_id | |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-988/TSI_AGRF_PacBio_C20083637/357366_TSI_AGRF_PacBio_DA052899_HiFi_metadata/ |
| birth_date | |
| cell_postion | D01 |
| certainty | 1.0 |
| class | |
| collection_date | 2020-08-24 |
| collection_method | |
| collector | Sam Yap |
| collector_sample_id | |
| common_name | native guava |
| contextual_data_submission_date | |
| coord_uncertainty_metres | |
| country | Australia |
| data_context | Reference genome for Rhodomyrtus psidioides |
| data_custodian | Jia-Yee Samantha Yap |
| data_generated | 2020-12-01 |
| data_type | Pacbio HiFi |
| dataset_id | 102.100.100/358866 |
| dataset_url | |
| date_of_transfer | |
| death_date | |
| decimal_latitude_public | |
| decimal_longitude_public | |
| description | |
| dna_treatment | SHEARING |
| experimental_design | NA |
| facility_sample_id | RP_2 |
| family | Myrtaceae |
| file_name | 355356_TSI_AGRF_PacBio_DA052899.subreads.bam |
| file_type | BAM |
| flowcell_id | DA052899 |
| flowcell_type | SMRT Cell 8M |
| folder_name | TSI_AGRF_PacBio_C20083637 |
| genotypic_sex | |
| genus | Rhodomyrtus |
| habitat | |
| identified_by | |
| insert_size_range | 16365.0 |
| institution_name | Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science |
| latitude | |
| library_comments | NA |
| library_construction_protocol | Preparing HiFi SMRTbell® Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_id | 102.100.100/357366 |
| library_index_id | NA |
| library_index_sequence | NA |
| library_layout | NA |
| library_location | AGRF |
| library_ng_ul | 96.2 |
| library_oligo_sequence | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2020-10-14 |
| library_prepared_by | Trent Peters |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_status | Library Sequenced |
| library_strategy | Preparing HiFi SMRTbell® Libraries using SMRTbell Express Template Prep Kit 2.0 |
| library_type | WGS |
| lifestage | |
| location_text | Bed 65i at Royal Botanic Gardens, Sydney |
| longitude | |
| material_conc_ng_ul | |
| material_extracted_by | |
| material_extraction_date | 2020-08-24 |
| material_extraction_method | modified CTAB method |
| material_extraction_type | DNA |
| method_of_determination | Observation (Adam & Williams 2001) |
| movie_length | 30HRS |
| n_libraries_pooled | 1.0 |
| order | Myrtales |
| phenotypic_sex | unknown (bisexual but self-incompatible) |
| phylum | |
| prior_genetics | |
| sample_custodian | |
| sample_id | 102.100.100/355356 |
| sample_quality | |
| sample_submission_date | |
| sequencing_facility | AGRF |
| sequencing_model | PacBio Sequel II |
| sequencing_platform | PACBIO_SMRT |
| source_population | unknown provenance |
| species | psidioides |
| specimen_id | AA16933 |
| specimen_id_description | Rhodomyrtus psidioides from the RBGSYD living collection |
| state_or_region | New South Wales |
| subspecies | |
| taxon_id | 375277.0 |
| taxonomic_group | Plant |
| ticket | BPAOPS-988 |
| tissue_collection | AA16933_RBGSYD |
| tissue_number | AA16933SYD_RBG_leaf |
| tissue_preservation | fresh |
| tissue_type | leaf tissue |
| type_status | |
| wild_captive | |
| work_order | 14002.0 |