there is no common name listed, Reference genome, PacBio-HiFi, leaf
Dataset size is: 1.07 TiB
This dataset is currently under a short embargo period until May 7, 2024 to enable primary access by research partners.
If you would like access during this period please contact us here or contact the project lead directly (see details in the table below) for collaboration opportunities.
Data and Resources
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:tsi-consortium-members |
| Access Control Date | 2024-05-07 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| access_rights | No restrictions |
| analysis_software | SMRT Link Analysis |
| analysis_software_version | 12.0.0.177059 |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-1387/2023053_TSI_AGRF_CAGRF221213172_DA235476/ |
| bioplatforms_project | Threatened Species Initiative |
| cell_postion | 1_A01 |
| certainty | NA |
| class | Equisetopsida |
| collection_method | snap freeze in liquid nitrogen from live plant |
| collector | Ton Stewart, University of the Sunshine Coast |
| common_name | there is no common name listed |
| country | Australia |
| data_context | Reference genome |
| data_custodian | Ton Stewart |
| data_type | PacBio-HiFi |
| dataset_id | 102.100.100/358811 |
| dataset_url | researcher informed |
| date_of_transfer | 2023-05-08 |
| date_of_transfer_to_archive | 2023-05-10 |
| description | Fontainea HiFi |
| dna_treatment | SHEARING |
| experimental_design | NA |
| facility_project_code | CAGRF221213172 |
| facility_sample_id | 460859.0 |
| family | Euphorbiaceae |
| fast5_compression | NA |
| file_type | BAM |
| flowcell_id | DA235476 |
| flowcell_type | SMRT Cell 8M |
| folder_name | 2023053_TSI_AGRF_CAGRF221213172_DA235476 |
| genotypic_sex | NA |
| genus | Fontainea |
| habitat | rain forest |
| health_state | healthy young plant |
| insert_size_range | 16000.0 |
| institution_name | University of the Sunshine Coast |
| library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell ® prep kit 3.0 |
| library_id | 102.100.100/460859 |
| library_index_id | NA |
| library_index_id_dual | NA |
| library_index_seq_dual | NA |
| library_index_sequence | NA |
| library_layout | NA |
| library_location | AGRF |
| library_ng_ul | 48.6 |
| library_oligo_sequence | NA |
| library_oligo_sequence_dual | NA |
| library_pcr_cycles | NA |
| library_pcr_reps | NA |
| library_prep_date | 2023-04-19 |
| library_prepared_by | Trent Peters |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | WGS |
| library_type | PacBio-HiFi |
| location_text | only two sites just north of Coffs Harbour on the NSW mid-north coast, Boambee Valley, along the coastal foothills to Coffs Creek, the Korora Basin |
| material_extracted_by | Ton Stewart |
| material_extraction_type | DNA |
| metadata_revision_date | 2023-11-30 |
| metadata_revision_filename | 20231130_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx |
| method_of_determination | NA |
| model_base_caller | NA |
| movie_length | 30HRS |
| n_libraries_pooled | 1.0 |
| order | Malpighiales |
| phenotypic_sex | NA |
| phylum | Streptophyta |
| sample_custodian | Ton Stewart, Gabes Conroy |
| sample_id | 102.100.100/458822 |
| sample_quality | don't know yet |
| sample_type | tissue sample |
| scientific_name | Fontainea sp. Coffs Harbour (A.S.Benwell 341, NSW1102027) |
| scientific_name_authorship | A.S.Benwell 341 |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | 11.1.0.154383 |
| sequencing_model | PacBio Sequel II |
| sequencing_platform | PACBIO_SMRT |
| species | Coffs harbour |
| specimen_id | UniSC FC0001 |
| specimen_id_description | UniSC is where the plant propagate, FC is Fontainea Coffs Harbour, number is plant number |
| state_or_region | New South Wales |
| subspecies | None |
| taxon_id | no taxon id in taxonomy website but there ie number from NSW as NSW1102027 |
| taxonomic_group | Plant |
| ticket | BPAOPS-1387 |
| tissue_collection | Botany |
| tissue_collection_type | living collection |
| tissue_number | UniSC FC0001_leaf1 |
| tissue_preservation | frozen |
| tissue_preservation_temperature | -80C |
| tissue_type | leaf |
| work_order | 14043 |