GAP PacBio-HiFi, Reference genomes, 378149
Dataset size is: 1.09 TiB
This dataset is currently under a short embargo period until June 27, 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
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378149_GAP_GWA_DA235355.subreads.bam Metadata Only BAM
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378149_GAP_GWA_DA235355_ccs_stat... Metadata Only CSV
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378149_GAP_GWA_DA235355.pdf Metadata Only PDF
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378149_GAP_GWA_DA235355-SeqQC.pdf Metadata Only PDF
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378149_GAP_GWA_DA235355.ccs.bam Metadata Only BAM
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378149_GAP_GWA_DA235355.xlsx Metadata Only XLSX
Additional Info Show Blank Fields
Field | Value |
---|---|
Resource Permissions | organization_member |
Access Control Date | 2024-06-27 |
Access Control Mode | date |
Sequence Data Type | pacbio-hifi |
analysis_software | SMRT Link |
analysis_software_version | 11.1.0.166339 |
base_url | https://downloads-qcif.bioplatforms.com/bpa/plants_staging/pacbio-hifi/BPAOPS-1433/20230622_GAP_GWA_GWA-AJ-845_DA235355/ |
cell_postion | A01 |
country | Australia |
data_type | Main dataset |
dataset_id | 102.100.100/83820 |
dataset_url | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1433 |
date_data_published | 12/07/2023 |
date_of_transfer | 2023-06-28 |
date_of_transfer_to_archive | 2023-07-11 |
description | PacBio-HiFi |
dna_treatment | Shearing on Diagenode megaruptor-3, FFPE repair with NEB kit, Blue Pippin Size selection > 15kB before library preparation |
facility | GWA |
facility_sample_id | iLab ID GWA-AJ-845 GYM RAW L249 PBS034 |
family | Casuarinaceae |
flowcell_id | DA235355 |
flowcell_type | 8M SMRT cell |
folder_name | 20230622_GAP_GWA_GWA-AJ-845_DA235355 |
genomic_material_associated_references | Jones et al (2021) PLOS ONE https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253830 |
genomic_material_preparation_date | 2022-02-01 |
genomic_material_preparation_materials | In the protocol |
genomic_material_preparation_process | Jones et al (2021) PLOS ONE https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253830 |
genomic_material_preparation_type | Leaf gDNA |
genomic_material_prepared_by | Ashley Jones |
herbarium_code | MEL |
id_vetting_by | Gareth Holmes |
id_vetting_date | 2022-09-19 |
insert_size_range | 21276.0 |
library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 PN 102-166-600 APR2022 |
library_id | 102.100.100/384042 |
library_layout | NA |
library_location | GWA FRIDGE 7 |
library_ng_ul | 83.2 |
library_prep_date | 2023-04-20 |
library_prepared_by | Ali Sadiq Cheema |
library_selection | RANDOM |
library_source | GENOMIC |
library_status | Library Sequenced |
library_strategy | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 PN 102-166-600 APR2022 with custom steps |
library_type | Long read Hi Fi library with custom steps |
living_collections_catalog_number | RBGC 144227.1 |
living_collections_event_date | 2022-09-19 |
living_collections_material_sample_rna | N/A |
living_collections_record_number | GDH146 |
living_collections_recorded_by | Gareth Holmes, Todd McLay |
location_id | Royal Botanic Gardens Victoria, Cranbourne, Gondwana Garden |
metadata_revision_date | 2024-02-28 |
metadata_revision_filename | 2024-02-28_Combined_plant_sample_metadata_forQCIF.xlsx |
movie_length | 30 hours |
nagoya_protocol_compliance | Yes |
nagoya_protocol_permit_number | 10008918.0 |
preservation_date_begin | 2022-11-01 |
preservation_temperature | Leaf −80°C (2022-11), DNA 4°C (2023-02) |
preservation_type | Freezing, fridge |
project_aim | Reference genomes |
sample_id | 102.100.100/378149 |
sample_submitter_email | David.Cantrill@rbg.vic.gov.au |
sample_submitter_name | David Cantrill |
scientific_name | Gymnostoma australianum |
scientific_name_authorship | L.A.S.Johnson |
sequencing_facility | Genomics WA |
sequencing_model | PacBio Sequel II |
sequencing_platform | PACBIO_SMRT |
silica_gel | No |
silica_gel_id | N/A |
silica_gel_pressed_sheet | N/A |
state_or_territory | Victoria |
ticket | BPAOPS-1433 |
voucher_herbarium_catalog_number | MEL 2524930A |
voucher_herbarium_collector_id | Gareth Holmes |
voucher_herbarium_event_date | 2022-09-19 |
voucher_herbarium_record_number | GDH146 |
voucher_herbarium_recorded_by | Gareth Holmes |