GAP PacBio-HiFi, Reference genomes, 378166
Dataset size is: 1.08 TiB
This dataset is currently under a short embargo period until August 10, 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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378166_GAP_GWA_DA266052.pdf Metadata Only PDF
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378166_GAP_GWA_DA266052-SeqQC.pdf Metadata Only PDF
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378166_GAP_GWA_DA266052.subreads.bam Metadata Only BAM
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378166_GAP_GWA_DA266052.ccs.bam Metadata Only BAM
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378166_GAP_GWA_DA266052_ccs_stat... Metadata Only CSV
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378166_GAP_GWA_DA266052.xlsx Metadata Only XLSX
Additional Info Show Blank Fields
Field | Value |
---|---|
Resource Permissions | organization_member |
Access Control Date | 2024-08-10 |
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-1455/20230731_GAP_GWA_GWA-AJ-847_DA266052/ |
cell_postion | A01 |
country | Australia |
data_type | Main dataset |
dataset_id | 102.100.100/83797 |
dataset_url | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1455 |
date_data_published | 21/06/2023 |
date_of_transfer | 2023-08-11 |
date_of_transfer_to_archive | 2023-08-17 |
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-847 Lepidosperma gladiatum L290 PBS036 |
family | Cyperaceae |
flowcell_id | DA266052 |
flowcell_type | 8M SMRT cell |
folder_name | 20230731_GAP_GWA_GWA-AJ-847_DA266052 |
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 | 2023-06-01 |
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 | David Cantrill |
id_vetting_date | 2023-04-03 |
insert_size_range | 20134.0 |
library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 PN 102-166-600 APR2022 |
library_id | 102.100.100/383173 |
library_layout | NA |
library_location | GWA FRIDGE 10 |
library_ng_ul | 125.5 |
library_prep_date | 2023-07-28 |
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 | RBGM 180608.6 |
living_collections_event_date | 2023-04-03 |
living_collections_material_sample_rna | N/A |
living_collections_record_number | DJC 2361 |
living_collections_recorded_by | David Cantrill, Todd McLay |
location_id | Royal Botanic Gardens Victoria, Melbourne, Australian Drylands Bed |
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 | 2023-04-01 |
preservation_temperature | Leaf −80°C (2023-04), DNA 4°C (2023-06) |
preservation_type | Freezing, fridge |
project_aim | Reference genomes |
sample_id | 102.100.100/378166 |
sample_submitter_email | David.Cantrill@rbg.vic.gov.au |
sample_submitter_name | David Cantrill |
scientific_name | Lepidosperma gladiatum |
scientific_name_authorship | Labill. |
sequencing_facility | Genomics WA |
sequencing_model | PacBio Sequel II |
sequencing_platform | PACBIO_SMRT |
state_or_territory | Victoria |
ticket | BPAOPS-1455 |
voucher_herbarium_catalog_number | MEL 2529500A |
voucher_herbarium_collector_id | David Cantrill |
voucher_herbarium_event_date | 2023-04-03 |
voucher_herbarium_record_number | DJC 2361 |
voucher_herbarium_recorded_by | David Cantrill |