Australian Microbiome Metagenomics Novaseq 102.100.100/401000
Dataset size is: 8.66 GiB
Data and Resources
This data is made available openly under a Creative Commons Attribution license.
Please see the initiative
Data Policy
for attribution information.
Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Geospatial Coverage |
Dataset extentMap tiles & Data by OpenStreetMap, under CC BY SA.
|
| Resource Permissions | organization_member_after_embargo:archive_ingestion_date:90:am-consortium-members |
| Access Control Date | 2022-12-12 |
| Access Control Mode | date |
| Sequence Data Type | illumina-shortread |
| Related Data | doi:10.25953/vp5c-pk95 |
| absorbance_260_230_ratio | 0.349 |
| absorbance_260_280_ratio | 1.84 |
| absorbance_260_280_ratio_submitter | 1.768 |
| absorbance_260_280_ratio_submitter_meth | meth_NanoPhotometer NP80 |
| am_environment | Marine |
| archive_ingestion_date | 2022-09-14 |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/amd/metagenomics-novaseq/ramaciotti/BPAOPS-1318/20220902_MGE_UNSW_H7KCJDSX5_Q0009190/ |
| bioplatforms_dataset_id | 102.100.100/401931 |
| bioplatforms_project | Australian Microbiome Initiative (AM) |
| bioplatforms_project_code | AM0015 |
| collection_date | 2020-11-01T12:00:00 |
| conversion_software | bcl2fastq |
| conversion_software_version | v2.20 |
| data_generated | 2022-09-14 |
| data_type | MGE |
| database_schema_definitions_url | https://github.com/AusMicrobiome/contextualdb_doc/raw/4.2.0/db_schema_definitions/db_schema_definitions.xlsx |
| dataset_id | 102.100.100/401931 |
| date_of_transfer | 2022-09-13 |
| depth (m) | 0.0 |
| depth_lower (m) | 0.01 |
| depth_upper (m) | 0.0 |
| description | NovaSeq data package |
| dna_concentration | 19.26 |
| dna_concentration_method | picogreen |
| dna_concentration_submitter (ng/μL) | 22.45 |
| dna_concentration_submitter_meth | meth_NanoPhotometer NP80 |
| env_broad_scale | 6 Water |
| env_local_scale | 6.6 Estuary/coastal waters |
| env_medium | Sediment [ENVO_00002007] |
| facility_code | ramaciotti |
| fine_sediment (%) | 10.0135021713 |
| fine_sediment_meth | meth_1. Transfer sediments into pre-weighed labelled aluminium trays. 2. Place in drying oven at 60°C for 24hrs. 3. Using a sediment shaker for 1 min; shake sample through 4mm; 2mm; 1mm; 500um; 250um; 125um and 63um size sieves. 4. Transfer sediments retained on each sieve into pre-weighed weighing boats. 5. Weigh each fraction and calculate % fines. |
| flowcell | H7KCJDSX5 |
| folder_name | 20220902_MGE_UNSW_H7KCJDSX5_Q0009190 |
| funding_agency | Australian Microbiome Initiative |
| general_env_feature | Coastal (coastal terrestrial including cliff; rocky shore) |
| geo_loc_name | Australia:New South Wales [GAZ_00002793] |
| insert_size_range | 350-500 |
| lat_lon (decimal_degrees) | -33.488115 151.35585 |
| latitude (decimal_degrees) | -33.488115 |
| library_construction_protocol | Illumina DNA Prep |
| longitude (decimal_degrees) | 151.35585 |
| nucl_acid_ext | Qiagen PowerSoil Kit |
| number_of_raw_reads | 58295384.0 |
| number_pcr_cycle | 5.0 |
| omics | metagenomics |
| org_matter (%) | 10.4070340332 |
| org_matter_meth | meth_1. Transfer sediment to pre-weighed labelled aluminium tray. 2. Dry in oven at 60°C for 24hrs. 3. Grind to a fine powder using a mixing mill (MM200). 4. Place samples in pre-weighed labelled crucibles and transfer to muffle furnace at 105°C for 24 hrs. 5. Remove samples; allow to cool and weigh. 6.Return crucibles to muffle furnace at 430°C for a further 24 hours. 7. Remove samples; cool and weigh. Calculate % organic matter. |
| samp_collect_device | meth_Sterile 15ml tube |
| samp_mat_process | Samples frozen at -80°C until DNA extraction. For DNA extraction samples were defrosted and a spatula (sterilised with 10% bleach) was used to weigh 0.25g of sediment into bead beating tubes. |
| sample_attribution | Alessandra Suzzi |
| sample_database_file | AM_db_v4.2_202410080900.db |
| sample_id | 102.100.100/401000 |
| sample_metadata_ingest_date | 2024-02-01 13:24:34 |
| sample_metadata_ingest_file | AM0015Huggett_Sample_Submission_sheet_20210916_schema_v3_vocab_2_0_3_SUZ9963_edited2_xlsx |
| sample_site_location_description | BrisbaneWater_Saratoga3 |
| sample_submission_date | 2022-09-13 |
| sample_submitter | Alessandra Suzzi |
| sample_type | Sediment |
| sequencer | NovaSeq 6000 |
| source_mat_id | 102.100.100/401000 |
| store_cond | frozen (-80°) |
| temp (degC) | 23.48 |
| temp_meth | meth_Horiba U-50 water quality meter |
| ticket | BPAOPS-1318 |
| url | https://data.bioplatforms.com//organization/australian-microbiome?q=sample_id:102.100.100/401000 |
| utc_date_sampled | 2020-11-01 |
| utc_time_sampled | 12:00:00 |
| vegetation_type | Seagrass bed/meadow |