Australian Microbiome Amplicons 16S 102.100.100/400973 K9KGY
Dataset size is: 76.48 MiB
Data and Resources
This data is made available openly under a Creative Commons Attribution license.
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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:date_of_transfer_to_archive:90:am-consortium-members |
| Access Control Date | 2022-07-28 |
| Access Control Mode | date |
| Sequence Data Type | illumina-amplicons |
| Related Data | doi:10.25953/vp5c-pk95 |
| absorbance_260_280_ratio_submitter | 1.766 |
| absorbance_260_280_ratio_submitter_meth | meth_NanoPhotometer NP80 |
| am_environment | Marine |
| amplicon | 16S |
| analysis_software | MiSeq Reporter |
| analysis_software_version | 2.6.2.3 |
| analytical_platform | MiSeq |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/amd/amplicons-miseq/16s/BPAOPS-1239/ |
| bioplatforms_dataset_id | 102.100.100/401931 |
| bioplatforms_project | Australian Microbiome Initiative (AM) |
| bioplatforms_project_code | AM0015 |
| ccg_jira_ticket | BPAOPS-1239 |
| collection_date | 2020-11-01T09:00:00 |
| comments | 400973_16S_K9KGY_TCGAGGAC-AAGCAGCA |
| data_type | 16S |
| 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 | 2022-04-29 |
| date_of_transfer_to_archive | 2022-05-03 |
| depth (m) | 0.0 |
| depth_lower (m) | 0.01 |
| depth_upper (m) | 0.0 |
| description | MiSeq data package |
| dilution_used | Neat |
| dna_concentration_submitter (ng/μL) | 5.65 |
| dna_concentration_submitter_meth | meth_NanoPhotometer NP80 |
| download | (non-BPA funded samples) |
| env_broad_scale | 6 Water |
| env_local_scale | 6.6 Estuary/coastal waters |
| env_medium | Sediment [ENVO_00002007] |
| fine_sediment (%) | 3.4515251016 |
| 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. |
| flow_id | K9KGY |
| folder_name | 20220429_AM_16S_UNSW_K9KGY_renamed |
| funding_agency | Australian Microbiome Initiative |
| general_env_feature | Coastal (coastal terrestrial including cliff; rocky shore) |
| geo_loc_name | Australia:New South Wales |
| index | TCGAGGAC-AAGCAGCA |
| lat_lon (decimal_degrees) | -31.428669 152.900727 |
| latitude (decimal_degrees) | -31.428669 |
| longitude (decimal_degrees) | 152.900727 |
| nucl_acid_ext | Qiagen PowerSoil Kit |
| omics | Genomics |
| org_matter (%) | 0.4251184258 |
| 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. |
| pass_fail | P |
| pcr_plate_name | SUZ10224_16S1_P4_SetD |
| reads | 153100.0 |
| 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_202402091224.db |
| sample_id | 102.100.100/400973 |
| 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 | HastingsRiver_S2_1 |
| sample_submitter | Alessandra Suzzi |
| sample_type | Sediment |
| sequencing_facility | Ramaciotti |
| source_mat_id | 102.100.100/400973 |
| store_cond | frozen (-80°) |
| target | 16S |
| temp (degC) | 21.53 |
| temp_meth | meth_Horiba U-50 water quality meter |
| ticket | BPAOPS-1239 |
| url | https://data.bioplatforms.com//organization/australian-microbiome?q=sample_id:102.100.100/400973 |
| utc_date_sampled | 2020-11-01 |
| utc_time_sampled | 09:00:00 |
| vegetation_type | Seagrass bed/meadow |