Australian Microbiome Amplicons 18S 102.100.100/401041 K77V8
Dataset size is: 14.00 MiB
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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 | 0.873 |
absorbance_260_280_ratio_submitter_meth | meth_NanoPhotometer NP80 |
am_environment | Marine |
amplicon | 18S |
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/18s/BPAOPS-1240/ |
bioplatforms_dataset_id | 102.100.100/401931 |
bioplatforms_project | Australian Microbiome Initiative (AM) |
bioplatforms_project_code | AM0015 |
ccg_jira_ticket | BPAOPS-1240 |
collection_date | 2020-11-01T08:00:00 |
comments | 401041_18S_K77V8_ATCTCAGG-CTCTCTAT |
data_type | 18S |
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) | 2.4 |
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] |
fine_sediment (%) | 6.6908421206 |
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 | K77V8 |
folder_name | 20220429_AM_18S_UNSW_K77V8 |
funding_agency | Australian Microbiome Initiative |
general_env_feature | Coastal (coastal terrestrial including cliff; rocky shore) |
geo_loc_name | Australia:New South Wales [GAZ_00002793] |
index | ATCTCAGG-CTCTCTAT |
lat_lon (decimal_degrees) | -32.994878 151.600376 |
latitude (decimal_degrees) | -32.994878 |
longitude (decimal_degrees) | 151.600376 |
nucl_acid_ext | Qiagen PowerSoil Kit |
omics | Genomics |
org_matter (%) | 1.1920884197 |
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 | WK |
pcr_plate_name | SUZ9963_18S4_P1_SetA |
reads | 38424.0 |
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_202408091431.db |
sample_id | 102.100.100/401041 |
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 | LakeMacquarie_FennellBay4 |
sample_submitter | Alessandra Suzzi |
sample_type | Sediment |
sequencing_facility | Ramaciotti |
source_mat_id | 102.100.100/401041 |
store_cond | frozen (-80°) |
target | 18S |
temp (degC) | 23.02 |
temp_meth | meth_Horiba U-50 water quality meter |
ticket | BPAOPS-1240 |
url | https://data.bioplatforms.com//organization/australian-microbiome?q=sample_id:102.100.100/401041 |
utc_date_sampled | 2020-11-01 |
utc_time_sampled | 08:00:00 |
vegetation_type | Seagrass bed/meadow |