Broad-toothed rat, Whole Genomes, Illumina TruSeq DNA, spleen
Dataset size is: 56.64 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:365:omg-consortium-members |
Access Control Date | 2020-09-16 |
Access Control Mode | date |
Sequence Data Type | illumina-shortread |
access_rights | no restrictions |
ala_specimen_url | https://biocache.ala.org.au/occurrences/b05dc893-7ec9-4e01-8908-1235d2585a40 |
ancillary_notes | DNA conc method = Qubit, DNA total µg = 10.332 |
archive_ingestion_date | 2019-09-17 |
associated_media | NA |
barcode_id | NA |
base_url | https://downloads-qcif.bioplatforms.com/bpa/omg_staging/genomics-novaseq/BPAOPS-856/ |
birth_date | unknown |
bpa_dataset_id | 102.100.100/52613 |
bpa_library_id | 102.100.100/54311 |
bpa_sample_id | 102.100.100/41600 |
bpa_work_order | 40047 |
class | Mammalia |
collection_date | 2013-11-28 |
collection_method | elliott trap |
collector | Karen Roberts |
collector_sample_id | KKR173 |
common_name | Broad-toothed rat |
coord_uncertainty_metres | 200.0 |
country | Australia |
custodian | Kevin C Rowe | Museums Victoria |
data_custodian | Kevin C. Rowe |
data_generated | 2019-09-17 |
data_type | Illumian FASTQ |
dataset_url | (ingested) |
date_of_transfer | 2019-09-17 |
ddrad_data | no |
ddrad_dataset_ids | NA |
death_date | 2013-11-28 |
description | NovaSeq 6000- Whole Genome - 41600 and 41597 |
dna_conc_ng_ul | 57.4 |
dna_extracted_by | Kevin C Rowe |
dna_extraction_date | 2019-05-15 |
dna_extraction_method | Qiagen DNEasy |
dna_treatment | Qiagen DNEasy Extraction |
exon_capture_data | no |
exon_capture_dataset_ids | NA |
experimental_design | 1x NovaSeq 6000 150 bp paired-end reads |
facility_sample_id | 9406-3 |
family | Muridae |
file | 41600_HT25VDSXX_TGGATCGA-GTGCGATA_S2_L003_R1, 41600_HT25VDSXX_TGGATCGA-GTGCGATA_S2_L003_R2 |
flowcell_id | HT25VDSXX |
folder_name | 20190912_AGRF_BPA_OMG_HT25VDSXX |
genome_data | yes |
genome_dataset_ids | 52613.0 |
genus | Mastacomys |
habitat | Alpine meadow |
identified_by | Kevin Rowe |
institution_name | Museums Victoria |
latitude | -36.65264 |
library_comments | DNA conc method = Qubit, DNA total µg = 10.332 (41600) or 0.72 (41601) |
library_index_id | UDI0008 |
library_index_sequence | TGGATCGA-GTGCGATA |
library_location | AGRF |
library_ng_ul | 29.1 |
library_oligo_sequence | GATCGGAAGAGCACACGTCTGAACTCCAGTCAC[i7]ATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT |
library_pcr_cycles | 8.0 |
library_prep_date | 2019-08-28 |
library_prep_method | Illumina TruSeq DNA Nano |
library_prepared_by | Justin Crockett |
library_status | Sequenced |
library_type | Illumina TruSeq DNA |
life_stage | adult organism |
location_text | Alpine National Park, Davies Plain Camp, 16.91km SE of Mt Pinnibar summit, and 6.70km NE of Davies Plain Track and Kings Plain 4WD Track junction |
longitude | 148.12485 |
n_libraries_pooled | 1 |
omg_project | Whole Genomes |
order | Rodentia |
phylum | Chordata |
prior_genetics | unknown |
sample_quality | Qiagen Standard Extraction Quality |
sample_submission_date | 2019-09-17 |
sequence_length | 150 bp PE |
sequencing_facility | AGRF |
sequencing_platform | NovaSeq |
sex | female |
software_version | Illumina RTA v3.4.4 |
source_population | unknown |
species | fuscus |
species_name | Mastacomys fuscus |
state_or_region | Victoria |
subspecies_or_variant | NA |
taxon_id | 337222 |
taxonomic_group | rodent |
ticket | BPAOPS-856 |
tissue_collection | Mammalogy |
tissue_number | NMV Z27367 QA |
tissue_preservation | RNALater |
tissue_type | spleen |
trace_lab | no |
type_status | unknown |
voucher_id | NMV_C37546 |
voucher_number | NMV C37546 |
voucher_or_tissue_number | NMV C37546 |
wild_captive | wild |