JSON

OMG Exon Capture Raw 102.100.100/364453 BHYCGCDRXX TTGAAGT

Notamacropus dorsalis, AM M.46612.001 Australia New South Wales

Data and Resources

Additional Info

Field Value
Geospatial Coverage

Dataset extent

Map tiles & Data by OpenStreetMap, under CC BY SA.
Resource Permissions organization_member
Sequence Data Type
access_rights
ala_species_name
ala_specimen_url
ancillary_notes Original notes: The specimen was collected with a joey that was euthanised by a vet. Other notes: The specimen came in with damage to the skull (probably hit by a car), damaged tail (bones exposed - probably predated on by a bird). It was brought in for ID confirmation - Dr Mark Eldridge commented, that although it was found pretty far north, the markings and appearance are consistent with M. parma(Note written: 01/05/2014). DNA sequencing by Greta Frankham found that this specimen is most consistent with Macropus dorsalis (WGM078_3)- the species has been updated accordingly (Note written: 15/01/2015).
archive_ingestion_date 2021-03-03
associated_media
barcode_id
base_url https://downloads-qcif.bioplatforms.com/bpa/omg_staging/exon_capture/brf/BPAOPS-1032/
birth_date
bpa_dataset_id 102.100.100/52647
bpa_library_id 102.100.100/364453
bpa_sample_id 102.100.100/362282
bpa_work_order 40074
class Mammalia
collection_date 2005
collection_method Found dead on the road
collector SUSANNE Ulyatt
collector_sample_id
common_name Black-striped wallaby
contextual_data_submission_date
coord_uncertainty_metres
country Australia
custodian Mark Eldridge
data_custodian Mark Eldridge
data_generated 2021-03-03
data_type Illumina FASTQ
dataset_url
date_of_transfer 2021-02-11
ddrad_data no
ddrad_dataset_ids NA
death_date
description Novaseq 6000 A00548_0147_LBroady_52647_Marsupial_gDNA
dna_conc_ng_ul 9.28
dna_extracted_by Liz Broady
dna_extraction_date 2020-09-20
dna_extraction_method salting out
dna_treatment 10 biorupter cycles
exon_capture_data yes
exon_capture_dataset_ids 52647.0
experimental_design Nimblegen Exon Capture, marsupial probes V2, dual indexed
facility brf
facility_sample_id 364453_BHYCGCDRXX_TTGAAGT
family Macropodidae
file
flowcell_id BHYCGCDRXX
folder_name A00548_0147_LBroady_52647_Marsupial_gDNA
genome_data no
genome_dataset_ids NA
genus Notamacropus
habitat
identified_by unknown
institution_name Australian Museum
latitude -28.863611
library_comments qPCR results indicate that the target capture and enrichment was successful
library_location EBL main freezer
library_ng_ul 56.2
library_pcr_cycles 12.0
library_pcr_reps 2.0
library_prep_date 2021-01-11
library_prep_method Meyer and Kircher protocol
library_prepared_by Liz Broady
library_status Ready for sequencing
library_type Exon Capture
life_stage Adult
location_generalisation
location_text 34km W of Casino, Bruxner Highway
longitude 152.784444
n_libraries_pooled 288
omg_project Marsupial phylogenetics
order Diprotodontia
p5_library_index_id P5_indexing22
p5_library_index_sequence GCATTGG
p5_library_oligo_sequence AATGATACGGCGACCACCGAGATCTACACccaatgcACACTCTTTCCCTACACGACGCTCTT
p7_library_index_id P7_indexing12
p7_library_index_sequence TTGAAGT
p7_library_oligo_sequence CAAGCAGAAGACGGCATACGAGATacttcaaGTGACTGGAGTTCAGACGTGT
phylum Chordata
prior_genetics
sample_quality unknown
sample_submission_date 2021-02-11
sequence_length 100bp PE
sequencing_facility BRF
sequencing_platform Illumina NovaSeq SP 200 cycle
sex Female
software_version unknown
source_population
species dorsalis
species_name Notamacropus dorsalis
state_or_region New South Wales
subspecies_or_variant
taxon_id 651581
taxonomic_group marsupial
ticket BPAOPS-1032
tissue_collection Mammalogy
tissue_number EBU 59140
tissue_preservation unknown
tissue_type muscle
trace_lab no
type_status
voucher_id
voucher_number AM M.46612.001
voucher_or_tissue_number AM M.46612.001
wild_captive unknown