Hooded Scaly-foot, Phylogenomics, Illumina Capture, liver

Pygopodidae, Pygopus nigriceps, WAM R136743, lizard | gecko, Project Lead: Ian Brennan

Dataset size is: 1.32 GiB

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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 extent

Map tiles & Data by OpenStreetMap, under CC BY SA.
Resource Permissions organization_member_after_embargo:date_of_transfer_to_archive:365:ausarg-consortium-members
Access Control Date 2022-05-04
Access Control Mode date
Sequence Data Type Illumina Capture
access_rights No restrictions
ala_specimen_url https://ozcam.ala.org.au/occurrences/f8d22e3c-41ed-4395-966a-dd8686040084
analysis_software Bcl2Fastq
ancillary_notes NA
associated_media NA
barcode_id NA
base_url https://downloads-qcif.bioplatforms.com/bpa/ausarg_staging/exon_capture/brf/BPAOPS-1066/
certainty high
class Reptilia
collection_date 2004-10-29
collection_method Pit Trap
collector M.A. Cowan
collector_sample_id NA
common_name Hooded Scaly-foot
country Australia
data_context Phylogenomics
data_custodian Ian Brennan
data_type Illumina Capture
dataset_id 102.100.100/351767
date_of_transfer 2021-05-04
date_of_transfer_to_archive 2021-05-10
decimal_latitude_public -26.281111
decimal_longitude_public 121.357222
description Short reads
dna_treatment Fragmentation by Covaris
experimental_design Perkin Elmer DNA-Seq Rapid 2.0 Libraries with Arbor (Daicel) Biosciences Exon Capture - dual index
facility BRF
facility_project_code NA
facility_sample_id 349779_AHHVV2AFX2_TACGCCAAGT
family Pygopodidae
file_type FASTQ
flowcell_id AHHVV2AFX2
flowcell_type Mid output 300 cycles
folder_name 20210504_AusARG_BRF_AHHVV2AFX2
genotypic_sex not determined
genus Pygopus
habitat unknown
identified_by Brad Maryan
insert_size_range 150 bp PE
institution_name Western Australian Museum
latitude -26.281111
library_comments Full library reaction; qubit 16.9 ng/uL
library_construction_protocol NEXTFLEX Rapid DNA-Seq Kit 2.0
library_id 102.100.100/350789
library_index_id P7_UDI_0001
library_index_id_dual P5_UID_0001
library_index_seq TACGCCAAGT
library_index_seq_dual TTCGGCTCCG
library_layout paired end
library_location ANU EBL Freezer
library_ng_ul 16.9
library_oligo_sequence GATCGGAAGAGCACACGTCTGAACTCCAGTCAC tacgccaagtATCTCGTATGCCGTCTTCTGCTTG
library_oligo_sequence_dual AATGATACGGCGACCACCGAGATCTACAC ttcggctccgACACTCTTTCCCTACACGACGCTCTTCCGATCT
library_pcr_cycles 4
library_pcr_reps 1
library_prep_date 2021-02-18
library_prepared_by Ian Brennan
library_selection Hybrid Selection
library_source GENOMIC
library_strategy Targeted-Capture
library_type Exon capture
lifestage adult
location_text Lorna Glen Station
longitude 121.357222
material_conc_ng_ul 140.0
material_extracted_by Ian Brennan
material_extraction_date 2020-09-01
material_extraction_method Salt extraction
material_extraction_type DNA
metadata_revision_date 2024-01-25
metadata_revision_filename AusARG_Metadata_master_QCIF_20240125_FORDATAPORTAL.xlsx
method_of_determination hemipenis eversion
n_libraries_pooled 32
order Squamata
phenotypic_sex male
phylum Chordata
prior_genetics NA
project_aim Phylogenomics
sample_custodian Paul Doughty
sample_id 102.100.100/349779
sample_quality unknown
sequencing_facility Biomolecular Research Facility - ANU
sequencing_kit_chemistry_version NextSeq 500 midoutput 300 cycles V2.5
sequencing_model NextSeq 500
sequencing_platform Illumina
source_population NA
species nigriceps
species_name Pygopus nigriceps
specimen_id WAM R136743
specimen_id_description Western Australian Museum
state_or_region Western Australia
subspecies NA
taxon_id 207568
taxonomic_group lizard | gecko
ticket BPAOPS-1066
tissue_collection Herpetology (R)
tissue_number WAM R136743
tissue_preservation -80C | ethanol
tissue_type liver
type_status non type
voucher_or_tissue_number WAM R136743
wild_captive wild
work_order 13018