Eungella Leaf-tailed Gecko, Reference genome, Illumina-HiC, liver

Carphodactylidae, Phyllurus nepthys, TBA, lizard, Project Lead: Megan Higgie

Dataset size is: 126.64 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
Resource Permissions organization_member_after_embargo:date_of_transfer_to_archive:10:ausarg-consortium-members
Access Control Date 2023-12-29
Access Control Mode date
Sequence Data Type illumina-hic
access_rights No restrictions
ala_specimen_url NA
analysis_software Bcl2Fastq
ancillary_notes individual for Phyllurus genome assembly
associated_media IMG_5138
barcode_id NA
base_url https://downloads-qcif.bioplatforms.com/bpa/ausarg_staging/genomics-hi-c/BPAOPS-1538/20231215_AusARG_BRF_222VJYLT4/20231215_AusARG_BRF_351905_222VJYLT4/
bioplatforms_dataset_id multiple (11x)
bioplatforms_library_id multiple (11x)
bioplatforms_sample_id multiple (11x)
certainty very high
class Lepidosauria
collection_date 2023-05-12
collection_method spotlighting
collector Conrad Hoskin
collector_sample_id CONX6659
common_name Eungella Leaf-tailed Gecko
country Australia
data_context Reference genome
data_custodian Megan Higgie
data_type Illumina-HiC
dataset_id 102.100.100/351905
date_of_transfer 2023-12-19
date_of_transfer_to_archive 2023-12-22
death_date 2023-05-18
decimal_latitude_public -21.09226
decimal_longitude_public 148.54085
description HiC
dna_treatment FA crosllinking restriction enzymes and sonication
experimental_design Arima HiC 2.0 single index
facility BRF
facility_project_code NA
facility_sample_id 456749_AusARG_BRF_222VJYLT4_AGTCGCGA
family Carphodactylidae
file_type fastq.gz
flowcell_id 222VJYLT4
flowcell_type NovaSeq X 25B
folder_name 20231215_AusARG_BRF_222VJYLT4
genotypic_sex not determined
genus Phyllurus
habitat tropical moist broadleaf forest (upland rainforest)
identified_by Conrad Hoskin
insert_size_range ~900bp
institution_name James Cook University
latitude -21.09226
library_comments Concentration and size was assesd by Bioanalyzer and Qubit
library_construction_protocol Arima HiC 2.0
library_id 456749
library_index_id index_3
library_index_seq AGTCGCGA
library_layout paierd-end
library_location Freezer at BRF
library_ng_ul 2.39
library_oligo_sequence GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCGCGA(AT)CTCGTATGCCGTCTTCTGCTTG
library_pcr_cycles 6
library_pcr_reps 1
library_prep_date 2023-11-23
library_prepared_by Max Nekrasov
library_selection Restriction Digest
library_source GENOMIC
library_strategy Hi-C
library_type Illumina-HiC
lifestage adult
location_text Dalrymple Heights Road, Eungella
longitude 148.54085
material_conc_ng_ul NA
material_extracted_by BRF ANU
material_extraction_method NA
material_extraction_type DNA
metadata_revision_date 2024-11-15
metadata_revision_filename AusARG_Metadata_master_QCIF_20241115_FORDATAPORTAL.xlsx
method_of_determination presence of developing eggs
n_libraries_pooled 11
order Squamata
phenotypic_sex female
phylum Chordata
prior_genetics HIFI and transcriptome
project_aim Reference genome
sample_custodian Megan Higgie | Conrad Hoskin
sample_id 102.100.100/458259
sample_quality freshly sampled
scientific_name Common eastern froglet (Crinia signifera), Eungella Leaf-tailed Gecko (Phyllurus nephtys), Southern ornate nursery frog (Cophixalus australis), Gehyra sp. x8
sequencing_facility BRF
sequencing_kit_chemistry_version NovaSeq X series 25B 300 cycles
sequencing_model Illumina NovaSeq X
sequencing_platform ILLUMINA
source_population Australia, Queensland, Eungella Uplands
species nepthys
specimen_id TBA
specimen_id_description Queensland Museum
state_or_region Queensland
subspecies NA
taxon_id 136855
taxonomic_group lizard
ticket BPAOPS-1538
tissue_collection Adaptation Lab (Higgie & Hoskin)
tissue_number CONX6655
tissue_preservation frozen | -80C
tissue_type liver
type_status no
voucher_or_tissue_number CONX6659
wild_captive wild
work_order 13072