Plain Tree Dtella, Reference genome, Illumina-HiC, tail muscle

Gekkonidae, Gehyra gemina, CCM8051, lizard, Project Lead: Emily Roycroft

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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 restriction
ala_specimen_url NA
analysis_software Bcl2Fastq
associated_media NA
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_351908_222VJYLT4/
bioplatforms_dataset_id multiple (11x)
bioplatforms_library_id multiple (11x)
bioplatforms_sample_id multiple (11x)
certainty high
class Reptilia
collection_date 2021-06-12
collection_method Captured by hand
collector Stephen Zozaya | Leonardo Tedeschi | Jéssica Fenker | Octavio Jiménez Robles
collector_sample_id CCM8051
common_name Plain Tree Dtella
country Australia
data_context Reference genome
data_custodian Emily Roycroft
data_type Illumina-HiC
dataset_id 102.100.100/351908
date_of_transfer 2023-12-19
date_of_transfer_to_archive 2023-12-22
decimal_latitude_public -18.1871
decimal_longitude_public 125.5836
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 456752_AusARG_BRF_222VJYLT4_TCAGCATC
family Gekkonidae
file_type fastq.gz
flowcell_id 222VJYLT4
flowcell_type NovaSeq X 25B
folder_name 20231215_AusARG_BRF_222VJYLT4
genotypic_sex female
genus Gehyra
identified_by Stephen Zozaya
insert_size_range ~900bp
institution_name Australian National University
latitude -18.1871
library_comments Concentration and size was assesd by Bioanalyzer and Qubit
library_construction_protocol Arima HiC 2.0
library_id 456752
library_index_id index_5
library_index_seq TCAGCATC
library_layout paierd-end
library_location Freezer at BRF
library_ng_ul 5.96
library_oligo_sequence GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCAGCATC(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 Fitzroy Crossing, Crossing Inn
longitude 125.5836
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 external and internal morphology
n_libraries_pooled 11
order Squamata
phenotypic_sex female
phylum Chordata
prior_genetics NA
project_aim Reference genome
sample_custodian Craig Moritz
sample_id 102.100.100/458262
sample_quality high
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 NA
species gemina
specimen_id CCM8051
specimen_id_description ANU tissue collection
state_or_region Western Australia
subspecies NA
taxon_id 2856562
taxonomic_group lizard
ticket BPAOPS-1538
tissue_collection Moritz Lab ANU
tissue_number CCM8051
tissue_preservation frozen -80
tissue_type tail muscle
type_status no
voucher_or_tissue_number CCM8051
wild_captive wild
work_order 13072