Lister's gecko, Reference genome (HiC), Illumina-HiC, Heart_liver_tail

408044 Lepidodactylus listeri, Australia New South Wales

Dataset size is: 70.10 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:365:tsi-consortium-members
Access Control Date 2023-07-13
Access Control Mode date
Sequence Data Type illumina-hic
access_rights Open Access
ala_specimen_url https://bie.ala.org.au/species/urn:lsid:biodiversity.org.au:afd.taxon:4e9782f1-53d6-47cd-9d01-7a04a78b94e9
analysis_software Bcl2Fastq
ancillary_notes NA
associated_media NA
barcode_id NA
base_url https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/genomics-hi-c/BPAOPS-1309/20220711_TSI_BRF_HG5YLDMXY/
ccg_jira_ticket BPAOPS-1309
certainty High
class Reptillia
collection_date 2021-02-09
collection_method Medical euthanasia
collector Claire Ford
collector_sample_id LG448
common_name Lister's gecko
country Australia
data_context Reference genome (HiC)
data_custodian Carolyn Hogg
data_type Illumina-HiC
dataset_id 102.100.100/358786
date_of_transfer 2022-07-13
date_of_transfer_to_archive 2022-08-09
death_date 2021-02-09
decimal_latitude_public -33.8
decimal_longitude_public 151.2
description Hi-C multiple species
dna_treatment FA crosllinking restriction enzymes and sonication
download researcher informed
experimental_design Arima HiC 2.0 single index
facility_project_code BRF
facility_sample_id 408044_AusARG_BRF_XXXXX_CCGTCC
family Gekkonidae
file_type FASTQ
flowcell_id HG5YLDMXY
flowcell_type Novaseq S2
folder_name 20220711_TSI_BRF_HG5YLDMXY
genus Lepidodactylus
habitat Rainforest
health_state Poor - severe gout
insert_size_range 150bp PE
institution_name University of Sydney
latitude -33.8
library_comments Concentration and size was assesd by Bioanalyzer and Qubit
library_construction_protocol Arima HiC 2.0
library_id 408044
library_index_id Index_16
library_index_seq CCGTCC
library_layout paired end
library_location Freezer at BRF
library_ng_ul 1.6
library_oligo_sequence GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCC(AT)CTCGTATGCCGTCTTCTGCTTG
library_pcr_cycles 6
library_pcr_reps 1
library_prep_date 2022-06-30
library_prepared_by Max Nekrasov
library_selection Restriction Digest
library_source GENOMIC
library_strategy Hi-C
library_type Illumina-HiC
lifestage adult
location_text Mosman
longitude 151.2
metadata_revision_date 2024-08-28
metadata_revision_filename 20240829_Sample_metadata_COMBINED-FOR-PORTAL_NOLATLON.xlsx
method_of_determination Dissection
n_libraries_pooled 6
order Squamata
phenotypic_sex male
phylum Chordata
prior_genetics ddRAD
sample_custodian Carolyn Hogg
sample_id 102.100.100/405659
sample_quality Poor
sample_type Organ
scientific_name Lepidodactylus listeri
scientific_name_authorship Boulenger
sequencing_facility BRF
sequencing_kit_chemistry_version NovaSeq v1.5
sequencing_model Illumina NovaSeq 6000
sequencing_platform ILLUMINA
source_population Taronga Zoo
species listeri
specimen_id LG448
specimen_id_description Taronga Zoo ID
state_or_region New South Wales
taxon_id 747221.0
taxonomic_group Reptile
ticket BPAOPS-1309
tissue_collection Euthanasia
tissue_collection_type Living collection - zoo
tissue_number LG448_heart_liver_tail
tissue_preservation Preserved in ethanol
tissue_preservation_temperature "-20C"
tissue_type Heart_liver_tail
wild_captive captive
work_order 13045