JSON

TSI Pacbio HiFi 102.100.100/357368

Macroderma gigas, Australia Northern Territory

Data and Resources

Additional Info

Field Value
Geospatial Coverage
Resource Permissions organization_member
access_rights exact site coordinates should not be released to public as it is an important conservation site for ghost bats
ala_specimen_url
analysis_software SMRT Link Analysis
analysis_software_version 9.0.0.92188
ancillary_notes The captured bat was clearly an older bat with very worn teeth, scarred wing membrane and a large notch missing from his ear.
archive_ingestion_date 2021-02-09
associated_media photos,videos
barcode_id
base_url https://downloads-qcif.bioplatforms.com/bpa/tsi_staging/pacbio-hifi/BPAOPS-1023/20210205_TSI_CAGRF20114490_DA060252/357368_TSI_AGRF_DA060252_HiFi_metadata/
birth_date
cell_postion C01
certainty certain
class Mammalia
collection_date 2020-09-23
collection_method A ghost bat was captured using a mist net in open woodland in the vicinity of a known roost. Bat was lured into the mist net using a playback protocol designed by Nicola Hanrahan during her PhD research. Bat was removed from net immediately and placed into a calico bag. The ghost bat was sedated by a trained vet to a workable sedation using isoflourane in a purpose-built chamber. Blood samples were taken using cranial vena cava venepuncture. The fully sedated bat was then euthanised using cervical dislocation. Once the bat was confirmed to be deceased, samples were taken from all identifiable organs, with the number of samples taken based on the size of the organ.
collector Nicola Hanrahan (Western Sydney University/Charles Darwin University), Simon Hollamby (Veterinary Surgeon; Territory Wildlife Park), Damian Stanioch (NT Parks & Wildlife), Sam Banks (Charles Darwin University), Brenton von Takach Dukai (Charles Darwin University)
collector_sample_id PC43
common_name Ghost Bat
contextual_data_submission_date
coord_uncertainty_metres ~20m
country Australia
data_context Reference genome
data_custodian Nicola Hanrahan
data_generated 2021-02-09
data_type Pacbio HiFi
dataset_id 102.100.100/358726
dataset_url
date_of_transfer 2021-02-08
death_date 2020-09-23
decimal_latitude_public
decimal_longitude_public
description
dna_treatment SHEARING
experimental_design NA
facility_sample_id 357368.0
family Megadermatidae
file_name 357368_TSI_AGRF_PacBio_DA060252.subreads.bam
file_type BAM
flowcell_id DA060252
flowcell_type SMRT Cell 8M
folder_name 20210205_TSI_CAGRF20114490_DA060254
genotypic_sex
genus Macroderma
habitat Undulating hills, Open Eucalypt woodland, historic gold mining area with multiple mine shafts.
identified_by Nicola Hanrahan
insert_size_range 15552.0
institution_name Charles Darwin University
latitude
library_comments NA
library_construction_protocol Preparing HiFi SMRTbell® Libraries using SMRTbell Express Template Prep Kit 2.0
library_id 102.100.100/357368
library_index_id NA
library_index_sequence NA
library_layout NA
library_location AGRF
library_ng_ul 97.0
library_oligo_sequence NA
library_pcr_cycles NA
library_pcr_reps NA
library_prep_date 2020-12-14
library_prepared_by Trent Peters
library_selection size fractionation
library_source GENOMIC
library_status Library Sequenced
library_strategy Preparing HiFi SMRTbell® Libraries using SMRTbell Express Template Prep Kit 2.0
library_type WGS
lifestage adult
location_text Pine Creek Township, Norhern Territroy
longitude
material_conc_ng_ul 66.0
material_extracted_by Elspeth McLennan (USYD); Kate Farquharson (USYD)
material_extraction_date 2020-11-10
material_extraction_method Circulomics Kit ("Nanobind Tissue Big DNA Kit v1.0 11/19"), with Liver Note for liver extraction
material_extraction_type DNA
method_of_determination genitals
movie_length 30HRS
n_libraries_pooled 1.0
order Chiroptera
phenotypic_sex male
phylum Chordata
prior_genetics none
sample_custodian Nicola Hanrahan
sample_id 102.100.100/355454
sample_quality High
sample_submission_date 2021-02-08
sequencing_facility AGRF
sequencing_model PacBio Sequel II
sequencing_platform PACBIO_SMRT
source_population Pine Creek
species gigas
specimen_id MG_PC43
specimen_id_description scientific name acronym_researcher assigned sample ID
state_or_region Northern Territory
subspecies NA
taxon_id 9411.0
taxonomic_group Mammal
ticket BPAOPS-1023
tissue_collection Charles Darwin University_Nicola Hanrahan
tissue_number MG_PC43_pooled_liver_heart_kidney_LN1
tissue_preservation Liquid Nitrogen - Placed in dry tube,flash frozen in liquid nitrogen, transported on dry ice and stored in -80 freezer
tissue_type Liver, heart and kidney
type_status
wild_captive wild_caught
work_order 14004.0