Giant white-tailed rat, Phylogenomics, exon capture, liver

Muridae, Uromys caudimaculatus, AM M.49883, rodent, Project Lead: Kevin Rowe

Dataset size is: 703.30 MiB

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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:archive_ingestion_date:365:omg-consortium-members
Access Control Date 2021-04-01
Access Control Mode date
Sequence Data Type illumina-exoncapture
access_rights no restrictions
ala_specimen_url NA
ancillary_notes NA
archive_ingestion_date 2020-04-01
associated_media NA
barcode_id NA
base_url https://downloads-qcif.bioplatforms.com/bpa/omg_staging/exon_capture/brf/BPAOPS-894/
birth_date unknown
bpa_dataset_id 102.100.100/52624
bpa_library_id 102.100.100/55170
bpa_sample_id 102.100.100/42010
bpa_work_order 40056
class Mammalia
collection_date 2006-08-30
collection_method unknown
collector Steve Hamilton
collector_sample_id NA
common_name Giant white-tailed rat
coord_uncertainty_metres unknown
country Papua New Guinea
custodian Mark Eldridge | Australian Museum
data_custodian Kevin Rowe
data_generated 2020-04-01
data_type Illumina FASTQ
dataset_url (ingested)
date_of_transfer 2020-04-01
ddrad_data no
ddrad_dataset_ids NA
death_date unknown
description Nextseq500 150PE - exon capture marsupial
dna_conc_ng_ul 5.9066666667
dna_extracted_by Amy Adams
dna_extraction_date 2019-07-02
dna_extraction_method Qiagen DNEasy
dna_treatment 10 bioruptor cycles
exon_capture_data yes
exon_capture_dataset_ids 52624.0
experimental_design Nimblegen Exon Capture – single index
facility brf
facility_sample_id 55170_H55FWAFX2_CAATATG
family Muridae
file 55170_H55FWAFX2_CAATATG_S22_L001_R1_001.fastq.gz | 55170_H55FWAFX2_CAATATG_S22_L001_R2_001.fastq.gz | 55170_H55FWAFX2_CAATATG_S22_L002_R1_001.fastq.gz | 55170_H55FWAFX2_CAATATG_S22_L002_R2_001.fastq.gz
flowcell_id H55FWAFX2
folder_name NB501086_0361_AMacDonald_OzMammals_Rodent_gDNA_exon_capture
genome_data no
genome_dataset_ids NA
genus Uromys
habitat unknown
identified_by Steve Hamilton
institution_name Australian Museum
library_comments library ng/µL for 200-800 bp range
library_location ANU EBL
library_ng_ul 17.274157534
library_pcr_cycles 12.0
library_pcr_reps 2.0
library_prep_date 2019-09-27
library_prep_method Meyer and Kircher protocol
library_prepared_by Kevin Rowe
library_status Data available
library_type exon capture
life_stage not determined
location_generalisation 1km
location_text Mibini
n_libraries_pooled 94
omg_project Phylogenomics
order Rodentia
p5_library_index_id NA
p5_library_index_sequence NA
p5_library_oligo_sequence NA
p7_library_index_id 24.0
p7_library_index_sequence CAATATG
p7_library_oligo_sequence CAAGCAGAAGACGGCATACGAGATcatattgGTGACTGGAGTTCAGACGTGT
phylum Chordata
prior_genetics unknown
sample_quality good
sample_submission_date 2020-04-01
sequence_length 150bp PE
sequencing_facility BRF
sequencing_platform Illumina NextSeq mid output 300 cycle
sex female
software_version unknown
source_population unknown
species caudimaculatus
species_name Uromys caudimaculatus
state_or_region Western Province
subspecies_or_variant NA
taxon_id 36800
taxonomic_group rodent
ticket BPAOPS-894
tissue_collection Mammalogy
tissue_number AM M.49883
tissue_preservation ethanol | frozen
tissue_type liver
trace_lab no
type_status unknown
voucher_number AM M.49883
voucher_or_tissue_number AM M.49883
wild_captive wild