delicate skink, Reference Genome, Illumina-HiC, liver
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Data and Resources
This data is made available openly under a Creative Commons Attribution license.
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Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:ausarg-consortium-members |
| Access Control Date | 2022-10-28 |
| Access Control Mode | date |
| Sequence Data Type | illumina-hic |
| access_rights | No restrictions |
| ala_specimen_url | unknown |
| analysis_software | Bcl2Fastq |
| ancillary_notes | NA |
| associated_media | NA |
| barcode_id | unknown |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/ausarg_staging/genomics-hi-c/BPAOPS-1154/ |
| bioplatforms_dataset_id | 351780, 351810, 351812, 351814, 351816 |
| bioplatforms_library_id | 350845, 353995, 353996, 353997, 353998 |
| bioplatforms_sample_id | 349834, 352981, 352982, 352983, 352984 |
| certainty | 1.0 |
| class | Reptilia |
| collection_date | 2021-02-11 |
| collection_method | By hand |
| collector | Camilla Whittington |
| collector_sample_id | Ld2003 |
| common_name | delicate skink |
| coord_uncertainty_metres | 20.0 |
| country | Australia |
| data_context | Reference Genome |
| data_custodian | Camilla Whittington |
| data_type | Illumina-HiC |
| dataset_id | 102.100.100/351810 |
| date_of_transfer | 2021-10-28 |
| date_of_transfer_to_archive | 2021-10-29 |
| death_date | 2021-02-23 |
| decimal_latitude_public | -33.883385 |
| decimal_longitude_public | 151.178649 |
| 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 | 353995_HMGMJDRXY_CGATGT |
| family | Scincidae |
| file_type | FASTQ |
| flowcell_id | HMGMJDRXY |
| flowcell_type | Novaseq S1 |
| folder_name | 20211027_AusARG_BRF_HMGMJDRXY |
| genotypic_sex | not determined |
| genus | Lampropholis |
| habitat | urban |
| identified_by | Glenn Shea |
| insert_size_range | 650.0 |
| institution_name | University of Sydney |
| latitude | -33.883385 |
| library_comments | Concentration and size was assesd by Bioanalyzer and Qubit |
| library_construction_protocol | Arima HiC 2.0 |
| library_id | 353995 |
| library_index_id | Index 2 |
| library_index_seq | CGATGT |
| library_layout | paired end |
| library_location | Freezer at BRF |
| library_ng_ul | 1.3 |
| library_oligo_sequence | GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT(AT)CTCGTATGCCGTCTTCTGCTTG |
| library_pcr_cycles | 7 |
| library_pcr_reps | 1 |
| library_prepared_by | Max Nekrasov |
| library_selection | Restriction Digest |
| library_source | GENOMIC |
| library_strategy | Hi-C |
| library_type | Illumina-HiC |
| lifestage | Adult |
| location_text | Camperdown |
| longitude | 151.178649 |
| metadata_revision_date | 2023-03-14 |
| metadata_revision_filename | AusARG_Metadata_master_QCIF_20230314.xlsx |
| method_of_determination | inspected gonads |
| n_libraries_pooled | 5 |
| order | Squamata |
| phenotypic_sex | male |
| phylum | Chordata |
| prior_genetics | unknown |
| project_aim | Reference genome |
| sample_custodian | Camilla Whittington |
| sample_id | 102.100.100/352981 |
| scientific_name | Hydrophis major, Lampropholis delicata, Pseudemoia entrecasteauxii, Saiphos equalis, Litoria serrata |
| sequencing_facility | BRF |
| sequencing_kit_chemistry_version | 300 cycles |
| sequencing_model | Illumina NovaSeq 6000 |
| sequencing_platform | ILLUMINA |
| source_population | Sydney |
| species | delicata |
| specimen_id | Ld2003 |
| specimen_id_description | University_of_Sydney_WhittingtonLab |
| state_or_region | New South Wales |
| subspecies | NA |
| taxon_id | 316451 |
| taxonomic_group | lizard |
| ticket | BPAOPS-1154 |
| tissue_collection | unknown |
| tissue_number | Ld2003_liver |
| tissue_preservation | none |
| tissue_type | liver |
| voucher_or_tissue_number | Ld2003 |
| wild_captive | wild |
| work_order | 13026 |