Broad-toothed rat, Phylogenomics, exon capture, 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 |
|---|---|
| Geospatial Coverage |
Dataset extentMap tiles & Data by OpenStreetMap, under CC BY SA.
|
| Resource Permissions | organization_member_after_embargo:archive_ingestion_date:365:omg-consortium-members |
| Access Control Date | 2020-01-14 |
| Access Control Mode | date |
| Sequence Data Type | illumina-exoncapture |
| access_rights | no restrictions |
| ala_specimen_url | NA |
| ancillary_notes | NA |
| archive_ingestion_date | 2019-02-14 |
| associated_media | NA |
| barcode_id | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/omg_staging/exon_capture/brf/BPAOPS-786/ |
| birth_date | unknown |
| bpa_dataset_id | 102.100.100/52602 |
| bpa_library_id | 102.100.100/54079 |
| bpa_sample_id | 102.100.100/41363 |
| bpa_work_order | 40032 |
| class | Mammalia |
| collection_date | 2013-11-28 |
| collection_method | elliott trap |
| collector | Kevin C Rowe |
| collector_sample_id | KCR2139 |
| common_name | Broad-toothed rat |
| coord_uncertainty_metres | unknown |
| country | Australia |
| custodian | Kevin C Rowe | Museums Victoria |
| data_custodian | Kevin Rowe |
| data_generated | 2019-02-14 |
| data_type | Illumina FASTQ |
| dataset_url | (ingested) |
| date_of_transfer | 2019-01-14 |
| ddrad_data | no |
| ddrad_dataset_ids | NA |
| death_date | unknown |
| description | HiSeq 2500 100bp PE - rodent exome DNA |
| dna_conc_ng_ul | unknown |
| dna_extracted_by | Emily Roycroft |
| dna_extraction_date | unknown |
| dna_extraction_method | unknown |
| dna_treatment | 10 bioruptor cycles |
| exon_capture_data | yes |
| exon_capture_dataset_ids | 52602 |
| experimental_design | Nimblegen Exon Capture – dual index |
| facility | brf |
| facility_sample_id | 54079_AHVWV3BCX2_CTGCGAC |
| family | Muridae |
| file | 54079_AHVWV3BCX2_CTGCGAC_S57_L001_R1_001.fastq.gz | 54079_AHVWV3BCX2_CTGCGAC_S57_L001_R2_001.fastq.gz | 54079_AHVWV3BCX2_CTGCGAC_S57_L002_R1_001.fastq.gz | 54079_AHVWV3BCX2_CTGCGAC_S57_L002_R2_001.fastq.gz |
| flowcell_id | AHVWV3BCX2 |
| folder_name | SN877_0621_AMacDonald_OzMammals_Rodent_gDNA_exome_capture |
| genome_data | no |
| genome_dataset_ids | NA |
| genus | Mastacomys |
| habitat | unknown |
| identified_by | Kevin Rowe |
| institution_name | Museums Victoria |
| latitude | -36.654838 |
| library_comments | NA |
| library_location | ANU EBL |
| library_ng_ul | 78.25 |
| library_pcr_cycles | 12.0 |
| library_pcr_reps | 2.0 |
| library_prep_date | 2018-11-09 |
| library_prep_method | Meyer and Kircher protocol |
| library_prepared_by | Emiy Roycroft |
| library_status | Submitted for sequencing |
| library_type | exon capture |
| life_stage | adult organism |
| location_text | Alpine National Park, Davies Plain, 13km S, 11km E of Mount Pinnibar |
| longitude | 148.127732 |
| n_libraries_pooled | 96 |
| omg_project | Phylogenomics |
| order | Rodentia |
| p5_library_index_id | NA |
| p5_library_index_sequence | NA |
| p5_library_oligo_sequence | NA |
| p7_library_index_id | 57.0 |
| p7_library_index_sequence | CTGCGAC |
| p7_library_oligo_sequence | CAAGCAGAAGACGGCATACGAGATgtcgcagGTGACTGGAGTTCAGACGTGT |
| phylum | Chordata |
| prior_genetics | unknown |
| sample_quality | good |
| sample_submission_date | 2019-01-14 |
| sequence_length | 100bp PE |
| sequencing_facility | BRF |
| sequencing_platform | Illumina HiSeq 2500 RAPID |
| sex | female |
| software_version | unknown |
| source_population | unknown |
| species | fuscus |
| species_name | Mastacomys fuscus |
| state_or_region | Victoria |
| subspecies_or_variant | NA |
| taxon_id | 337222 |
| taxonomic_group | rodent |
| ticket | BPAOPS-786 |
| tissue_collection | Mammalogy |
| tissue_number | NMV Z27372 |
| tissue_preservation | frozen | RNALater |
| tissue_type | liver |
| trace_lab | no |
| type_status | unknown |
| voucher_id | NMV C37548 |
| voucher_number | NMV C37548 |
| voucher_or_tissue_number | NMV C37548 |
| wild_captive | wild |