/
Rattus_norvegicus.yaml
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Rattus_norvegicus.yaml
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---
species:
short_name: mRatNor
name: Rattus norvegicus
taxon_id: 10116
common_name: Norway rat
order:
name: Rodentia
family:
name: Muridae
individuals:
-
short_name: mRatNor1
biosample_id: SAMEA7524397
alt_ids:
- SAN0001274
sex: male
project: [ vgp ]
-
short_name: mRatNor2
alt_ids:
- WKY/Bbb
-
short_name: mRatNor3
alt_ids:
- SHR/Utx (SHR-B2)
-
short_name: mRatNor4
biosample_id: null
strain: SHRSP/BbbUtx
alt_ids:
- RGD_8142383
- SHRA3/Utx
- SHR-A3
sex: male
birth_date: various, 2022-2023
birth_location: Texas, USA
breeding_method: natural
description: >
This "individual" represents the rat strain SHRSP/BbbUtx maintained at
UTHealth by Dr. Peter Doris. Multiple individuals are grouped together
because the strain is fully inbred and the genome is pseudohaploid.
Collections from various inviduals have occurred at multiple
timepoints, but they are generally being treated as coming from the
same source (similar to having a cell line) for the purpose of genome
assembly. A cell line was avoided so that somatic recombination could
be studied. For the purpose of this Tree of Life ID (ToLID), all
samples are from specimens at the same location and in the same
conditions. A reference genome assembly has already been generated using
PacBio HiFi and CLR (with other supporting data, e.g. Hi-C). The same
strain is being used for a T2T assembly effort.
provider: Dr. Peter Doris, University of Texas Health (UTHealth) Houston
samples:
-
sample_id: mRatNor4.liver1
tissue: liver
age: 18 weeks
dev_stage: adult
sample_biosample_id: SAMN24538170
birth_date: 2020-10-29
collection_date: 2021-03-08
provider: Dr. Peter Doris, University of Texas Health (UTHealth) Houston
-
sample_id: mRatNor4.kidney1
tissue: kindey
age: late gestational
dev_stage: late gestational
sample_biosample_id: null
collection_date: various, 2022-2023
provider: Dr. Peter Doris, University of Texas Health (UTHealth) Houston
description: >
Multiple samples were collected throughout 2022-2023 from multiple male
specimens. Intrabdominal testes are used to determine sex from these
late gestational fetuses. These samples were used for DNA sequencing
for the rat T2T project.
project: [ t2t ]
genome_size: 2900000000
genome_size_method: Expert estimate and existing assembly size
project: [ vgp, t2t ]