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Model organism or animal sample from Elephas maximus indicus (Indian elephant) for VGP reference genome, mEleMax1

Identifiers
BioSample: SAMN29174328; Sample name: Animal sample from Elephas maximus indicus (Indian elephant) for VGP reference genome, mEleMax1; SRA: SRS18690681
Organism
Elephas maximus indicus
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Afrotheria; Proboscidea; Elephantidae; Elephas; Elephas maximus
Package
Model organism or animal; version 1.0
Attributes
isolatemEleMax1
development stageadult
sexmale
tissuefibroblast cells from skin
biomaterial providerFrozen Zoo, San Diego Zoo
birth date1966
birth locationIndia
cell typefibroblast
collected bySan Diego Zoo
collection date2016
geographic locationUSA: San Diego Zoo
latitude and longitude32.7353 N 117.1490 W
treatmentfrozen cell pellets, -80C
sub speciesindicus
Description

The Indian elephant is one of the three subspecies of the Asian Elephant. It has been classified as Endangered on the IUCN realist since 1986 due to habitat loss and environmental degradation mainly caused by human activities. This assembly has been produced as part of the G10K-VGP Project, and supported by Virpi Lummaa (Professor, Ecology and Evolutionary Biology, university of Turku, Finland), Camila Mazzoni (group leader at the Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany), and by Colossal Biosciences. Work was done in collaboration with Sara Ord, Eriona Hysolli, and Larissa Souza Arantes. Skin tissue was collected from a 50 years old adult male at the San Diego zoo, California (SB-218, and GAN # 26734787; ZIMS/Species 360) and fibroblast cells were cultured by the Frozen Zoo. The sample was sequenced using the VGP 2.0 individual pipeline at the Rockefeller University Vertebrate Genome Lab, led by Olivier Fedrigo and Erich Jarvis. The primary haplotype contigs were generated from PacBio Hifi reads, scaffolded with Bionano optical maps, and Arima HiC reads. Genome was assembled by Diego De Panis. Manual curation of chromosomes and other genomic features was conducted by Nadolina Brajuka and led by Giulio Formenti. The raw data and assembly are currently under a G10K-VGP publication embargo until removed from this description, following the G10K data use policy at the following URL: https://genome10k.soe.ucsc.edu/about/data_use_policy

BioProjects
PRJNA1008098
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PRJNA861314 Elephas maximus isolate:mEleMax1
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PRJNA850270 Elephas maximus isolate:mEleMax1
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PRJNA850184 Elephas maximus isolate:mEleMax1
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Submission
G10K, Erich Jarvis; 2022-06-17
Accession:
SAMN29174328
ID:
29174328

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