91 Works

The Rice 3000 Genomes Project Data

The 3000 Rice Genomes Project
Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, rice production must increase by at least 25% to keep pace with population growth. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land and to ensure global food supply. Here, we include data from an international effort resequencing a core collection of 3,000 rice accessions from 89 countries as...

Bacterial whole-genome read data from the Oxford Nanopore Technologies MinION™ nanopore sequencer.

J Quick & Loman N.J
Genomic data sequenced at x times coverage with an Oxford Nanopore Technologies MinION™ nanopore sequence of E. coli K-12 MG1655, and assembled using poretools. Three sequencing runs of the MinION were performed, one with a standard library and two with an ONI library. The standard library resulted in xxx forward only reads (xx%), xxx bi-direction (2D) reads (xx%) and xxx high quality 2D reads (xx%). The combined ONI runs resulted in xxx forward only reads...

Supporting material for: De novo assembly of a haplotype-resolved human genome

HZ Cao, H Wu, R Luo, S Huang, Y Sun, X Tong, Y Xie, B Liu, H Yang, H Zheng, J Li, B Li, Y Wang, F Yang, P Sun, S Liu, P Gao, H Huang, J Sun, D Chan, G Ha, W Huang, Z Huang, Y Li, LCAM Tellier … & J Wang
Here we provide the first de novo haplotype-resolved diploid genome sequence of an Asian individual using a unique de novo assembly pipeline. Our pipeline uses fosmid pooling and whole genome shotgun strategies, based on next generation sequencing (NGS) technology. The assembled genome contains 5.15 Gb, with a haplotype N50 of 484 kb. This haplotype-resolved genome represents the most complete genome assembly so far. Our analysis further identified previously undetected indels and novel coding sequences, and...

GigaDB promoting data dissemination and reproducibility

Hunter Chris, Edmunds Scott, Li Peter, SZ Xiao, LDavidson Robert & Goodman Laurie
GigaDB promoting data dissemination and reproducibility.

Genomic data of the Bar-tailed trogon (Apaloderma vittatum)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Bar-tailed Trogon (Apaloderma vittatum) belongs to the Trogonidae family of birds and lives in forests at a preferred altitude of around 1600 metres, and who's vocalisations are described "a yelping crescendo". It is found in several African countries - Angola, Burundi, Cameroon, Democratic Republic of the Congo, Equatorial Guinea, and Kenya, to name a few. These data have been produced as part of the avian phylogenomic project. DNA from the Apaloderma vittatum was collected...

Genomic data of the American Crow (Corvus brachyrhynchos)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The American Crow (Corvus brachyrhynchos) is a large passerine bird and part of the Corvidae family. It is commonly found throughout North America, and despite being common and widespread, they are highly susceptible to West Nile Virus. These data have been produced as part of the avian phylogenomic project. DNA from the Corvus brachyrhynchos was collected in Asheboro, North Carolina, USA. We sequenced the 1.26Gb genome to a depth of approximately 80X with short reads...

Genomic data of the plum (Prunus mume).

Q Zhang, W Chen, L Sun, F Zhao, B Huang, W Yang, Y Tao, J Wang, Z Yuan, G Fan, Z Xing, C Han, H Pan, X Zhong, W Shi, X Liang, D Du, F Sun, Z Xu, R Hao, T Lv, Y Lv, Z Zheng, M Sun, L Luo … & J Wang
The Plum (Prunus mume), was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae to be sequenced. DNA from the plum was collected in Tongmai town, Tibet, China. We sequenced the genome to a depth of approximately 101.4 X with short reads from a series of libraries with various insert sizes ( 180bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and...

Genomic data of the green sea turtle (Chelonia mydas)

Z Wang, J Pascual-Anaya, A Zadissa, W Li, Y Niimura, Z Huang, C Li, S White, Z Xiong, D Fang, B Wang, Y Ming, Y Chen, Y Zheng, S Kuraku, M Pignatelli, J Herrero, K Beal, M Nozawa, Q Li, J Wang, H Zhang, L Yu, S Shigenobu, J Wang … & N Irie
Green turtles are long-lived and may take up to 59 years to reach sexual maturity. Undertaking tremendous feats of navigation, adults return to the same beach to breed each season. DNA from the green sea turtle was collected in Hong Kong. We sequenced the 2.24 Gb genome to a depth of approximately 82.3 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb,20kb and 40kb)...

Genomic data of the Great black cormorant (Phalacrocorax carbo)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Great Cormorant (Phalacrocorax carbo) is a widespread member of the cormorant family and is known by several different names around the world - the Black Shag in New Zealand, the Black Cormorant in Australia and the Large Cormorant in India. It is a large black bird that can be distinguished from the Common Shag by its larger size, heavier build and thicker bill. They are mostly silent birds but can produce various guttural noises...

Genomic data of the Anna's Hummingbird (Calypte anna)

G Zhang, B Li, C Li, M.T.P. Gilbert, C.V. Mello, E.D. Jarvis, The Avian Genome Consortium & J Wang
The Anna's Hummingbird (Calypte anna (Lesson, 1829)) is a medium-sized hummingbird native to the west coast of North America and is the only North American hummingbird species with a red crown. It belongs to one of the rare groups of vocal learning birds. The bird was named after Anna Massena, Duchess of Rivoli. These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from from a female, which...

Genomic data of the Red throated loon (Gavia stellata)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Red-throated Loon (Gavia stellata), also known as the Red-throated Diver, is a migratory aquatic bird that breeds mainly in the Arctic regions and spends winters in the northern coastal waters. The Red-throated loon has a large global population, making it the most widely distributed member of the Gaviidae (Loon or Diver) family.These data have been produced as part of the avian phylogenomic project. DNA from the Gavia stellata was collected in Denmark. We sequenced...

The genome of the American aligator (Alligator mississippiensis)

RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, MW Vandewege, JA St John, S Capella-Gutiérrez, TA Castoe, C Kern, MK Fujita, JC Opazo, J Jurka, KK Kojima, J Caballero, RM Hubley, AF Smit, RN Platt, CA Lavoie, MP Ramakodi, Finger Jr., JW, A Suh, Isberg, L Miles … & DA Ray
The American alligator (Alligator mississippiensis)), as the name suggests, is endemic to North America, specifically to the South-East United States, where it inhabits wetlands on the Atlantic coast from North Carolina to Florida, and in the Northern Gulf of Mexico west to Texas. These data have been produced as part of the Crocodilian Genomes Project. Genomic DNA was isolated using blood from two wild-caught individuals. Briefly, the alligator data consisted of Illumina sequences from five...

Genomic data of the Diamondback moth (Plutella xylostella)

M You, Z Yue, W He, X Yang, G Yang, M Xie, D Zhan, SW Baxter, L Vasseur, GM Gurr, CJ Douglas, J Bai, P Wang, K Cui, S Huang, X Li, Q Zhou, Z Wu, Q Chen, C Liu, B Wang, X Li, X Xu, C Lu, M Hu … & J Wang
How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood. P. xylostella has become the most destructive pest of economically important food crops, including rapeseed, cauliflower and cabbage. This insect is the first species to have evolved...

Genomic data of the Angola turaco (Tauraco erythrolophus)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Red-crested Turaco (Tauraco erythrolophus) is a group of African near-passerines endemic to western Angola. It's call has been described to be somewhat like a jungle monkey.These data have been produced as part of the avian phylogenomic project. DNA from the Tauraco erythrolophus was collected in Denmark. We sequenced the genome to a depth of approximately 30X. The assembled scaffolds of high quality sequences total 1.17Gb, with the contig and scaffold N50 values of 18kb...

Supporting material for: "Event-related potential datasets based on three-stimulus paradigm".

L Vareka, P Bruha & R Moucek
The event-related potentials technique is widely used in cognitive neuroscience research. The P300 waveform has been explored in many research articles because of its wide applications including lie detection or brain-computer interfaces. However, a very few datasets are publicly available. Therefore, most researchers use only their private datasets for their analysis. This leads to hardly comparable results, particularly in brain-computer interfaces research. This article presents the electroencephalography/event-related potentials (EEG/ERP) data. These were acquired using an...

Genomic data of the domestic donkey (Equus asinus)

L Orlando, A Ginolhac, G Zhang, D Froese, A Albrechtsen, M Stiller, M Schubert, E Cappellini, B Petersen, I Moltke, PLF Johnson, M Fumagalli, JT Vilstrup, M Raghavan, T Korneliussen, AS Malaspinas, J Vogt, D Szklarczyk, CD Kelstrup, J Vinther, A Dolocan, J Stenderup, AMV Velazquez, J Cahill, M Rasmussen … & E. Willerslev
The domestic donkey is derived from the African Wild Ass. As with most domesticated species there are a wide variety of coat colours and sizes. They can live for upto 40years. We sequenced the genome to a depth of approximately 19.4 X with short reads from a series of libraries with various insert sizes ( 800bp and 2kb) on a HiSeq 2000 sequencer.The assembled scaffolds of high quality sequences total 48.6 Gb.

Genomic data of the Kea (Nestor notabilis)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Kea (Nestor notabilis) is known as the cheeky parrot of New Zealand and is a large bird belonging to the superfamily Strigopoidea. It inhabits the alpine regions of the South Island and is known for its intelligence and curiosity - they can solve logical puzzles and can push and pull things in order to get food. These data have been produced as part of the avian phylogenomic project. DNA from the Nestor notabilis was...

Genomic data of the Macqueen's Bustard (Chlamydotis macqueenii)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
MacQueen's Bustard (Chlamydotis macqueenii) is a large bird that breeds in southwest Asia in deserts and similarly arid sandy areas. It has recently split as a separate species from the Houbara Bustard of the Canary Islands and Africa, and one difference is that the MacQueen's Bustard has a tendancy to wander compared with the Houbara.These data have been produced as part of the avian phylogenomic project. DNA from the Chlamydotis macqueenii was sequenced to a...

Genomic data of the Speckled mousebird (Colius striatus)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Speckled Mousebird (Colius striatus) is the largest species of mousebird and named because of its overall mousey-brown colour. The bird can be found from Cameroon to Eritrea and Ethiopia, and southern South Africa. Described as a noisy creature, it is not however, known for its voice, and is a rather social bird often observed feeding in groups. These data have been produced as part of the avian phylogenomic project. DNA from the Colius striatus...

Supporting materials for: "Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing".

Y Tan, X Yin, S Zhang, H Jiang, K Tan, J Li, B Xiong, F Gong, C Zhang, X Pan, F Chen, S Chen, C Gong, C Lu, K Luo, Y Gu, X Zhang, W Wang, X Xu, G Vajta, L Bolund, H Yang, G Lu, Y Du & Lin G
A total of 395 couples were subjected to IVF-PGD treatment, including 129 couples with NGS-based test and 266 couples with SNP array based test for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole genome sequencing with HiSeq 2000 platform. And the SNP array test was using Affymetrix Gene Chip Mapping Nsp I 262K. The average age of patients was 32.1 years (age range 20-44 years). Due to the...

Genomic data of the Hoazin (Opisthocomus hoazin)

G Zhang, B Li, C Li, M.T.P. Gilbert, P. Houde, E.D. Jarvis, The Avian Genome Consortium & J Wang
The Hoazin (Opisthocomus hoazin (Müller, 1776)) is a pheasant-sized tropical bird found in swamps, forest and mangroves of the Amazon and Orinoco Delta in South America. It is known by other names, such as the Hoactzin, Stinkbird or Canje Pheasant and is notable for having chicks that possess claws on two of their wings. These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a female obtained...

Genomic data of the Javan rhinoceros hornbill (Buceros rhinoceros silvestris)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Javan rhinoceros hornbill (Buceros rhinoceros silvestris ) is a sub species of the Rhinoceros Hornbill (Buceros rhinoceros), one of the world's largest hornbills that has lived in captivity for over 90 years. It is found it lowland and tropical and sub-tropical mountain rainforests in Borneo, Sumatra, Java, the Malay Peninsula, Singapore and southern Thailand. It is also the state bird of the Malaysian state, Sarawak. These data have been produced as part of the...

Genomic data of the Sunbittern (Eurypyga helias)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Sunbittern (Eurypyga helias) is the sole member of the family Eurypygidae and is found in Central to South America from Mexico, Peru to Brasil. It has similar morphological features to the Kagu of New Caledonia and is a non-migrant bird that is normally found on the ground scratching for insects. These data have been produced as part of the avian phylogenomic project. DNA from the Eurypyga helias was collected in Denmark. We sequenced the...

Genome sequence of the duck (Anas platyrhynchos)

Y Huang, Y Li, DW Burt, H Chen, Y Zhang, W Qian, H Kim, S Gan, Y Zhao, J Li, K Yi, H Feng, P Zhu, B Li, Q Liu, S Fairley, KE Magor, Z Du, X Hu, L Goodman, H Tafer, A Vignal, T Lee, K Kim, Z Sheng … & N Li
Available here is the first draft genomic sequence of the duck (Anas platyrhynchos). Duck is a member of Anatidae, a family of birds that include geese and swans. However, duck is an economically important waterfowl serving as a source of meat, eggs and feathers; though, of special interest to agriculture and medicine is that fact that the duck is a principal natural host of influenza A viruses and harbours all subtypes of 16 haemagglutinin and...

Genomic data of the Chuk-will's-widow (Antrostomus carolinensis)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Chuck-will's-widow (Antrostomus carolinensis) is a nocturnal bird and part of the Caprimulgidae family. It's name is derived from a continuous repetitive song often heard at night, and is often confused with Whippoorwills due to their similar calls and unusual names.These data have been produced as part of the avian phylogenomic project. DNA from the Antrostomus carolinensis was collected in Louisiana, USA. We sequenced the genome to a depth of approximately 30X. The assembled scaffolds...

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  • 2014
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