1,867 Works

Supporting data for "Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle"

Rice Stallknecht Edward, Koren Sergey, Rhie Arang, Heaton P Michael, Kalbfleisch S Theodore, Hardy Timothy, Hackett H Peter, Bickhart M Derek, Rosen D Benjamin, Vander Ley Brian, Maurer W Nicholas, Green E Richard, Phillippy M Adam, Petersen L Jessica & Smith PL Timothy
The development of trio binning as an approach for assembling diploid genomes has enabled creation of fully haplotype-resolved reference genomes. Unlike other methods of assembly for diploid genomes, this approach is enhanced, rather than hindered, by the heterozygosity of the individual sequenced. In order to maximize heterozygosity and simultaneously assemble reference genomes for two species, we applied trio binning to an interspecies F1 hybrid of yak (Bos grunniens) and cattle (Bos taurus), two species that...

Genomic data from the Eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)

Li Qiye, Guo Qunfei, Zhou Yang, Tan Huishuang, Bertozzi Terry, Zhu Yuanzhen, Li Ji, Donnellan Stephen & Zhang Guojie
Amphibian genomes are usually challenging to assemble due to large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap....

Supporting data for "Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration"

McGowan Thomas, Johnson E James, Kumar Praveen, Sajulga Ray, Mehta Subina, Jagtap D Pratik & Griffin J. Timothy
Proteogenomics integrates genomics, transcriptomics and mass spectrometry (MS)- based proteomics data to identify novel protein sequences arising from gene and transcript sequence variants. Proteogenomic data analysis requires integration of disparate ‘omic software tools, as well as customized tools to view and interpret results. The flexible Galaxy platform has proven valuable for proteogenomic data analysis. Here, we describe a novel Multi-omics Visualization Platform (MVP) for organizing, visualizing and exploring proteogenomic results, adding a critically needed tool...

Supporting data for "Bioentity2vec: Attribute- and Behavior-driven Representation for Multi-type Relationship Prediction between Various Bioentities"

Guo Zhen-Hao, You Zhu-Hong, Huang De-Shuang, Yi Hai-Cheng, Wang Yan-Bin & Chen Zhan-Heng
The explosive growth of genomic, chemical and pathological data provides new opportunities and challenges for humans to reexamine life activities in cells. However, there exist few computational models that aggregate various bioentities to comprehensively reveal the physical and functional landscape of biological system. Here, we construct a graph called Molecular Association Network (MAN) and a representation method called Bioentity2vec. Specifically, MAN is a heterogeneous attribute network consists of 18 kinds of edges (relationships) among 8...

Supporting data for "Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping and Hi-C"

Field A Matt, Rosen D Benjamin, Dudchenko Olga, Chan K.F. Eva, Minoche E. Andre, Edwards J. Richard, Barton Kirston, Lyons J. Ruth, Enosi Tuipulotu Daniel, Hayes M. Vanessa, Omer Arina, Colaric Zane, Keilwagen Jens, Skvortsova Ksenia, Bogdanovic Ozren, Smith A M, Aiden Lieberman Erez, Smith P.L. Timothy, Zammit A. Robert & J. O. Ballard William
The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance and search-and-rescue. Yet, GSD’s are well known to be afflicted with a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully...

Supporting data for "*-DCC: A platform to collect, annotate and explore a large variety of sequencing experiments"

Hörtenhuber Matthias, Mukarram Kadir Abdul, Stoiber Marcus, Brown B James & Daub Oliver Carsten
Over the last few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To assure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is of outstanding importance.
We first developed an annotation structure which captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure and...

Supporting data for "PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes"

Zafeiropoulos Haris, Quoc Ha Viet, Vasileiadou Katerina, Potirakis Antonis, Arvanitidis Christos, Topalis Pantelis, Pavloudi Christina & Pafilis Evangelos
Environmental DNA (eDNA) and metabarcoding allow the identification of a mixture of species individuals and launch a new era in bio- and eco-assessment. A great number of steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool’s execution parameters need to be tailored to reflect each experiment’s idiosyncrasy. Adding to this complexity, the computation capacity of High Performance Computing systems is frequently...

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...

Supporting data for "Genomic bases for colonizing the freezing Southern Ocean revealed by the genomes of Antarctic toothfish and Patagonia robalo"

Cheng Christina Chi-Hing, Wang Jian, Murphy R Katherine, Bilyk T Kevin, Chen Liangbiao, Hune Mathias, Yu Mengchao, Xu Qianghua, Jiang Shouwen, Peng Sihua, Zhai Wanying, Wang Wen, Li Wenhao, Zhuang Xuan, Ren Yandong, Fu Yanxia & Lu Ying
The Southern Ocean is the coldest ocean on Earth but a hotspot of evolution. The bottom-dwelling Eocene ancestor of Antarctic notothenioid fishes survived polar marine glaciation and underwent adaptive radiation forming >120 species that fill all water column niches today. Genome-wide changes enabling physiological adaptations and rapid expansion of the Antarctic Notothenioids remain poorly understood. To advance our understanding, we sequenced and compared two notothenioid genomes - the cold-adapted and neutrally buoyant Antarctic toothfish Dissostichus...

Supporting data for "Comparative Proteomics Analysis of Tibetan Hulless Barley under Osmotic Stress via Data-Independent Acquisition Mass Spectrometry"

Wang Yulin, Sang Zha, Xu Shaohang, Xu Qijun, Zeng Xingquan, Jabu Dunzhu & Yuan Hongjun
Tibetan hulless barley (Hordeum vulgare L. var. nudum ) is one of the primary crops cultivated in the mountains of Tibet and encounters low temperature, high salinity, and drought. Specifically, drought is one of the major abiotic stresses that affect and limit Tibetan barley growth. Osmotic stress is often simultaneously accompanied by drought conditions. Thus, to improve crop yield, it is critical to explore the molecular mechanism governing the responses of hulless barley to osmotic/drought...

Genomic data of Nanmaohu Park vascular plant specimen, RL0290

Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fu, Xuebin Wang, Guohai Hu, Wangsheng Li, Hongcheng Zhou, Yue Chang, Xiaoli Chen, Hongyun Chen, Le Cheng, Xuefei He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Jinlong Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao … & Xin Liu
We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).In total,...

Image data of Nanmaohu Park vascular plant specimen, RL0789

Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fu, Xuebin Wang, Guohai Hu, Wangsheng Li, Hongcheng Zhou, Yue Chang, Xiaoli Chen, Hongyun Chen, Le Cheng, Xuefei He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Jinlong Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao … & Xin Liu
We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).In total,...

Supporting data for "Multi-Dimensional Machine Learning Approaches for Fruit Shape Phenotyping in Strawberry"

Feldmann J Mitchell, Hardigan A Michael, Famula A Randi, López M Cindy, Tabb Amy, Cole S Glenn & Knapp J Steven
Shape is a critical element of the visual appeal of strawberry fruit and influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is inherently multi-dimensional, continuously variable trait, and not adequately described by a single categorical or quantitative feature. Morphometric approaches enable the study of complex, multi-dimensional forms but are often abstract and difficult to...

Supporting data for "Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism"

Zhang Jin, Hu Rongbin, Garcia Travis, Lipzen Anna, Wang Mei, Yerramsetty Pradeep, Liu Degao, Ng Vivian, Schmutz Jeremy, Cushman John, Borland Anne, Pasha Asher, Provart Nicholas, Chen Jin-Gui, Muchero Wellington, Tuskan Gerald & Yang Xiaohan
Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoe fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied.
Here we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12h/12h photoperiod with different light quality (blue, red, far-red,...

Supporting data for "SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees"

Morgulis Aleksandr & Agarwala Richa
Alignment of sequence reads generated by next-generation sequencing (NGS) is an integral part of most pipelines analyzing NGS data. A number of tools designed to quickly align large volume of sequences are already available. However, most existing tools lack explicit guarantees about their output. They also do not support searching genome assemblies, such as the human genome assembly GRCh38, that include primary and alternate sequences and placement information for alternate sequences to primary sequences in...

Genomic data of Nanmaohu Park vascular plant specimen, RL0104

Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fu, Xuebin Wang, Guohai Hu, Wangsheng Li, Hongcheng Zhou, Yue Chang, Xiaoli Chen, Hongyun Chen, Le Cheng, Xuefei He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Jinlong Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao … & Xin Liu
We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).In total,...

Supporting data for "A novel k-FLBPCM method for detecting morphologically similar crops and weeds based on the combination of contour masks and Local Binary Pattern operators"

Le Nguyen Thanh Vi, Ahderom Selam, Apopei Beniamin & Alameh Kamal
Weeds are a major cause of low agricultural productivity. Some weeds have morphological features similar to crops making them difficult to discriminate. This paper proposes a novel method using a combination of filtered-features extracted by combined Local Binary Pattern operators and features extracted by plant-leaf contour masks to improve the discrimination rate between broadleaf plants. Opening and closing morphological operators were applied to filter noise in plant images. The images at four stages of growth...

Supporting data for "Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs"

Chen Hao, Huang Min, Yang Bin, Wu Zhongping, Deng Zheng, Hou Yong, Ren Jun & Huang Lusheng
Pigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. Chinese indigenous pigs have been historically introduced to improve Europe local pigs. However, the geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown. Here we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. We...

Supporting data for "The chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome"

Jiang Shuang, An Haishan, Xu Fangjie & Zhang Xueying
The loquat (Eriobotrya japonica) is a species of flowering plant in the family Rosaceae that is widely cultivated in Asian, European, and African countries. It blossoms in the winter and ripens in the early summer. The genome of loquat has not been reported, which limits the study of molecular biology in the loquat. Here, we used the third-generation sequencing technology of Nanopore and High-through chromosome conformation capture (Hi-C) technology to sequence the genome of Eriobotrya...

Supporting data for "drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes"

Hsin-Hung Lin & Yu-Chieh Liao
Virus discovery using high-throughput next-generation sequencing (NGS) has become more commonplace. However, although analysis of deep NGS data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Here we present a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes),...

Genomic data of Nanmaohu Park vascular plant specimen, RL0100

Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fu, Xuebin Wang, Guohai Hu, Wangsheng Li, Hongcheng Zhou, Yue Chang, Xiaoli Chen, Hongyun Chen, Le Cheng, Xuefei He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Jinlong Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao … & Xin Liu

Genomic data for the domestic cucumber (Cucumis sativus var sativus L)

S Huang, R Li, Z Zhang, L Li, X Gu, W Fan, WJ Lucas, X Wang, B Xie, P Ni, Y Ren, H Zhu, J Li, K Lin, W Jin, Z Fei, G Li, J Staub, A Kilian, EA Van Der Vossen, Y Wu, J Guo, J He, Z Jia, Y Ren … & S Li
Here we present genomic data for the domestic cucumber (Cucumis sativus var. sativus L.). The cucumber is a member of the Cucurbitaceae or cucurbit family, a family of great agricultural and horticultural importance that also includes species such as melons, gourds and squashes. A biologically interesting as well as an economically relevant species, it is used as a model system for plant sex determination and vascular biology studies. The domestic cucumber has seven pairs of...

Supporting data for "An image dataset related to automated macrophage detection in immunostained lymphoma tissue samples"

Wagner Marcus, Reinke Sarah, Hänsel René, Klapper Wolfram & Braumann Ulf-Dietrich
We present an image dataset related to automated segmentation and counting of macrophages in diffuse large B-cell lymphoma {(DLBCL)} tissue sections. For the classification of DLBCL subtypes as well as for as for providing a prognosis of the clinical outcome, the analysis of the tumor microenvironment and, particularly, of the different types and functions of tumor-associated macrophages, is indispensable. Until now, however, most information about macrophages is obtained either in a completely indirect way by...

High quality chimpanzee reference genome (Pan_tro_30) from hybrid assembly approach

Lukas FK Kuderna, Chad Tomlinson, LaDeana W Hillier, Annabel Tran, Ian Fiddes, Joel Armstrong, Hafid Laayouni, David Gordon, John Huddleston, Raquel Garcia Perez, Inna Povolotskaya, Aitor Serres Armero, Jessica Gomez Garrido, Daniel Ho, Paolo Ribeca, Tyler Alioto, Richard E Green, Benedict Paten, Arcadi Navarro, Jaume Betranpetit, Javier Herrero, Evan E Eichler, Andrew J Sharp, Lars Feuk, Wesley C Warren … & Tomas Marques-Bonet
The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high quality reference genome assembly. The current iteration of the chimpanzee reference genome assembly (Pan_tro_2.1.4) is highly fragmented, with more than 183,000 contigs and incorporating over 159,000 gaps, with a genome wide contig N50 of 51 Kbp. In this work we produce an extensive and diverse array of sequencing datasets to rapidly assemble...

Supporting data for "Learning improves decoding of odor identity with phase-referenced oscillations in the olfactory bulb"

Losacco Justin, Ramirez-Gordillo Daniel, Gilmer Jesse & Restrepo Diego
Local field potential oscillations reflect temporally coordinated neuronal ensembles coupling distant brain regions, gating processing windows, and providing a reference for spike timing-based codes. In phase amplitude coupling (PAC), the amplitude of the envelope of a faster oscillation is larger within a phase window of a slower carrier wave.
Here, we characterized PAC, and the related theta phase-referenced high gamma and beta power (PRP), in the olfactory bulb of mice learning to discriminate odorants. PAC...

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