3,943 Works

Peer review of "Live time-lapse dataset of in vitro wound healing experiments"

Juliane Zimmermann
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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...

Peer review of "Common Workflow Language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data"

Leszek Pryszcz
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Filling reference gaps via assembling DNA barcodes using high-throughput sequencing – moving toward barcoding the world"

Akifumi Tanabe
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization"

Johannes Lenstra
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Integrated metabolomics and phytochemical genomics approaches for studies on rice"

Ellen Zuther
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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,...

Peer review of "Evaluating stably expressed genes in single cells"

George Tseng
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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...

Peer review of "YAMP: a containerised workflow enabling reproducibility in metagenomics research"

Konstantinos Krampis
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise"

Dominic Wright
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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),...

Peer review of "VaDiR: an integrated approach to Variant Detection in RNA"

Terry Speed
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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

Peer review of "Computer vision-based phenotyping for improvement of plant productivity: A machine learning perspective"

Andrew French
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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

Simon Roux
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization"

Benjamin Marie
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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...

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