6,073 Works

Drosophila ananassae Transcriptome or Gene expression

BGI
single end RNA sequencing for D. ananassae reference strain

Peer review of "Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembl"

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

Peer review of "The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly"

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

Whole genome sequencing of Juniperus communis (common juniper) to construct a draft genome assembly.

BGI
Conifers have dominated forests for more than 200 million years and are of huge ecological and economical importance. We present the draft assembly of the 20 Gbp genome of Norway spruce (Picea abies), the first genome sequence available for any gymnosperm. The number of well-supported genes (28,354) was similar to the >100 times smaller genome of Arabidopsis thaliana and there was no evidence of a recent whole-genome duplication. Instead, the large genome size has resulted...

Image data of Nanmaohu Park vascular plant specimen, RL0231

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,...

The Sequencing of Salmonella enterica strains.

BGI
None

Peer review of "SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast"

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

Pterocles gutturalis Genome sequencing and assembly

BGI
The whole genome sequencing of Pterocles gutturalis

Setaria italica strain:Zhang gu Genome sequencing

BGI
Foxtail millet (Setaria italica) is one of the oldest domesticated species and provides food and fodder, especially in semi-arid regions.

Genomic data of Nanmaohu Park vascular plant specimen, RL0622

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

Bombus impatiens genome sequencing project

BGI
Bombus impatiens is the #2 pollinator in the United States. The genome was sequenced by the Biotechnology Center, University of Illinois (BCUI), using genomic DNA from haploid males. The assembly was done by the Center for Bioinformatics and Computational Biology at University of Maryland.

Genomic data of Nanmaohu Park vascular plant specimen, RL0723

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 "A micro X-ray computed tomography dataset of fossil echinoderms in an ancient obrution bed: a robust method for taphonomic and palaeoecologic analyses "

Michael Bruce Meyer
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Whole genome assembly of Pacific Walrus using multiple sequencing platform

BGI
Whole genome assembly of Odobenus rosmarus (Pacific Walrus) by the BCM-HGSC and collaborators in the Marine Mammals Genome Projects using multiple sequencing platforms.

The Sequencing of Salmonella enterica strains.

BGI
None

Peer review of "Extensive evaluation of the generalized relevance network approach to inferring gene regulatory networks"

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

Peer review of "A reference gene set construction using RNA-seq of multiple tissues of Chinese Giant Salamander, Andrias davidianus"

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

Pooled CRISPR screening with single-cell transcriptome read-out

BGI
We combined CRISPR genome editing with single-cell RNA sequencing to assess complex phenotypes in pooled cellular screens. Our method for CRISPR droplet sequencing (CROP-seq) comprises four key components: a gRNA vector that makes individual gRNAs detectable in single-cell transcriptomes, a high-throughput assay for single-cell RNA-seq, a computational pipeline for assigning single-cell transcriptomes to gRNAs, and a bioinformatic method for analyzing and interpreting gRNA-induced transcriptional profiles. CROP-seq allowed us to link gRNA expression to the associated...

Peer review of "Nighres: Processing tools for high-resolution neuroimaging"

Christin Y. Sander
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Caligus rogercresseyi Genome sequencing and assembly

BGI
Caligus rogercresseyi has become an important model for the study of ectoparasitic infestations on salmon. The process of disease due to C. rogercresseyi on farmed Atlantic salmon (Salmo salar) in Chile is a result of their feeding behavior and the secretion of bioactive compounds into the host. Clinical signs include physical damage to the epidermis and underlying tissue, changes in the blood electrolyte composition, physiological stress, immune dysfunction, loss of locomotive capacity and sometimes, death....

Bloodstream_surveillence_across_Africas

BGI
A survey across centres in Africa into the main bacterial causes of bloodstream infections.

Peer review of "The draft genome sequence of forest musk deer (Moschus berezovskii)"

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

Peer review of "Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)"

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

Elysia chlorotica stage-specific gene expression

BGI
Here we used RNA-Seq analysis to test the idea that plastid sequestration leaves a significant signature on host gene expression during E. chlorotica development

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

BGI
A large number of computational methods have been recently developed for analyzing differential gene expression (DE) in RNA-seq data. We report on a comprehensive evaluation of the commonly used DE methods using the SEQC benchmark data set and data from ENCODE project. We evaluated a number of key features including: normalization, accuracy of DE detection and DE analysis when one condition has no detectable expression. We found significant differences among the methods. Furthermore, computational methods...

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