321 Works

Additional file 6 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 6: Table S3. Summary of 639 main-effect QTL affecting 12 traits identified in the combined population across three environments by inclusive composite interval mapping.

Additional file 6 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 6: Table S3. Summary of 639 main-effect QTL affecting 12 traits identified in the combined population across three environments by inclusive composite interval mapping.

Additional file 8 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 8: Table S5. Classification of 2,736 epistatic QTL pairs into 13 types according to their gene actions identified in the Q9311/WSSM combined population.

Additional file 1 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 1: Table S1. Phenotypic performance and heterosis of traits in Q9311B/WSSM RILs and backcross F1s (Q9311A × RIL).

Additional file 11 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 11. Summary statistics for the differential expression analysis. DE: differentially expressed. LS: lateral septum, MPOA: medial preoptic area, NAc: nucleus accumbens.

Additional file 9 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 9. Functional enrichment across structures and phenotypes. For each pairwise comparison, the functional enrichments in gene ontologies of the biological processes (BP), cellular components (CC), and molecular functions (MF) categories as well as in pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were tested for the differentially expressed genes up- or down-regulated (UP, and DOWN, respectively). The labels of pairwise comparisons were coded in two letters: the first one represents the...

Additional file 7 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 7. Detailed results from the linear regressions between all behaviors scored during the parental behaviors test, testing for an interaction of Group (Mothers/Fathers/Paternal).

Effects of SLCO1B1 on elimination and toxicities of high-dose methotrexate in pediatric acute lymphoblastic leukemia - Supplementary Material

Fei-Fei Yang, Tian-Lin Xue, Chao Gao, Ying Wu, Wei Lin, Jun Li, Rui-Dong Zhang, Hu-Yong Zheng & Shu-Guang Liu
Supplementary Table S1. Treatment elements of consolidation therapy in CCLG-ALL-2018. Supplementary Table S2. Leucovorin rescue and MTX concentration

Additional file 6 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 6: Supplemental Table 4. Per-study and meta-analytically aggregated effect sizes of per-feature differential abundance tests performed.

Additional file 5 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 5: Supplemental Table 3. Detailed specification for omnibus and per-feature differential abundance testing models.

Additional file 6 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 6: Supplemental Table 4. Per-study and meta-analytically aggregated effect sizes of per-feature differential abundance tests performed.

Additional file 9 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 9: Supplemental Table 7. Consensus loadings for the two identified continuous scores characterizing the IBD gut microbiome population structure.

Additional file 7 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 7: Supplemental Table 5. Per-study and meta-analytically aggregated effect sizes of tests on per-feature abundance associated with disease phenotypic severity.

Additional file 1 of Community composition and trophic mode diversity of fungi associated with fruiting body of medicinal Sanghuangporus vaninii

Yanjun Ma, Weiqian Gao, Fan Zhang, Xuetai Zhu, Weibao Kong, Shiquan Niu, Kun Gao & Hongqin Yang
Supplementary material 1: Table S1. Taxonomic classification of OTUs detected from Sanghuangporus vaninii fruiting body with total ITS rDNA read numbers. Table S2. The fungal OTUs associated with S. vaninii fruiting body were annotated into trophic modes. Table S3. Trophic modes annotation of associated fungi at genus level. Table S4. Trophic modes and their guilds annotation of fungi associated with S. vaninii fruiting body.

Additional file 8 of Circulating N-formylmethionine and metabolic shift in critical illness: a multicohort metabolomics study

Martin Ingi Sigurdsson, Hirotada Kobayashi, Karin Amrein, Kiichi Nakahira, Angela J. Rogers, Mayra Pinilla-Vera, Rebecca M. Baron, Laura E. Fredenburgh, Jessica A. Lasky-Su & Kenneth B. Christopher
Additional file 8. Additional metabolomics results from VITdAL-ICU and RoCI Cohorts. Nine individual worksheets include Linear regression results of Day 0 data from the VITdAL-ICU cohort adjusted for age, sex, baseline 25(OH)D, SAPS II, admission diagnosis, with additional adjustment for total bilirubin, creatinine, sepsis or propofol exposure. Day 0 data from the VITdAL-ICU cohort is also shown adjusted for age, sex, baseline 25(OH)D, and admission diagnosis but without SAPS II. Linear regression results of Day...

Delocalization State-Induced Selective Bond Breaking for Efficient Methanol Electrosynthesis from CO2

Shuyi Kong, Ximeng Lv, Xin Wang, Zhengzheng Liu, Zichuang Li, Bingquan Jia, Du Sun, Chao Yang, Lijia Liu, Anxiang Guan, Jiacheng Wang, Gengfeng Zheng & Fuqiang Huang
Source data of XRD, .hkl file from 3D electron diffraction, and electrolysis data.

Measuring protected-area effectiveness using vertebrate distributions from leech iDNA

Yinqiu Ji, Christopher C. M. Baker, Viorel D. Popescu, Jiaxin Wang, Chunying Wu, Zhengyang Wang, Yuanheng Li, Lin Wang, Chaolang Hua, Zhongxing Yang, Chunyan Yang, Charles C. Y. Xu, Alex Diana, Qingzhong Wen, Naomi E. Pierce & Douglas W. Yu
Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases...

Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies

Alexandre A. Lussier, Yiwen Zhu, Brooke J. Smith, Andrew J. Simpkin, Andrew D.A.C. Smith, Matthew J. Suderman, Esther Walton, Kerry J. Ressler & Erin C. Dunn
Biomedical research has grown increasingly cooperative through the sharing of consortia-level epigenetic data. Since consortia preprocess data prior to distribution, new processing pipelines can lead to different versions of the same dataset. Similarly, analytic frameworks evolve to incorporate cutting-edge methods and best practices. However, it remains unknown how different data and analytic versions alter the results of epigenome-wide analyses, which could influence the replicability of epigenetic associations. Thus, we assessed the impact of these changes...

Additional file 2 of Maternal blood pressure associates with placental DNA methylation both directly and through alterations in cell-type composition

Lucile Broséus, Daniel Vaiman, Jörg Tost, Camino Ruano San Martin, Milan Jacobi, Joel D. Schwartz, Rémi Béranger, Rémy Slama, Barbara Heude & Johanna Lepeule
Additional file 2: Supplementary tables ST1-ST12. ST1 – Participants’ characteristics; ST2 - Global methylation analyses; ST3 - Inflation Factors; ST4 - Top 100 DMPs; ST5 - Replication Analysis; ST6 - DMRs; ST7 - Trait Enrichment; ST8 - Gene enrichment; ST9 - Sensitivity analyses of DMRs; ST10 - Association between blood pressure and cell-type composition; ST11 – Compositional mediation analysis; ST12 - Mediation analysis: role of the ratio Stromal/Syncytiotrophoblasts.

Limited increases in savanna carbon stocks over decades of fire suppression

Yong Zhou, Jenia Singh, John Butnor, Corli Coetsee, Peter Boucher, Madelon Case, Evan Hockridge, Andrew Davies & Carla Staver
Savannas cover a fifth of the land surface and contribute a third of terrestrial net primary production, accounting for three quarters of global area burned and over half of global fire-driven carbon emissions. Fire suppression and afforestation have been proposed as tools to increase carbon sequestration in these ecosystems. A robust quantification of whole-ecosystem carbon storage in savannas is lacking, however, especially under altered fire regimes. Here, we provide the first direct estimates of whole-ecosystem...

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

Lerato Magosi, Yinfeng Zhang, Tanya Golubchik, Victor DeGruttola, Eric Tchetgen Tchetgen, Vladimir Novitsky, Janet Moore, Pam Bachanas, Tebogo Segolodi, Refeletswe Lebelonyane, Molly Pretorius Holme, Sikhulile Moyo, Joseph Makhema, Shahin Lockman, Christophe Fraser, Myron Essex & Marc Lipsitch
Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. Methods: To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664). Results: Deep-sequence phylogenetic analysis...

A dataset of 5 million city trees from 63 US cities: species, location, nativity status, health, and more.

Dakota McCoy, Benjamin Goulet-Scott, Weilin Meng, Bulent Atahan, Hana Kiros, Misako Nishino & John Kartesz
Sustainable cities depend on urban forests. City trees -- a pillar of urban forests -- improve our health, clean the air, store CO2, and cool local temperatures. Comparatively less is known about urban forests as ecosystems, particularly their spatial composition, nativity statuses, biodiversity, and tree health. Here, we assembled and standardized a new dataset of N=5,660,237 trees from 63 of the largest US cities. The data comes from tree inventories conducted at the level of...

Data from: Species tree estimation and the impact of gene loss following whole-genome duplication

Liang Liu, Haifeng Xiong, Danying Wang, Chen Shao, Xuchen Yang, Jialin Yang, Tao Ma, Charles Davis & Zhenxiang Xi
Whole-genome duplication (WGD) has been demonstrated to occur broadly and repeatedly in the evolutionary history of eukaryotes, and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD, however, differential loss of paralogs may lead to spurious phylogenetic inference resulting...

Dopamine activity in the tail of the striatum, DeepLabCut and MoSeq during novel object exploration

Mitsuko Watabe-Uchida, Korleki Akiti, Iku Tsutsui-Kimura, Yudi Xie, Alexander Mathis, Jeffrey Markowitz, Rockwell Anyoha, Sandeep Robert Datta, Mackenzie Weygandt Mathis & Naoshige Uchida
In this study, we characterized dynamics of novelty exploration using multi-point tracking (DeepLabCut) and behavioral segmentation (MoSeq). Mice were habituated in an arena, and then a object was placed at the corner of the arena. We compared 4 groups of mice: one with presentation of a novel object (stimulus novelty), one with a presentation of a familiar object (contextual novelty), one with presentation of a novel object after ablation of dopamine neuorns that project to...

Additional file 5 of Candidate genes screening based on phenotypic observation and transcriptome analysis for double flower of Prunus mume

Huanhuan Zhu, Yan Shi, Junwei Zhang, Manzhu Bao & Jie Zhang
Additional file 5.

Registration Year

  • 2022
    321

Resource Types

  • Dataset
    321

Affiliations

  • Harvard University
    311
  • Shanghai Jiao Tong University
    128
  • Sichuan University
    124
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    119
  • Fudan University
    118
  • Jilin University
    111
  • Sun Yat-sen University
    108
  • Capital Medical University
    108
  • Chongqing Medical University
    108
  • West China Hospital of Sichuan University
    85