962 Works

Data from: Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement

Jun Huang, Youjun Gao, Haitao Jia, Lei Liu, Dan Zhang & Zuxin Zhang
Background: Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement. Results In maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By...

Data from: Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

Weidong Chen, Renuka N. Attanayake, Vidhura Tennekoon, Dennis A. Johnson, Lyndon D. Porter, Luis Del Río-Mendoza & Daohong Jiang
The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, 8 population samples comprising 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for...

Data from: Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs

Chao Wang, Hongyang Wang, Yu Zhang, Zhonglin Tang, Kui Li & Bang Liu
Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome-wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions...

Circular RNA ZFR accelerates non-small cell lung cancer progression by acting as a miR-101-3p sponge to enhance CUL4B expression

Haifeng Zhang, Xiaolong Wang, Baoli Hu, Feng Zhang, Haitao Wei & Li Li
Non-small-cell lung carcinoma (NSCLC) is the most common type of lung cancer. Circular RNA ZFR (circZFR) is an identified circular RNA (circRNA) that is correlated with cancer progression. However, the role of circZFR in NSCLC remains unknown. In the present study, we aimed to investigate the function of circZFR in NSCLC and the underlying mechanism. The expression patterns of circZFR were determined using qRT-PCR in NSCLC samples and cell lines. The subcellular distribution of circZFR...

Circular RNA ZFR accelerates non-small cell lung cancer progression by acting as a miR-101-3p sponge to enhance CUL4B expression

Haifeng Zhang, Xiaolong Wang, Baoli Hu, Feng Zhang, Haitao Wei & Li Li
Non-small-cell lung carcinoma (NSCLC) is the most common type of lung cancer. Circular RNA ZFR (circZFR) is an identified circular RNA (circRNA) that is correlated with cancer progression. However, the role of circZFR in NSCLC remains unknown. In the present study, we aimed to investigate the function of circZFR in NSCLC and the underlying mechanism. The expression patterns of circZFR were determined using qRT-PCR in NSCLC samples and cell lines. The subcellular distribution of circZFR...

BNIP3L/NIX degradation leads to mitophagy deficiency in ischemic brains

Xiaoli Wu, Yanrong Zheng, Mengru Liu, Yue Li, Shijia Ma, Weidong Tang, Wenping Yan, Ming Cao, Wanqing Zheng, Lei Jiang, Jiaying Wu, Feng Han, Zhenghong Qin, Liang Fang, Weiwei Hu, Zhong Chen & Xiangnan Zhang
Mitophagy, the elimination of damaged mitochondria through autophagy, promotes neuronal survival in cerebral ischemia. Previous studies found deficient mitophagy in ischemic neurons, but the mechanisms are still largely unknown. We determined that BNIP3L/NIX, a mitophagy receptor, was degraded by proteasomes, which led to mitophagy deficiency in both ischemic neurons and brains. BNIP3L exists as a monomer and homodimer in mammalian cells, but the effects of homodimer and monomer on mitophagy are unclear. Site-specific mutations in...

Additional file 1 of Revealing the characteristics of ZIKV infection through tissue-specific transcriptome sequencing analysis

Zhi-lu Chen, Zuo-jing Yin, Tian-yi Qiu, Jian Chen, Jian Liu, Xiao-yan Zhang & Jian-qing Xu
Additional file 1.

Additional file 6 of CCHCR1-astrin interaction promotes centriole duplication through recruitment of CEP72

Zhenguang Ying, Kaifang Wang, Junfeng Wu, Mingyu Wang, Jing Yang, Xia Wang, Guowei Zhou, Haibin Chen, Hongwu Xu, Stephen Cho Wing Sze, Feng Gao, Chunman Li & Ou Sha
Additional file 6. Individual data values. Raw data of Fig. 3A,B,F,G,7C and 7I.

Additional file 1 of Surface fungal diversity and several mycotoxin-related genes’ expression profiles during the Lunar Palace 365 experiment

Jianlou Yang, Zikai Hao, Lantao Zhang, Yuming Fu & Hong Liu
Additional file 1: Supplementary Table S1. qPCR primer sequences, mycotoxin types, producers, and toxic effects in humans. Supplementary Table S2. ASV abundances and potential ecological functions (F01-F70). Supplementary Table S3. ISS dust, AIT, ILMAH, and LP1 surfaces merged fungal ASV table. Supplementary Table S4. Species abundance tables at the phylum level. Supplementary Table S5. Species abundance tables at the genus level. Supplementary Table S6. Trophic modes of the fungal microbiome in the different crew groups...

Additional file 4 of Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Huanhuan Xie, Lei Zhang, Cheng Zhang, Hong Chang, Zhenxiang Xi & Xiaoting Xu
Additional file 4: Table S1. GC content of the CPGs of the six subgenus Gynopodium species.

Additional file 4 of Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Huanhuan Xie, Lei Zhang, Cheng Zhang, Hong Chang, Zhenxiang Xi & Xiaoting Xu
Additional file 4: Table S1. GC content of the CPGs of the six subgenus Gynopodium species.

Additional file 6 of Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Huanhuan Xie, Lei Zhang, Cheng Zhang, Hong Chang, Zhenxiang Xi & Xiaoting Xu
Additional file 6: Table S3. List of SSRs in the CPGs of six subgenus Gynopodium species.

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 4 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

Erbao Chen, Jing Yi, Jing Jiang, Zhilin Zou, Yuqian Mo, Qingqi Ren, Zewei Lin, Yi Lu, Jian Zhang & Jikui Liu
Additional file4: Supplementary excel 4. The mutation profiles in the TCGA LIHC cohort.

Additional file 4 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

Erbao Chen, Jing Yi, Jing Jiang, Zhilin Zou, Yuqian Mo, Qingqi Ren, Zewei Lin, Yi Lu, Jian Zhang & Jikui Liu
Additional file4: Supplementary excel 4. The mutation profiles in the TCGA LIHC cohort.

RIOK3-Mediated Akt phosphorylation facilitates synergistic replication of Marek’s disease and reticuloendotheliosis viruses

Xusheng Du, Defang Zhou, Jing Zhou, Jingwen Xue & Ziqiang Cheng
Co-infection of Marek’s disease virus (MDV) and reticuloendotheliosis virus (REV) synergistically drives disease progression, yet little is known about the mechanism of the synergism. Here, we found that co-infection of REV and MDV increased their replication via the RIOK3-Akt pathway. Initially, we noticed that the viral titres of MDV and REV significantly increased in REV and MDV co-infected cells compared with single-infected cells. Furthermore, tandem mass tag peptide labelling coupled with LC/MS analysis showed that...

Circular RNA–microRNA–mRNA network identified circ_0007618 and circ_0029426 as new valuable biomarkers for lung adenocarcinoma

Qiang Zhang, Yungang Sun, Zhao Wang & Feng Shao
Circular RNAs (circRNAs) are involved in multiple physiological processes. However, whether circRNAs function as the indicators of lung adenocarcinoma (LUAD) remains unclear. Three LUAD-related microarray datasets were downloaded from the Gene Expression Omnibus database, and overlapping differentially expressed circRNAs (DECs) in LUAD were identified. circ_0007618 and circ_0029426 were revealed to be significantly dysregulated in LUAD and verified in LUAD tissues and serum obtained in this study. Subsequently, the overall survival curve and receiver operating characteristics...

Transcriptome analysis of strawberry (Fragaria × ananasa) responsive to Colletotrichum gloeosporioides inoculation and mining of resistance genes

Wenwei Liang, Mingjie Wang, Binghao Du, Lei Ling, Yingdong Bi, Jinghua Zhang, Yimin Sun, Shuang Zhou, Lili Zhang, Xiao Ma, Jun Ma, Liren Wu & Changhong Guo
Strawberry has high nutritional and economic value and is an important horticultural crop widely cultivated worldwide. Strawberry anthracnose is the most harmful disease in strawberry production, which causes huge production losses every year. Mining disease resistance genes and breeding high-quality strawberry varieties are the fundamental way to solve the problem of strawberry anthracnose. In this study, transcriptome analysis and disease resistance-related genes mining were targeted on strawberry anthracnose. The main results are as follows: (1)...

Additional file 9 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 9: Table S4. The 21 prognositc DE-MRGs based on the TCGA GBM cohort.

Additional file 10 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 10: Table S5. GO enrichment analysis by using DAVID.

Additional file 5 of Identification of TLN1 as a prognostic biomarker to effect cell proliferation and differentiation in acute myeloid leukemia

Di Cui, Xilong Cui, Xiaoliang Xu, Wenjing Zhang, Yu Yu, Yingxin Gao, Chuanzhong Mei & Weiwei Zheng
Additional file 5.

Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits

Xiaoyang Lv, Weihao Chen, Shanhe Wang, Xiukai Cao, Zehu Yuan, Tesfaye Getachew, Joram M. Mwacharo, Aynalem Haile & Wei Sun
Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (Fst) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in...

Additional file 2 of Novel six-gene prognostic signature based on colon adenocarcinoma immune-related genes

Rui Zhou, Zhuowei Gao & Yongle Ju
Additional file2. Table S2: DEIGs (multivariate Cox regression analysis) and regression coefficient.

Data from \" Chemical Origin of Temperature-Dependent Phase Transition and Conductivity in Hydroxyapatite\"

Dingguo Xu & Jing Wang
This dataset contains data relates to the publication " Chemical Origin of Temperature-Dependent Phase Transition and Conductivity in Hydroxyapatite", by Wang et al., 2022. In this work, we use deep potential molecular dynamics simulation to study Temperature-Dependent Phase Transition and Conductivity in Hydroxyapatite. The deep neural network potential is trained on DFT calculations. This dataset contains the deep potential models and the DFT training data reported in the publication, the input files of vasp, lammps,...

Flexible hyperspectral surface plasmon resonance microscopy

Ziwei Liu, Jingning Wu, Chen Cai, Bo Yang & Zhi-mei Qi
Dataset of the raw hyperspectral SPR datacube supporting the article titled 'Flexible Hyperspectral Surface Plasmon Resonance Microscopy'.

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