New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, wh...New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process;2) adaptation and development of new protocols for sample preparation;3) the assignment of a degree of confidence to the data generated;and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.展开更多
In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower...In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.展开更多
In this paper, a new partial transmit sequence（PTS）scheme with low computational complexity is proposed for the problems of high computational complexity in the conventional PTS method. By analyzing the relationship...In this paper, a new partial transmit sequence（PTS）scheme with low computational complexity is proposed for the problems of high computational complexity in the conventional PTS method. By analyzing the relationship of candidate sequences in the PTS method under the interleaved partition method, it has been discovered that some candidate sequences generated by phase factor sequences have the same peak average power ratio（PAPR）. Hence, phase factor sequences can be optimized to reduce their searching times. Then, the computational process of generating candidate sequences can be simplified by improving the utilization of data and minimizing the calculations of complex multiplication. The performance analysis shows that, compared with the conventional PTS scheme, the proposed approach significantly decreases the computational complexity and has no loss of PAPR performance.展开更多
Efforts have been made to establish various human pluripotent stem cell lines.However,such methods have not yet been duplicated in non-human primate cells.Here,we introduce a multiplexed single-cell sequencing techniq...Efforts have been made to establish various human pluripotent stem cell lines.However,such methods have not yet been duplicated in non-human primate cells.Here,we introduce a multiplexed single-cell sequencing technique to profile the molecular features of monkey pluripotent stem cells in published culture conditions.The results demonstrate suboptimized maintenance of pluripotency and show that the selected signaling pathways for resetting human stem cells can also be interpreted for establishing monkey cell lines.Overall,this work legitimates the translation of novel human cell line culture conditions to monkey cells and provides guidance for exploring chemical cocktails for monkey stem cell line derivation.展开更多
This paper deals with optimal training design and placement over multiple orthogonal frequency division multiplexing(OFDM) symbols for the least squares(LS) channel estimation in multiple-input multipleoutput(MIMO) OF...This paper deals with optimal training design and placement over multiple orthogonal frequency division multiplexing(OFDM) symbols for the least squares(LS) channel estimation in multiple-input multipleoutput(MIMO) OFDM systems.First,the optimal pilot sequences over multiple OFDM symbols are derived by co-cyclic Jacket matrices based on the minimum mean square error(MSE) of the LS channel estimation.Then,an enhanced channel estimation method using sliding window is proposed to improve further the performance for the optimal pilot sequences in fast-varying channels.Simulation results show that the enhancedmethod can efficiently improve the performances for the optimal pilot sequences over two and four OFDM symbols,especially in fast-varying channels.展开更多
Partial transmit sequence (PTS) is a promising technique for peak-to-average power ratio (PAPR) re-duction in orthogonal frequency division multiplexing (OFDM). While in optimal PTS, an exhaustive search for all combi...Partial transmit sequence (PTS) is a promising technique for peak-to-average power ratio (PAPR) re-duction in orthogonal frequency division multiplexing (OFDM). While in optimal PTS, an exhaustive search for all combinations of phase factor sequences is required, this results in huge computation. In this paper, by introducing the orthogonal design, a phase factor sequences algorithm is proposed. The algorithm uses orthogonal table to gen-erate phase factor sequences, and the regular PAPR computation result is then followed by the parameter estima-tion. The simulation result shows that the proposed algorithm reduces the computation notably and obtains a good PAPR performance approaching the optimal PTS.展开更多
本研究根据公开发表的烟草K326基因组和烟草430K SNP固相芯片检测数据,以7份种质两两组合之间每条染色体上20个多态标记为目标,基于多重PCR扩增的精准定位测序分型技术(mGPS,Genotyping by Pinpoint Sequencing of multiplex PCR produc...本研究根据公开发表的烟草K326基因组和烟草430K SNP固相芯片检测数据,以7份种质两两组合之间每条染色体上20个多态标记为目标,基于多重PCR扩增的精准定位测序分型技术(mGPS,Genotyping by Pinpoint Sequencing of multiplex PCR products)开发出烟草1.8K育种液相芯片(YT1.8K.1)。利用该芯片对上述7份种质两两之间杂交的21个杂交组合进行基因分型检测,每个杂交组合之间的平均差异位点数为650个,能同时满足每个组合定向改良筛选高遗传背景回复率单株的需要。利用该芯片对23个烟草品种进行基因型分型检测和聚类分析,聚类分类结果与品种系谱基本吻合;利用该芯片从367个BC2F1群体中筛选出5个背景回复率高于94.96%的单株,高于理论均值87.5%,表明该育种芯片可应用于烟草种质资源聚类分析、定向改良育种的遗传背景筛选。展开更多
建立A组轮状病毒(Group A rotavirus,RVA)全基因组单管多重RT⁃PCR扩增方法,并比较其与双链cDNA合成方法在RVA临床标本全基因组二代测序中的应用。对2022年某哨点医院的18份腹泻住院患儿RVA阳性粪便标本进行核酸提取,分别用单管多重RT⁃PC...建立A组轮状病毒(Group A rotavirus,RVA)全基因组单管多重RT⁃PCR扩增方法,并比较其与双链cDNA合成方法在RVA临床标本全基因组二代测序中的应用。对2022年某哨点医院的18份腹泻住院患儿RVA阳性粪便标本进行核酸提取,分别用单管多重RT⁃PCR扩增方法对RVA全基因组进行扩增,用随机引物对病毒核酸进行反转录及双链cDNA合成,最后采用Illumina平台对这2种不同类型的产物进行二代测序。用CLC软件对测序数据进行拼接,分析有效数据量、测序深度及全基因组覆盖度等参数,并用IGV软件查看全基因组测序深度覆盖轨迹。多重RT⁃PCR扩增产物测序和双链cDNA测序获得的RVA有效数据量分别为69.39%~99.83%和0.38%~92.99%,平均测序深度分别为10172×~68156×和35×~61783×,全基因组测序深度10×以上的位点覆盖度分别为98.93%~100.00%和86.28%~100.00%。从全基因组测序深度情况来看,多重RT⁃PCR扩增产物测序在同一个基因节段内部测序深度较为均匀,在11个节段之间测序深度差别较大;而双链cDNA测序在不同基因节段之间的测序深度较为均匀,但同一个基因节段内部靠近5'和3'末端测序深度较低。2种方法所获得的病毒核苷酸序列基本一致,部分基因节段在5'或3'末端100 bp区域内存在2个以内的核苷酸位点差异。在多重RT⁃PCR扩增方法中鉴于引物在不同基因型别间的特异性,对本研究中未涉及到的基因型别的扩增效率还有待进一步验证。单管多重RT⁃PCR扩增方法和双链cDNA合成方法虽然各有优缺点,但均适用于轮状病毒全基因组二代测序在基层的推广。展开更多
文摘New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process;2) adaptation and development of new protocols for sample preparation;3) the assignment of a degree of confidence to the data generated;and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.
文摘In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.
基金supported by the National Natural Science Foundation of China(6167309361370152)the Science and Technology Project of Shenyang(F16-205-1-01)
文摘In this paper, a new partial transmit sequence（PTS）scheme with low computational complexity is proposed for the problems of high computational complexity in the conventional PTS method. By analyzing the relationship of candidate sequences in the PTS method under the interleaved partition method, it has been discovered that some candidate sequences generated by phase factor sequences have the same peak average power ratio（PAPR）. Hence, phase factor sequences can be optimized to reduce their searching times. Then, the computational process of generating candidate sequences can be simplified by improving the utilization of data and minimizing the calculations of complex multiplication. The performance analysis shows that, compared with the conventional PTS scheme, the proposed approach significantly decreases the computational complexity and has no loss of PAPR performance.
基金supported by the National Key R&D Program of China(Nos.2021YFA0805700 and 2021YFA1102000)the National Natural Science Foundation of China(No.U2102204)the Natural Science Foundation of Yunnan Province,China(Nos.202001BC070001 and 202102AA100053)。
文摘Efforts have been made to establish various human pluripotent stem cell lines.However,such methods have not yet been duplicated in non-human primate cells.Here,we introduce a multiplexed single-cell sequencing technique to profile the molecular features of monkey pluripotent stem cells in published culture conditions.The results demonstrate suboptimized maintenance of pluripotency and show that the selected signaling pathways for resetting human stem cells can also be interpreted for establishing monkey cell lines.Overall,this work legitimates the translation of novel human cell line culture conditions to monkey cells and provides guidance for exploring chemical cocktails for monkey stem cell line derivation.
基金the National Natural Science Foundation of China (Nos. 60332030 and 60625103)the Science and Technology Commission of Shanghai Municipality (STCSM) (No. 05DZ22102)the National High Technology Research and Development Program(863) of China (No. 2007AA01Z237)
文摘This paper deals with optimal training design and placement over multiple orthogonal frequency division multiplexing(OFDM) symbols for the least squares(LS) channel estimation in multiple-input multipleoutput(MIMO) OFDM systems.First,the optimal pilot sequences over multiple OFDM symbols are derived by co-cyclic Jacket matrices based on the minimum mean square error(MSE) of the LS channel estimation.Then,an enhanced channel estimation method using sliding window is proposed to improve further the performance for the optimal pilot sequences in fast-varying channels.Simulation results show that the enhancedmethod can efficiently improve the performances for the optimal pilot sequences over two and four OFDM symbols,especially in fast-varying channels.
基金Supported by Tianjin Natural Science Foundation (No. 043600611)Key Scientific and Technological Training Program of Tianjin (No. 043102911).
文摘Partial transmit sequence (PTS) is a promising technique for peak-to-average power ratio (PAPR) re-duction in orthogonal frequency division multiplexing (OFDM). While in optimal PTS, an exhaustive search for all combinations of phase factor sequences is required, this results in huge computation. In this paper, by introducing the orthogonal design, a phase factor sequences algorithm is proposed. The algorithm uses orthogonal table to gen-erate phase factor sequences, and the regular PAPR computation result is then followed by the parameter estima-tion. The simulation result shows that the proposed algorithm reduces the computation notably and obtains a good PAPR performance approaching the optimal PTS.
文摘本研究根据公开发表的烟草K326基因组和烟草430K SNP固相芯片检测数据,以7份种质两两组合之间每条染色体上20个多态标记为目标,基于多重PCR扩增的精准定位测序分型技术(mGPS,Genotyping by Pinpoint Sequencing of multiplex PCR products)开发出烟草1.8K育种液相芯片(YT1.8K.1)。利用该芯片对上述7份种质两两之间杂交的21个杂交组合进行基因分型检测,每个杂交组合之间的平均差异位点数为650个,能同时满足每个组合定向改良筛选高遗传背景回复率单株的需要。利用该芯片对23个烟草品种进行基因型分型检测和聚类分析,聚类分类结果与品种系谱基本吻合;利用该芯片从367个BC2F1群体中筛选出5个背景回复率高于94.96%的单株,高于理论均值87.5%,表明该育种芯片可应用于烟草种质资源聚类分析、定向改良育种的遗传背景筛选。
文摘建立A组轮状病毒(Group A rotavirus,RVA)全基因组单管多重RT⁃PCR扩增方法,并比较其与双链cDNA合成方法在RVA临床标本全基因组二代测序中的应用。对2022年某哨点医院的18份腹泻住院患儿RVA阳性粪便标本进行核酸提取,分别用单管多重RT⁃PCR扩增方法对RVA全基因组进行扩增,用随机引物对病毒核酸进行反转录及双链cDNA合成,最后采用Illumina平台对这2种不同类型的产物进行二代测序。用CLC软件对测序数据进行拼接,分析有效数据量、测序深度及全基因组覆盖度等参数,并用IGV软件查看全基因组测序深度覆盖轨迹。多重RT⁃PCR扩增产物测序和双链cDNA测序获得的RVA有效数据量分别为69.39%~99.83%和0.38%~92.99%,平均测序深度分别为10172×~68156×和35×~61783×,全基因组测序深度10×以上的位点覆盖度分别为98.93%~100.00%和86.28%~100.00%。从全基因组测序深度情况来看,多重RT⁃PCR扩增产物测序在同一个基因节段内部测序深度较为均匀,在11个节段之间测序深度差别较大;而双链cDNA测序在不同基因节段之间的测序深度较为均匀,但同一个基因节段内部靠近5'和3'末端测序深度较低。2种方法所获得的病毒核苷酸序列基本一致,部分基因节段在5'或3'末端100 bp区域内存在2个以内的核苷酸位点差异。在多重RT⁃PCR扩增方法中鉴于引物在不同基因型别间的特异性,对本研究中未涉及到的基因型别的扩增效率还有待进一步验证。单管多重RT⁃PCR扩增方法和双链cDNA合成方法虽然各有优缺点,但均适用于轮状病毒全基因组二代测序在基层的推广。
