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1. 发明专利

IL271454D0 High-throughput single-cell sequencing with reduced amplification bias 未知
公开(公告)号：IL271454D0
公开(公告)日：2020-01-30
申请号：IL27145419
申请日：2019-12-15
申请人： ILLUMINA INC , STEEMERS FRANK J , UNIV WASHINGTON , SHENDURE JAY , YIN YI
发明人： STEEMERS FRANK J , SHENDURE JAY , YIN YI
IPC分类号： C12N20060101
摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the methods include linear amplification of the nucleic acids. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences

2. 发明专利

IL272234D0 High-throughput single-cell transcriptome libraries and methods of making and of using 未知
公开(公告)号：IL272234D0
公开(公告)日：2020-03-31
申请号：IL27223420
申请日：2020-01-24
申请人： ILLUMINA INC , STEEMERS FRANK J , UNIV WASHINGTON , SHENDURE JAY , CAO JUNYUE
发明人： STEEMERS FRANK J , SHENDURE JAY , CAO JUNYUE
摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes nucleic acids that represent the whole transcriptomes from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences.

3. 发明专利

AU2019282158A1 High-throughput single-cell transcriptome libraries and methods of making and of using 未知
公开(公告)号：AU2019282158A1
公开(公告)日：2020-01-16
申请号：AU2019282158
申请日：2019-06-04
申请人： CAO JUNYUE , ILLUMINA INC , SHENDURE JAY , UNIV WASHINGTON
发明人： SHENDURE JAY , CAO JUNYUE , STEEMERS FRANK J
IPC分类号： C12N1/00
摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes nucleic acids that represent the whole transcriptomes from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences.

4. 发明公开

EP3049557A4 METHODS AND SYSTEMS FOR LARGE SCALE SCAFFOLDING OF GENOME ASSEMBLIES 有权转让
标题翻译： VERFAHREN UND SYSTEMEFÜRGROSS ANGELEGTES SCAFFOLDING VON GENOMASSEMBLIERUNGEN
公开(公告)号：EP3049557A4
公开(公告)日：2017-06-14
申请号：EP14846949
申请日：2014-09-27
申请人： SHENDURE JAY , ADEY ANDREW , BURTON JOSHUA , KITZMAN JACOB , DUNHAM MAITREYE J , LIACHKO IVAN
发明人： SHENDURE JAY , ADEY ANDREW , BURTON JOSHUA , KITZMAN JACOB , DUNHAM MAITREYE J , LIACHKO IVAN
IPC分类号： G06F19/22 , C40B20/00 , C40B20/04 , C40B40/06 , G06F19/18
CPC分类号： G06F19/12 , G06F19/18 , G06F19/22
摘要： Computational methods used for large scale scaffolding of a genome assembly are provided. Such methods may include a step of applying a location clustering model to a test set of contigs to form two or more location cluster groups, each location cluster group comprising one or more location-clustered contigs; a step of applying an ordering model to each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group; and a step of applying an orienting model to each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group. In some aspects, the test set of contigs are generated from aligning a set of reads generated by a chromosome conformation analysis technique (e.g., Hi-C) with a draft assembly, a reference assembly, or both.
摘要翻译：提供了用于大规模基因组组装的脚手架的计算方法。这样的方法可以包括将位置聚类模型应用于重叠群的测试集合以形成两个或更多个位置聚类组的步骤，每个位置聚类组包括一个或更多位置聚类重叠群; 将排序模型应用于所述两个或更多个位置簇组中的每一个以形成每个簇群内的一个或更多个位置群集重叠群的有序集合的步骤; 以及将定向模型应用于每个有序集合的一个或多个位置聚类重叠群以向每个位置聚类群组内的每个位置聚类重叠群分配相对定向的步骤。在一些方面，通过将由染色体构象分析技术（例如，Hi-C）产生的一组读数与草案组件，参考组件或两者对齐来生成重叠群测试集。

5. 发明专利

BR112021019640A2 Bibliotecas de células únicas de alto rendimento e métodos de preparo e uso 未知
公开(公告)号：BR112021019640A2
公开(公告)日：2022-06-21
申请号：BR112021019640
申请日：2020-12-18
申请人： ILLUMINA INC , UNIV WASHINGTON
发明人： CUSANOVICH DARREN , STEEMERS FRANK , SHENDURE JAY , DAZA RIZA
IPC分类号： C12N15/10
摘要： bibliotecas de células únicas de alto rendimento e métodos de preparo e uso. a presente invenção se refere a métodos para preparar uma biblioteca de sequenciamento que inclui ácidos nucleicos de uma pluralidade de células únicas. em uma modalidade, a biblioteca de sequenciamento inclui ácidos nucleicos que representam a acessibilidade à cromatina a partir da pluralidade de células únicas. em uma modalidade, os ácidos nucleicos incluem três sequências de índice. em outra modalidade, a presente revelação fornece métodos para caracterizar eventos raros em células e núcleos isolados.

6. 发明专利

BR112019027750A2 Bibliotecas transcriptônicas de célula única altorendimento, e métodos de fabricação e de usos 未知
公开(公告)号：BR112019027750A2
公开(公告)日：2022-06-14
申请号：BR112019027750
申请日：2019-06-04
申请人： ILLUMINA INC , JAY SHENDURE , JUNYUE CAO , UNIV WASHINGTON
发明人： FRANK J STEEMERS , SHENDURE JAY , CAO JUNYUE
IPC分类号： C12N15/10 , C12Q1/6806 , C12Q1/6813 , C12Q1/6816 , C12Q1/6844 , C12Q1/6869
摘要： bibliotecas transcriptônicas de célula única alto-rendimento, e métodos de fabricação e de usos. são aqui fornecidos métodos para preparar uma biblioteca de sequenciamento que inclui ácidos nucleicos de uma pluralidade de células únicas. em uma concretização, a biblioteca de sequenciamento inclui ácidos nucleicos que representam os transcriptomas inteiros da pluralidade de células únicas. em uma concretização, os ácidos nucleicos incluem três sequências índice. também são fornecidas aqui composições, tais como composições que incluem os ácidos nucleicos com três sequências índice.

7. 发明专利

AU2020407641A1 High-throughput single-cell libraries and methods of making and of using 未知
公开(公告)号：AU2020407641A1
公开(公告)日：2021-09-23
申请号：AU2020407641
申请日：2020-12-18
申请人： ILLUMINA INC , UNIV WASHINGTON
发明人： SHENDURE JAY , CUSANOVICH DARREN , DAZA RIZA , STEEMERS FRANK
IPC分类号： C12N15/10
摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes nucleic acids that represent the chromatin accessibility from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. In another embodiment, the present disclosure provides methods for characterizing rare events in isolated cells and nuclei.

8. 发明专利

AU2022202739A1 High-Throughput Single-Cell Sequencing With Reduced Amplification Bias 未知
公开(公告)号：AU2022202739A1
公开(公告)日：2022-05-19
申请号：AU2022202739
申请日：2022-04-26
申请人： ILLUMINA INC , UNIV WASHINGTON
发明人： SHENDURE JAY , YIN YI , STEEMERS FRANK
IPC分类号： C12Q1/68
摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the methods include linear amplification of the nucleic acids. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences.

9. 发明专利

AU2020232618A1 High-throughput single-nuclei and single-cell libraries and methods of making and of using 未知
公开(公告)号：AU2020232618A1
公开(公告)日：2021-04-08
申请号：AU2020232618
申请日：2020-03-02
申请人： ILLUMINA INC , UNIV WASHINGTON
发明人： SRIVATSAN SANJAY , MCFALINE-FIGUEROA JOSE , RAMANI VIJAY , CAO JUNYUE , BOOTH GREGORY , SHENDURE JAY , TRAPNELL COLE , STEEMERS FRANK J
IPC分类号： C12N15/10
摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the method includes nuclear or cellular hashing which permits increased sample throughput and increased doublet detection at high collision rates. In one embodiment, the method includes normalization hashing which aids in estimating and removing technical noise in cell to cell variation and increases sensitivity and specificity.

10. 发明专利

AU2019270185A1 High-throughput single-cell sequencing with reduced amplification bias 未知
公开(公告)号：AU2019270185A1
公开(公告)日：2020-01-16
申请号：AU2019270185
申请日：2019-05-17
申请人： ILLUMINA INC , UNIV WASHINGTON
发明人： SHENDURE JAY , YIN YI , STEEMERS FRANK J
IPC分类号： C12Q1/68
摘要： Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the methods include linear amplification of the nucleic acids. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences

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