公开(公告)号：US20220112553A1

公开(公告)日：2022-04-14

申请号：US17500060

申请日：2021-10-13

Applicant: Massachusetts Institute of Technology ,  The Broad Institute, Inc.

Inventor： Edward S. Boyden ,  Fei Chen ,  Nikita Obidin ,  Andrew Colin Payne

IPC: C12Q1/6874 ,  C12Q1/6806

Abstract: Methods for single-molecule analysis of structure and sequence of linearized polynucleotides are provided.

公开(公告)号：US20170067096A1

公开(公告)日：2017-03-09

申请号：US15229539

申请日：2016-08-05

Applicant: Massachusetts Institute of Technology

Inventor： Asmamaw Wassie ,  Fei Chen ,  Edward Stuart Boyden ,  Shahar Alon

IPC: C12Q1/68

CPC classification number: C12Q1/6841 ,  C12Q1/6806 ,  G01N1/36 ,  G01N2001/364

Abstract: The invention enables in situ genomic and transcriptomic assessment of nucleic acids to be conducted in biological specimens that have been physically expanded. The invention leverages the techniques for expansion microscopy (ExM) to provide new methods for in situ genomic and transcriptomic assessment of nucleic in a new process referred to herein as “expansion fluorescent in situ hybridization” (ExFISH).

Abstract translation: 本发明使得能够在物理扩展的生物标本中进行核酸的原位基因组和转录组学评估。 本发明利用扩展显微镜技术（ExM）提供了在本文称为“扩增荧光原位杂交”（ExFISH）的新方法中对核酸进行原位基因组和转录组学评估的新方法。

公开(公告)号：US20160305856A1

公开(公告)日：2016-10-20

申请号：US15098799

申请日：2016-04-14

Applicant: Massachusetts Institute of Technology

Inventor： Edward Stuart Boyden ,  Jae-Byum Chang ,  Fei Chen ,  Paul Warren Tillberg

IPC: G01N1/30 ,  G01N33/58

CPC classification number: G01N33/582 ,  G01N1/36 ,  G01N1/4044 ,  G01N2001/302 ,  G01N2001/307

Abstract: The present invention leverages the techniques for expansion microscopy (ExM) to provide improved high-throughput super-resolution whole-organ imaging methodology to image protein architectures over whole organs with nanoscale resolution by using high-throughput microscopes in combination with samples that have been iteratively expanded more than once, in a method referred to herein as “iterative expansion microscopy” (iExM). In the ExM method, biological samples of interest are permeated with a swellable material that results in the sample becoming embedded in the swellable material, and then the sample can be expanded isotropically in three dimensions The process of iteratively expanding the samples can be applied to samples that have been already expanded using ExM techniques one or more additional times to iteratively expand them such that, for example, a 5-fold expanded specimen can be expanded again 3- to 4-fold, resulting in as much as a 17- to 19-fold or more linear expansion.

Abstract translation: 本发明利用扩展显微镜技术（ExM）来提供改进的高通量超分辨率全器官成像方法，以通过使用高通量显微镜与已经迭代的样品组合来对纳米尺度分辨率的整个器官进行成像蛋白质结构 在这里称为“迭代显微镜”（iExM）的方法中多次扩展。 在ExM方法中，感兴趣的生物样品渗透出可膨胀的材料，导致样品变得嵌入可溶胀材料中，然后样品可以在三维方向上各向同性地膨胀。迭代扩展样品的过程可以应用于样品 已经使用ExM技术已经扩展了一个或多个时间来迭代地扩展它们，使得例如5倍扩展的样本可以再次扩展3到4倍，导致17到19 倍或更多的线性膨胀。

公开(公告)号：US20230123513A1

公开(公告)日：2023-04-20

申请号：US17806879

申请日：2022-06-14

Applicant: Massachusetts Institute of Technology ,  The Broad Institute, Inc. ,  President and Fellows of Harvard College

Inventor： Kaiyi Jiang ,  Rohan Neil Krajeski ,  Omar Osama Abudayyeh ,  Jonathan S. Gootenberg ,  Yifan Zhang ,  Fei Chen ,  Xi Chen ,  Jeremy G. Koob

IPC: C12N15/113 ,  C12Q1/6897 ,  C12N15/10 ,  C12N9/78 ,  C12N9/50

Abstract: RNA editing tools for use in systems designed to measure RNA in vivo and manipulate specific cell types are disclosed herein. An RNA sensor system comprising a) a single-stranded RNA (ssRNA) sensor comprising a stop codon and a payload; optionally wherein the ssRNA sensor further comprises a normalizing gene; and b) an adenosine deaminase acting on RNA (ADAR) deaminase; wherein the sensor is capable of binding to a ssRNA target to form a double-stranded RNA (dsRNA) duplex that becomes a substrate for the ADAR deaminase; wherein the substrate comprises a mispairing within the stop codon; and wherein the mispairing is editable by the ADAR deaminase, which editing can effectively remove the stop codon so as to enable translation and expression of the payload. A method of quantifying ribonucleic acid (RNA) levels using the RNA sensor system is also disclosed.

公开(公告)号：US10526649B2

公开(公告)日：2020-01-07

申请号：US15789419

申请日：2017-10-20

Applicant: Massachusetts Institute of Technology ,  President and Fellows of Harvard College

Inventor： Fei Chen ,  Shahar Alon ,  Andrew Payne ,  Asmamaw Wassie ,  Daniel Goodwin ,  Edward Stuart Boyden ,  Evan Daugharthy ,  Jonathan Scheiman

IPC: C12Q1/6874 ,  C12Q1/6841

Abstract: The invention provides in situ nucleic acid sequencing to be conducted in biological specimens that have been physically expanded. The invention leverages the techniques for expansion microscopy (ExM) to provide new methods for in situ sequencing of nucleic acids in a process referred to herein as “expansion sequencing” (ExSEQ).

公开(公告)号：US10317321B2

公开(公告)日：2019-06-11

申请号：US15229545

申请日：2016-08-05

Applicant: Massachusetts Institute of Technology

Inventor： Paul Warren Tillberg ,  Fei Chen ,  Edward Stuart Boyden ,  Chih-Chieh Yu

IPC: G01N1/30 ,  G01N1/36 ,  G01N33/58 ,  G01N33/68

Abstract: The invention provides a method termed protein retention ExM (proExM), in which proteins, rather than labels, are anchored to the swellable gel, using a cross-linking molecule. This proExM strategy can be used to perform nanoscale imaging of immunostained cells and tissues as well as samples expressing various FPs as fluorescent signals from genetically encoded fluorescent proteins and/or conventional fluorescently labeled secondary antibodies and streptavidin that are directly anchored to the gel are preserved even when subjected to the nonspecific proteolytic digestion.

公开(公告)号：US20190032128A1

公开(公告)日：2019-01-31

申请号：US16043950

申请日：2018-07-24

Applicant: Massachusetts Institute of Technology ,  President and Fellows of Harvard College

Inventor： Fei Chen ,  Andrew C. Payne ,  Jason D. Buenrostro ,  Paul Reginato ,  Edward Stuart Boyden

IPC: C12Q1/6874 ,  C12N15/10

Abstract: The present invention provides methods for analyzing polynucleotides such as genomic DNA. In some embodiments, the disclosure provides a method for preparing and amplifying a genomic DNA library in situ in a fixed biological sample. The method comprises treating a fixed biological sample with an insertional enzyme complex to produce tagged fragments of genomic DNA. The method further comprises circularizing the tagged fragments of genomic DNA. The method further comprises amplifying the tagged fragments of genomic DNA.

公开(公告)号：US20180119219A1

公开(公告)日：2018-05-03

申请号：US15789419

申请日：2017-10-20

Applicant: Massachusetts Institute of Technology

Inventor： Fei Chen ,  Shahar Alon ,  Andrew Payne ,  Asmamaw Wassie ,  Daniel Goodwin ,  Edward Stuart Boyden

IPC: C12Q1/6874

CPC classification number: C12Q1/6874 ,  C12Q1/6841 ,  C12Q2545/113

Abstract: The invention provides in situ nucleic acid sequencing to be conducted in biological specimens that have been physically expanded. The invention leverages the techniques for expansion microscopy (ExM) to provide new methods for in situ sequencing of nucleic acids in a process referred to herein as “expansion sequencing” (ExSEQ).

公开(公告)号：US20170089811A1

公开(公告)日：2017-03-30

申请号：US15229545

申请日：2016-08-05

Applicant: Massachusetts Institute of Technology

Inventor： Paul Warren Tillberg ,  Fei Chen ,  Edward Stuart Boyden ,  Chih-Chieh Yu

IPC: G01N1/30 ,  G01N33/58

CPC classification number: G01N1/30 ,  G01N1/36 ,  G01N33/582 ,  G01N33/6803 ,  G01N2001/302 ,  G01N2001/307 ,  G01N2333/95

Abstract: The invention provides a method termed protein retention ExM (proExM), in which proteins, rather than labels, are anchored to the swellable gel, using a cross-linking molecule. This proExM strategy can be used to perform nanoscale imaging of immunostained cells and tissues as well as samples expressing various FPs as fluorescent signals from genetically encoded fluorescent proteins and/or conventional fluorescently labeled secondary antibodies and streptavidin that are directly anchored to the gel are preserved even when subjected to the nonspecific proteolytic digestion.