Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells

Nature Protocols
Lixin Wang, Kevin A Janes

Abstract

Single-cell variations in gene and protein expression are important during development and disease. Such cell-to-cell heterogeneities can be directly inspected one cell at a time, but global methods are usually not sensitive enough to work with the starting material of a single cell. Here we provide a detailed protocol for stochastic profiling, a method that infers single-cell regulatory heterogeneities by repeatedly sampling small collections of cells selected at random. Repeated stochastic sampling is performed by laser-capture microdissection or limiting dilution, followed by careful exponential cDNA amplification, hybridization to microarrays and statistical analysis. Stochastic profiling surveys the transcriptome for programs that are heterogeneously regulated among cellular subpopulations in their native tissue context. The protocol is readily optimized for specific biological applications and takes about 1 week to complete.

References

Jan 7, 2014·Nature Materials·Jing GuoYing Jiang
Mar 19, 2013·Nature Nanotechnology·Georg Heimel, Jean-Luc Brédas
Jul 16, 2014·PeerJ·Linda E KippnerMelissa L Kemp
Sep 1, 2014·Nature Nanotechnology·Mickael L PerrinHerre S J van der Zant
Jul 24, 2014·Nucleic Acids Research·Antoine-Emmanuel SalibaJörg Vogel
Jan 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Sameer S BajikarKevin A Janes
Jun 21, 2016·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Vladimir Espinosa Angarica, Antonio Del Sol
Jul 22, 2016·PLoS Computational Biology·Manikandan NarayananJohn S Tsang
Sep 10, 2017·Cell and Tissue Research·Ting Zhou, Hiroaki Matsunami
Apr 9, 2015·Science Signaling·Kevin A Janes
Mar 22, 2019·Scientific Reports·Shambhavi SinghKevin A Janes

Citations

Jan 1, 1993·Methods in Enzymology·G Brady, Norman N Iscove
Nov 8, 1996·Science·M R Emmert-BuckLance A Liotta
Jan 23, 1999·The American Journal of Pathology·F FendM Raffeld
Mar 30, 2002·Nature Biotechnology·Christoph A KleinGert Riethmüller
Apr 23, 2002·Nature Genetics·Ertugrul M OzbudakAlexander van Oudenaarden
Aug 17, 2002·Science·Michael B ElowitzPeter S Swain
Mar 15, 2003·Developmental Cell·Ming-Ko Chiang, Douglas A Melton
Apr 30, 2003·Neuron·Ian TietjenCatherine Dulac
Jan 17, 2004·Clinical Chemistry·Anders StåhlbergMikael Kubista
May 5, 2004·PLoS Biology·Hunter B FraserMichael B Eisen
Jul 22, 2004·Analytical Biochemistry·W Gregory CoxJerry L Ruth
Dec 20, 2005·Cell·Ido GoldingEdward C Cox
Apr 15, 2006·Science·X Sunney XieWei Yuan Yang
Oct 3, 2006·PLoS Genetics·Carlos A RamosMargaret A Goodell
Oct 21, 2006·Proceedings of the National Academy of Sciences of the United States of America·Roger A O'NeillPeter B Vander Horn
Oct 31, 2006·Nucleic Acids Research·Claudia H Hartmann, Christoph A Klein
Nov 14, 2006·Proceedings of the National Academy of Sciences of the United States of America·Luigi WarrenStephen R Quake
Feb 28, 2007·Genome Biology·Shobhit GuptaWilliam Stafford Noble
Apr 5, 2007·Nature Protocols·Virginia EspinaLance A Liotta
Apr 5, 2007·Nature Protocols·Fuchou TangM Azim Surani
Apr 21, 2007·The Journal of Comparative Neurology·Jeffrey M TrimarchiConstance L Cepko
May 10, 2007·Nature Protocols·Shigeyuki EsumiTakeshi Yagi
Jul 20, 2007·Nature·Kathryn Miller-JensenDouglas A Lauffenburger
Feb 14, 2008·PloS One·Jeffrey M TrimarchiConstance L Cepko
Apr 5, 2008·Science·Richard Losick, Claude Desplan
Apr 23, 2008·Current Protocols in Human Genetics·Christoph A KleinNicole Wendler
Oct 30, 2008·Cell·Arjun Raj, Alexander van Oudenaarden
Apr 8, 2009·Nature Methods·Fuchou TangM Azim Surani
Apr 14, 2009·Nature·Sabrina L SpencerPeter K Sorger
May 7, 2009·Annual Review of Biophysics·Arjun Raj, Alexander van Oudenaarden
May 7, 2009·Lab on a Chip·Angela R WuStephen R Quake
Jun 16, 2009·Nature Methods·Kiyomi TaniguchiHideki Kambara
Jul 7, 2009·Nature·Avigdor EldarMichael B Elowitz

Related Concepts

Stochastic Processes
Nucleic Acid Hybridization Procedure
Transcription, Genetic
Nucleic Acid Amplification Tests
Neoplasms
Gene Amplification Technique
Laser Capture Microdissection
Cryonic Suspension
Surgical Pathology Microdissection
Gene Amplification Abnormality

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Synapse Loss as Therapeutic Target in MS

As we age, the number of synapses present in the human brain starts to decline, but in neurodegenerative diseases this occurs at an accelerated rate. In MS, it has been shown that there is a reduction in synaptic density, which presents a potential target for treatment. Here is the latest research on synapse loss as a therapeutic target in MS.

Artificial Intelligence in Cardiac Imaging

Artificial intelligence (ai) techniques are increasingly applied to cardiovascular (cv) medicine in cardiac imaging analysis. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

Social Learning

Social learning involves learning new behaviors through observation, imitation and modeling. Follow this feed to stay up to date on the latest research.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Single Cell Chromatin Profiling

Techniques like ATAC-seq and CUT&Tag have the potential to allow single cell profiling of chromatin accessibility, histones, and TFs. This will provide novel insight into cellular heterogeneity and cell states. Discover the latest research on single cell chromatin profiling here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Sameer S BajikarKevin A Janes
Nature Protocols
Virginia EspinaLance A Liotta
© 2020 Meta ULC. All rights reserved