Data from: A Living Vector Field Reveals Constraints on Galactose Network Induction in Yeast
Code
MATLAB scripts
File Size |
|
File Format |
|
Scope And Content | The MATLAB scripts were used to process the raw images and store the abstracted data in a MySQL database. |
R scripts
File Size |
|
File Format |
|
Scope And Content |
The R scripts took the data from the MySQL database and analyzed it to generate the results and figures in the paper. |
Technical Details | This package is a packrat bundle (https://rstudio.github.io/packrat/) containing everything needed to reproduce the analysis including data files and R scripts and the R libraries used at the time the analysis was done. It should be possible to unbundle the package in R or extract it using standard unarchiving tools and run it. |
MySQL database
Database
File Size |
|
File Format |
|
Scope And Content |
This contains the data that was collected on the raw images by the MATLAB scripts. |
Experiment number 2: glucose to galactose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 3: glucose to galactose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 4: glycerol to galactose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 7: reinduction
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 8: glycerol to galactose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 13: glucose to galactose, 0.15% glucose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 16: glucose to galactose, 0.3% glucose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 23: glucose to galactose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 24: glucose to galactose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
Experiment number 25: glucose to galactose
Scope And Content | The experiments are referenced by a unique number and a type (e.g. glucose to galactose). |
Raw data
File Size |
|
File Format |
|
Scope And Content |
This contains TIFF images of fields of fluorescence or bright-field images over time. There is metadata associated with each image that describes microscope settings. |
Date Collected |
|
Image Analysis
File Size |
|
File Format |
|
Scope And Content |
These are intermediate images generated as part of the MATLAB processing, including information on segmentation, normalization, classification, and tracking. |
- Collection
- Cite This Work
-
Stockwell, Sarah R.; Rifkin, Scott A. (2017). Data from: A Living Vector Field Reveals Constraints on Galactose Network Induction in Yeast. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0C24TCX
- Description
-
Abstract: When a cell encounters a new environment, its transcriptional response can be constrained by its history. For example, yeast cells in galactose induce GAL genes with a speed and unanimity that depends on previous nutrient conditions. Cellular memory of long-term glucose exposure delays GAL induction and makes it highly variable with in a cell population, while other nutrient histories lead to rapid, uniform responses. To investigate how cell-level gene expression dynamics produce population-level phenotypes, we collected thousands of microscopy images of fields of cells as they switched to galactose from various nutrient histories, extracted time series of thousands of individual cells undergoing this shift, and used these to build living vector fields as the cells moved across the state space of the proteins Gal3p and Gal1p. We show that, after sustained glucose exposure, the lack of these GAL transducers leads to induction delays that are long but also variable; that cellular resources constrain induction; and that bimodally distributed expression levels arise from lineage selection - a subpopulation of cells induces more quickly and outcompetes the rest. Our results illuminate cellular memory in this important model system and illustrate how resources and randomness interact to shape the response of a population to a new environment.
- Scope And Content
-
This data set consists of analysis code and data used in the related paper.
- Date Collected
- 2015 to 2016
- Date Issued
- 2017
- Authors
- Note
-
This work relies on external software packages, modules/libraries, or programs, use of which may carry specific license requirements. Users should comply with any licenses specified within the contents of this work.
- Topics
Formats
View formats within this collection
- Language
- No linguistic content; Not applicable
- Identifier
- Related Resources
- Sarah R. Stockwell, Scott A. Rifkin. A living vector field reveals constraints on galactose network induction in yeast. bioRxiv 073817. https://doi.org/10.1101/073817
- Stockwell, Sarah R. and Rifkin, Scott A. 2017. A living vector field reveals constraints on galactose network induction in yeast. Molecular Systems Biology 13(908). https://doi.org/10.15252/msb.20167323
- Rifkin Laboratory Website: https://labs.biology.ucsd.edu/rifkin
Primary associated publication
Other resource
- License
-
Creative Commons Attribution 4.0 International Public License
- Rights Holder
- UC Regents
- Copyright
-
Under copyright (US)
Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.
Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.
- Digital Object Made Available By
-
Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
- Last Modified
2023-08-25