User:J. Steen Hoyer: Difference between revisions
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==Contact Info== | ==Contact Info== | ||
*J. Steen Hoyer | *J. Steen Hoyer, Duffy lab, Rutgers University | ||
* | *PhD, Computational and Systems Biology Program, Washington University in St. Louis | ||
*[[Special:Emailuser/J. Steen Hoyer|Email me through OpenWetWare]] | *[[Special:Emailuser/J. Steen Hoyer|Email me through OpenWetWare]] | ||
*http://orcid.org/0000-0002-1338-8900 | *http://orcid.org/0000-0002-1338-8900 | ||
**My Zenodo records are linked from this page. They include a number of time-lapse imaging datasets and begomovirus multiple sequence alignments. | |||
*https://scholar.google.com/citations?user=AWRhHlsAAAAJ&hl=en&oi=sra | |||
*https://www.zotero.org/jshoyer | |||
I previously worked in the Kaplinsky lab at Swarthmore College and the Meyers lab at the University of Delaware. I was in the Molecular and Cellular Biology Program at Oregon State University prior to transferring to WUSTL. | I previously worked | ||
in the Carrington Lab (Donald Danforth Plant Science Center), | |||
the Kaplinsky lab at Swarthmore College, | |||
and the Meyers lab at the University of Delaware. | |||
(Blake Meyers subsequently moved his lab to the Danforth Center.) | |||
I was in the Molecular and Cellular Biology Program at Oregon State University prior to transferring to WUSTL. | |||
I used the model plant <i>Arabidopsis thaliana</i> | |||
in all three labs | |||
and am currently focused | |||
on evolution of viruses infecting cassava and tomato. | |||
I enjoy reading about history | |||
and have authored a few wikipedia pages. | |||
I am interested in protocols | |||
for (in-field) extraction of RNA | |||
and (high-molecular-weight) DNA, | |||
and for detection of rare variants | |||
in populations of viruses | |||
and/or somatic cells | |||
by sequencing. | |||
==Links and notes== | ==Links and notes== | ||
[[Arabidopsis]] | ''[[Arabidopsis]] thaliana''---maybe move or rename page. | ||
===''S. cerevisiae'' (budding yeast)=== | ===''S. cerevisiae'' (budding yeast)=== | ||
Clontech Yeast Protocols Handbook | I recommend | ||
the Clontech Yeast Protocols Handbook | |||
and Matchmaker Handbook | |||
(takarabio.com), | |||
and the introductory guides | |||
by the late Fred Sherman. | |||
Introduction by Duina et al. (2014): | Introduction by Duina et al. (2014): | ||
http://doi.org/10.1534/genetics.114.163188 | http://doi.org/10.1534/genetics.114.163188 | ||
==== Different names for dropout media ==== | ==== Different names for dropout media ==== | ||
| Line 29: | Line 50: | ||
Some people (e.g. Sherman) reserve the term 'SD' for minimal media without amino acids, and refer to the corresponding media with amino acids as 'SC'. Others (e.g. Clontech) refer to both as 'SD'. Still others refer to these (I think) as 'CSM' or 'CM'. | Some people (e.g. Sherman) reserve the term 'SD' for minimal media without amino acids, and refer to the corresponding media with amino acids as 'SC'. Others (e.g. Clontech) refer to both as 'SD'. Still others refer to these (I think) as 'CSM' or 'CM'. | ||
Abbreviation 1 for Yeast Extract/Peptone/Dextrose (YEPD) is easy to confuse with YEP media, and | Abbreviation 1 for Yeast Extract/Peptone/Dextrose (YEPD) is easy to confuse with YEP media, and abbreviation 2 (YPDA [with Adenine]) is easy to confuse with Potato Dextrose Agar (PDA) media! | ||
Some people use 'YCM', which seems to just be YPD with 1% peptone instead of 2% peptone. Why? | Some people use 'YCM', which seems to just be YPD with 1% peptone instead of 2% peptone. Why? | ||
| Line 35: | Line 56: | ||
Doubling times in YPD typically about 90 minutes, reaching stationary phase at around 16-18 hours. | Doubling times in YPD typically about 90 minutes, reaching stationary phase at around 16-18 hours. | ||
Doubling times in synthetic media typically about 140 minutes, reaching stationary phase at around 32-36 hours. | Doubling times in synthetic media typically about 140 minutes, reaching stationary phase at around 32-36 hours. | ||
My sense is that Difco media | |||
are a bit expensive | |||
but are well worth it. | |||
==== Other yeasts ==== | |||
High-molecular-weight DNA extraction protocol | |||
(zymolyase, phenol-chloroform) | |||
from the group of Lois L. Hoyer | |||
(no known relation), | |||
UIUC: | |||
https://www.protocols.io/view/extraction-of-yeast-high-molecular-weight-genomic-rm7vzb1b4vx1/v1 | |||
The [[yeast]] page mainly links to [[McClean:Protocols]] | The [[yeast]] page mainly links to [[McClean:Protocols]] | ||
Latest revision as of 12:57, 1 July 2023
Contact Info
- J. Steen Hoyer, Duffy lab, Rutgers University
- PhD, Computational and Systems Biology Program, Washington University in St. Louis
- Email me through OpenWetWare
- http://orcid.org/0000-0002-1338-8900
- My Zenodo records are linked from this page. They include a number of time-lapse imaging datasets and begomovirus multiple sequence alignments.
- https://scholar.google.com/citations?user=AWRhHlsAAAAJ&hl=en&oi=sra
- https://www.zotero.org/jshoyer
I previously worked in the Carrington Lab (Donald Danforth Plant Science Center), the Kaplinsky lab at Swarthmore College, and the Meyers lab at the University of Delaware. (Blake Meyers subsequently moved his lab to the Danforth Center.) I was in the Molecular and Cellular Biology Program at Oregon State University prior to transferring to WUSTL. I used the model plant Arabidopsis thaliana in all three labs and am currently focused on evolution of viruses infecting cassava and tomato. I enjoy reading about history and have authored a few wikipedia pages. I am interested in protocols for (in-field) extraction of RNA and (high-molecular-weight) DNA, and for detection of rare variants in populations of viruses and/or somatic cells by sequencing.
Links and notes
Arabidopsis thaliana---maybe move or rename page.
S. cerevisiae (budding yeast)
I recommend the Clontech Yeast Protocols Handbook and Matchmaker Handbook (takarabio.com), and the introductory guides by the late Fred Sherman.
Introduction by Duina et al. (2014): http://doi.org/10.1534/genetics.114.163188
Different names for dropout media
Some people (e.g. Sherman) reserve the term 'SD' for minimal media without amino acids, and refer to the corresponding media with amino acids as 'SC'. Others (e.g. Clontech) refer to both as 'SD'. Still others refer to these (I think) as 'CSM' or 'CM'.
Abbreviation 1 for Yeast Extract/Peptone/Dextrose (YEPD) is easy to confuse with YEP media, and abbreviation 2 (YPDA [with Adenine]) is easy to confuse with Potato Dextrose Agar (PDA) media!
Some people use 'YCM', which seems to just be YPD with 1% peptone instead of 2% peptone. Why?
Doubling times in YPD typically about 90 minutes, reaching stationary phase at around 16-18 hours. Doubling times in synthetic media typically about 140 minutes, reaching stationary phase at around 32-36 hours.
My sense is that Difco media are a bit expensive but are well worth it.
Other yeasts
High-molecular-weight DNA extraction protocol (zymolyase, phenol-chloroform) from the group of Lois L. Hoyer (no known relation), UIUC: https://www.protocols.io/view/extraction-of-yeast-high-molecular-weight-genomic-rm7vzb1b4vx1/v1
The yeast page mainly links to McClean:Protocols
