We are happy to share ALL original material that we have published.
Yeast strains:
We use a variety of yeast strains in the lab, particularly laboratory, industrial and wild isolates of S. cerevisiae. All strains we have used/published are available upon request.
Plasmids and constructs:
We are happy to share all published plasmids and constructs. Some may already be available on addgene.
Some SOPs for requesting reagents:
Yeast strains:
We use a variety of yeast strains in the lab, particularly laboratory, industrial and wild isolates of S. cerevisiae. All strains we have used/published are available upon request.
Plasmids and constructs:
We are happy to share all published plasmids and constructs. Some may already be available on addgene.
Some SOPs for requesting reagents:
- Please specify the exact publication you are referring to, as well as the strain/plasmid/construct name. Send your request to Sunil Laxman, along with a digital MTA signed by your institute representative.
- Please provide your full postal address, as well as your appropriate FEDEX or other shipment number, if from outside India. Indian scientists please provide only your postal address.
- We can only honor requests from institutional email accounts and not personal ones.
Software from the lab, source data sets from publications, mathematical models, other goodies:
Datasets from manuscripts:
Mathematical models - Yeast colonies with spatially organized, metabolic heterogeneity (glycolytic and gluconeogenic cells)
Lab resources (internal)
Lab: Protocols, method resources, strains, plasmids, primers
Lab intranet: ordering & inventory
Useful grant resources within India:
Grants compilation from NCBS RDO
Videos of lectures (undergrad level) (SL)
Biological oscillators: The yeast metabolic cycle Part I (with Sandeep Krishna)
Biological oscillators: The yeast metabolic cycle Part II (with Sandeep Krishna)
Popular science lectures for anyone (SL):
Science communication (on amazing fungi, what we've learned from them, a bit of history about biochemistry and more): Breaking bread, and other breakthroughs (on youtube)
Science cafe: Life in the extreme (on extreme metabolism and cell survival in conditions that should not support life).
Other resources/general:
Online yeast & genome resources
Saccharomyces genome database (SGD) Alliance of genome resources
YeastMine on SGD
Yeast Metabolic Cycle (YMC) db (Sceptrans)
KEGG metabolic pathway database
Generic GO term mapper
Yeast biochemical pathways database
Primers-4-yeast
Dan Gottschling's collection of useful resources, and protocols
Botstein lab protocols
Detailed setting up of chemostats (Dunham lab)
Metabolic & Genome Scale modeling resources
COBRA toolbox & tutorials (FBA, constrained FBA etc)
Perspective in FEMS 2022 on Genome Scale Metabolic Modeling in yeast
Consensus Yeast-GEM for Genome Scale Metabolic Modeling and latest release
Protein localization, abundance:
LoQAtE db Yeast protein localization DB Yeast GFP DB CYCLoPs: protein abundance and localization
Kinase interaction DBC
tRNA & RNA databases
tRNA database RNA modifications database Modomics
Metabolomics/mass spec resources
OMIC tools
METLIN DB at Scripps
METLIN tested SIGMA metabolites
A simple mass spectrometry tutorial
Software/freeware for mass spec
General biochemistry and molecular biology tools:
Phosphate buffer calculator
Oligo calculator
Ammonium sulfate calculator
SDS PAGE gel calculator
NEB restriction enzyme tools
NEB building tools
Cloning: DNA insert:vector calculator
Antibodies validated for yeast (ABCAM)
EnCor codon optimization calculator
Interactive Dotplot/graphing software
Article collection: Recombinant protein expression in microbial systems
Datasets from manuscripts:
- Proteomic and phosphoproteomic datasets from Niphadkar et al, Plos Genetics 2024 are at PRIDE ProteomeXchanger with identifiers PXD049793 (Ppg1 interactors) and PXD049989 (FAR complex phosphoproteomics).
- Proteomic datasets from Prasad et al, Plos Biology 2023 are at PRIDE ProteomeXchanger identifier PXD044525
- RNA-seq data sets for wild-type and Kog1 mutants, related to SNF1 activity, from Rashida et al. Science Advances 2021: NCBI SRA number PRJNA645282
- RNA-seq and ChIP-seq data for wild type and Gcn4 deficient yeast cells, growing in minimal glucose medium with methionine, from Srinivasan R et al, Plos Genetics 2020: NCBI SRA number PRJNA599001
- Ribosome profiling (transcript and ribosome footprint) data sets for wild type and tRNA thiolation mutant yeast cells, from Gupta R et al, eLIFE 2019: NCBI GEO number GSE124428
- Gene expression datasets for cells growing in excess methionine (with lactate as a carbon source), from Walvekar A et al, MBoC, 2018: NCBI SRA accession number SRP101768
Mathematical models - Yeast colonies with spatially organized, metabolic heterogeneity (glycolytic and gluconeogenic cells)
- Colony simulator code 2: Improved yeast colony simulation model (to simulate 'light' glycolytic and 'dark' gluconeogenic cells, based on amino acid availability), from Varahan S et al, eLIFE 2020: GITHIB code download link
- Colony simulator code 1: Yeast colony simulation software (to simulate 'light' and 'dark' cells, based on resource availability), from Varahan S et al, eLIFE 2019: GITHUB code download link
- Colonizer: An Android based app for counting microbial colonies (CFUs): in this preprint. We apologize, but we are no longer developing or supporting colonizer.
Lab resources (internal)
Lab: Protocols, method resources, strains, plasmids, primers
Lab intranet: ordering & inventory
Useful grant resources within India:
Grants compilation from NCBS RDO
Videos of lectures (undergrad level) (SL)
Biological oscillators: The yeast metabolic cycle Part I (with Sandeep Krishna)
Biological oscillators: The yeast metabolic cycle Part II (with Sandeep Krishna)
Popular science lectures for anyone (SL):
Science communication (on amazing fungi, what we've learned from them, a bit of history about biochemistry and more): Breaking bread, and other breakthroughs (on youtube)
Science cafe: Life in the extreme (on extreme metabolism and cell survival in conditions that should not support life).
Other resources/general:
Online yeast & genome resources
Saccharomyces genome database (SGD) Alliance of genome resources
YeastMine on SGD
Yeast Metabolic Cycle (YMC) db (Sceptrans)
KEGG metabolic pathway database
Generic GO term mapper
Yeast biochemical pathways database
Primers-4-yeast
Dan Gottschling's collection of useful resources, and protocols
Botstein lab protocols
Detailed setting up of chemostats (Dunham lab)
Metabolic & Genome Scale modeling resources
COBRA toolbox & tutorials (FBA, constrained FBA etc)
Perspective in FEMS 2022 on Genome Scale Metabolic Modeling in yeast
Consensus Yeast-GEM for Genome Scale Metabolic Modeling and latest release
Protein localization, abundance:
LoQAtE db Yeast protein localization DB Yeast GFP DB CYCLoPs: protein abundance and localization
Kinase interaction DBC
tRNA & RNA databases
tRNA database RNA modifications database Modomics
Metabolomics/mass spec resources
OMIC tools
METLIN DB at Scripps
METLIN tested SIGMA metabolites
A simple mass spectrometry tutorial
Software/freeware for mass spec
General biochemistry and molecular biology tools:
Phosphate buffer calculator
Oligo calculator
Ammonium sulfate calculator
SDS PAGE gel calculator
NEB restriction enzyme tools
NEB building tools
Cloning: DNA insert:vector calculator
Antibodies validated for yeast (ABCAM)
EnCor codon optimization calculator
Interactive Dotplot/graphing software
Article collection: Recombinant protein expression in microbial systems