BUSRP Laboratory Reagents and Resources

In an effort to stimulate collaboration and increase the accessibility of research tools, the Research Translation Core is providing the following list of reagents and tools that have been developed by BUSRP researchers with support from the Superfund Research Program (grant #5 P42 ES007381) and can be distributed without permission.

If you are interested in obtaining any of these items please email the appropriate contact person, or contact the Research Translation Core.

For reagents from Dr. David Sherr’s lab, see Sherr Lab Resources.

 

Fundulus heteroclitus

As a life-long resident of estuaries, the fish Fundulus heteroclitus (Atlantic killifish) is routinely exposed to high levels of contaminants from industrial, agricultural, and municipal sources. Fundulus populations harbor natural variation in tolerance to pollution, and can serve as models to study the genomic basis of sensitivity to the toxic effects of pollution. Below we make available the genomic and transcriptomic information as part of the Fundulus Genomics Consortium and microRNA sequences from killifish embryos from contaminated (NBH) and pristine (Scorton Creek, MA (SC)) sites.

See full Fundulus heteroclitus genome.

See microRNA profiling in Atlantic killifish (Fundulus heteroclitus).

Strain or tissue of origin Genetic Info/Construct Data Notes Contact
aryl hydrocarbon receptor-1 antibodies Mark Hahn
aryl hydrocarbon receptor-2 antibodies Mark Hahn
aryl hydrocarbon receptor repressor antibodies Mark Hahn
heart cDNA library Sibel Karchner
liver  cDNA library Sibel Karchner
SC aryl hydrocarbon receptor-1*1A (AHR1*1A) expression construct in pcDNA Mark Hahn
NBH aryl hydrocarbon receptor-1*3A expression construct in pcDNA Mark Hahn
aryl hydrocarbon receptor-2 expression construct in pcDNA Mark Hahn
hypoxia inducible factor-2alpha (HIF-2a) cDNA in pGEM-T Mark Hahn
aryl hydrocarbon receptor repressor (AHRR) expression construct in pcDNA Mark Hahn
aryl hydrocarbor receptor nuclear translocator-2 (ARNT2) expression construct in pcDNA Mark Hahn
B-actin cDNA in pGEM-T Sibel Karchner
Estrogen receptor-related receptor (ERR)-alpha cDNA construct Ann Tarrant
ERR-beta-a cDNA construct Ann Tarrant
ERR-beta-b cDNA construct Ann Tarrant
ERR-gamma cDNA construct Ann Tarrant


Zebrafish

Strain or tissue of origin Genetic Info/Construct Data Notes Contact
TL CYP1C1 clones John Stegeman
TL CYP1C2 clones John Stegeman
TL CYP1D1 clones John Stegeman

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Danio rerio

Genetic Info/Construct Data Notes Contact
aryl hydrocarbon receptor repressor-1 expression construct in pcDNA Mark Hahn
aryl hydrocarbon receptor repressor-2 expression construct in pcDNA Mark Hahn
aryl hydrocarbon receptor-1B (AHR1B) expression construct in pcDNA Mark Hahn
AHRR1-Y9F and other mutant constructs expression construct in pcDNA Mark Hahn

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Open Source Software

Item (description) Utility of Tool/application Limitations (known) Notes Contact
S-Plus code for estimating surfaces based on spatial binary data using generalized additive models. Text file of S-Plus code for reproducing our analysis using synthetic data Requires S-Plus. The output of this file can be mapped with GIS software such as ArcView. Synthetic data are also available. Thomas Webster
R code for estimating surfaces based on spatial binary data using generalized additive models. Text file of R code for reproducing our analysis using synthetic data Although R is freely downloadable, the R version of the gam software performs something similar to stepwise regression; this is not always desirable when trying to control potential confoudners. The output of this file can be mapped with GIS software such as ArcView. Synthetic data are also available. Thomas Webster
Hydra: A Flexible Pipeline for the Processing of RNA-seq data github repository of the source Python code implementing the pipeline: Requires Python See github repository for documentation Stefano Monti
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Synthetic Data Sets

Item (description) Utility of Tool/application Limitations (known) Notes Contact
Excel file of synthetic data Used with S-Plus (or R code) to generate surfaces. Files of crude and adjusted maps based on these data are also available Thomas Webster
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Reagents

Item Contact
15dPGJ Stefano Monti
1-hydroxyphenazine Stefano Monti
3,3-diindolemethane (DIM) Stefano Monti
4,8-Dihydroxy-2-quinolinecarboxylic acid (Xanthurenic Acid) Stefano Monti
9-cis-retinoic acid Stefano Monti
Acid Orange 156 Stefano Monti
Arolcolr Stefano Monti
beta-naphthoflavone Stefano Monti
Bexarotene Stefano Monti
Butyl benzyl phthalate Stefano Monti
CB7950998 (discovered agonist) Stefano Monti
CW-051 Stefano Monti
FICZ Stefano Monti
Flutamide Stefano Monti
FM550 Stefano Monti
Galangin Stefano Monti
galangin with TCDD Stefano Monti
HP163 Stefano Monti
Indirubin Stefano Monti
Indole Stefano Monti
leflunomide Stefano Monti
LG100268 Stefano Monti
LG100754 Stefano Monti
nifedipine Stefano Monti
nTZDpa Stefano Monti
Omeprazole Stefano Monti
PCB 153 Stefano Monti
PCB126 Stefano Monti
PCB126 with TBT Stefano Monti
PCB66 Stefano Monti
PCB77 Stefano Monti
PCB95 Stefano Monti
Prallethrin Stefano Monti
Pregnenolone 16alpha-carbonitrile Stefano Monti
Quinoxyfen Stefano Monti
Rosi with TPhP Stefano Monti
S26948 Stefano Monti
serotonin Stefano Monti
shAHRm Stefano Monti
Spironolactone Stefano Monti
SR1664 Stefano Monti
sulforaphane Stefano Monti
tranilast Stefano Monti
Tributyltin chloride Stefano Monti
Triclosan Stefano Monti
tryptamine Stefano Monti

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