University of Michigan Center for Gastrointestinal Research


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Protein Localization, Identification and Folding Core

In Vivo Animal and Human Studies Core

Molecular Biology Core
Facilities and Resources

Microbiome and Metabolomics Core

Molecular Biology Core


Juanita Merchant, M.D., Ph.D.

Linda Samuelson, Ph.D.


Transgenic Rodent Program
The Transgenic Rodent Program utilizes a centralized facility ( supported by the University of Michigan and staffed by highly trained technicians who provide timely access to transgenic and embryonic stem (ES) cell technology at an affordable cost.  (Service Request Form)

Program services available to membership include:
a)  Generate mouse and rat transgenics and mouse ES cell-derived strains.

b)  Work with the Genome Editing Program to generate gene-edited mouse and rat models.

c)  Produce transgenic mice from BAC constructs with similar efficiencies to plasmid transgene vectors.

d)  Produce gene-targeted (knockout) mice from ES cells and establish de novo ES cell lines.

e)  Provide assisted reproduction (e.g. in vitro fertilization), cryopreservation, and clean up contaminated strains by conversion to specific pathogen free (SPF) status.

f)  Maintain a database of genetically-engineered mouse models used in UMCGR member labs.


Genome Editing Program

Genome editing technology, primarily CRISPR/Cas9, is a new program offered by the Molecular Core to generate gene-targeted mice, organoids and cell lines. Access to this Core is restricted to UMCGR and Michigan Diabetes Research Center members and as such members will receive full support in the execution of this technology.  (Service Request Form)

Program services available to membership include:

a) Work with members to design CRISPR/Cas9 genome editing approaches to engineer novel rodent (mouse and rat) strains, organoids (human and mouse) and cell lines.

b) Collaborate with the Transgenic Rodent and Viral Vector Programs to access plasmids and targeting libraries appropriate to generate constructs for genome-editing and to execute the project.

c) Coordinate with the UMCGR In Vivo Core to provide gene-editing tools for human and mouse organoids.

d) Screen genomic DNA (blastocyst, mouse tail or cell/organoid) for successful gene editing.

e) Generate basic cloning and luciferase reporter plasmids for cell transfection.


Viral Vector Program

The Viral Vector Program provides recombinant viral vectors for in vitro and in vivo gene transfer into mammalian cells. (Service Request Form)

Program services available to membership include:

a)   Construct, purify, concentrate and characterize recombinant adenoviral, retroviral, rabies and lentiviral vectors.

b)   Expand and distribute shRNA library clones (GE Dharmacon and Sigma) in lentiviral backbones.

c)   Provide access to ready-made stocks of certain recombinant viruses, including reporters (e.g., dsRed, GFP) and constructs (e.g., p53) to manipulate cell function.

d)   Maintain a database of GI-relevant vectors previously built by the Vector Core or ready-made for expression of selected mammalian proteins (e.g., human and mouse interleukins).


Integrated Genomics Program

The Integrated Genomics Program provides complete services for UMCGR members to implement a wide array of genomic techniques through coordinated bioinformatics analysis of genomic sequence data (see: ). (Service Request Form)

Program services available to membership include:

a)  Develop a rigorous experimental design and plan for genomic sequence acquisition and bioinformatics analysis. This includes decisions on comparison groups and sequencing approach, e.g., exome versus whole genome sequencing, the number of samples needed, length of the reads and whether the reads should be single or double-stranded.

b)  Receive raw data files from the DNA sequencing core, e.g., Microarray, RNA-Seq, ChIP-Seq, Exome-Seq, SNP analysis, genome methylation analysis, whole genome sequencing and execute prescribed analysis.

c)  Custom-design bioinformatics algorithms to analyze UMCGR member sequencing data, e.g., define transcription factor function by comparing ChIP-Seq to RNA-Seq data.

d)  Apply bioinformatics algorithms to identify genome signatures from archived University or publicly available databases.

e)  Generate data plots for publication.

Additional Molecular Core Tools and Services

Drs. Merchant and Samuelson together with the four Program Managers and the UMCGR Administrative Core maintain GI-centric databases to facilitate member research programs and stimulate collaborative interactions between Center members. These are made accessible through the UMCGR internal website in a password-protected section. Restricting access protects member projects and resources that are not yet published. (Service Request Form)

These databases available to membership include:

a)   Genetically-engineered mouse strains maintained in Center-member laboratories. This list includes strains generated by the UMCGR Transgenic Rodent Program (e.g., Villin-Cre, Cdx2-CreERT2, Gastrin-CreERT2, Tph1-CreERT2), by member collaborators (e.g., H,K-ATPase-Cre, GFAP-CreERT2, Lrig1-CreERT2; Olfm4-CreERT2) or through commercial sources (e.g., Lgr5-eGFP-IRES-CreERT2, ROSA lineage-tracing strains). This list also includes many strain combinations (e.g., Lgr5-eGFP-IRES-CreERT2; ROSA-loxSTOPlox-tdTomato), which when shared can save substantial breeding time for investigators wanting to study strains carrying multiple alleles.

b)   Viral vector constructs and plasmids (e.g., lentivirus-expressing WT and S33Y oncogenic beta-catenin).

c)   GI-relevant genomic sequence information generated by members (e.g., RNA-Seq database of LGR5+ (actively-cycling) and BMI+ (slowly-cycling) stem cells from mouse intestine) or publically available databases that UMCGR investigators can include in their studies.




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