The Stanford Center for Clinical and Translational Research and Education

Analysis of Gene/Protein Function

High School Student

Have Questions?

Please see the individual resource websites for contact information. If you cannot find what you are looking for, please
contact Bruce D. Koch, PhD  email

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Analysis of Gene/Protein Function

Identification and characterization of functional perturbants (antibody, siRNA, peptide, small molecule).

Shared Facilities:

Gene Virus Vector Core (GVVC)
  • Description — Provides virus production (e.g., AAV, lentiviruses, retroviruses, and others) and associated molecular biology (e.g., plasmid construction, plasmid production, PCR, Q-PCR, mutagenesis, and others) services.
  • Location — Lorry I. Lokey Stem Cell Research Building, Room G1027
  • Questions — Javier Alcudia, PhD  email or Keiko Takahashi, PhD  email
  • Website
  • Selected References

    The neurexin ligands, neuroligins and leucine-rich repeat transmembrane proteins, perform convergent and divergent synaptic functions in vivo. Soler-Llavina GJ, Fuccillo MV, Ko J, Südhof TC, Malenka RC. Proc Natl Acad Sci U S A. 2011 Sep 27. [Epub ahead of print]  PubMedID: 21953696: PMCID: PMC3189075

    Neuroligins/LRRTMs prevent activity- and Ca2+/calmodulin-dependent synapse elimination in cultured neurons. Ko J, Soler-Llavina GJ, Fuccillo MV, Malenka RC, Südhof TC. J Cell Biol. 2011 Jul 25;194(2):323-34. PubMedID: 21788371; PMCID: PMC3144410

    A calcineurin/AKAP complex is required for NMDA receptor-dependent long-term depression. Jurado S, Biou V, Malenka RC. Nat Neurosci. 2010 Sep;13(9):1053-5. Epub 2010 Aug 8. PubMedID: 20694001; PMCID: PMC2943866

High Throughput Bioscience Center (HTBC)
  • Description — Fully automated high-throughput screening (HTS) and high content screening of compound, genomic cDNA, and genomic siRNA libraries. Consultation and assistance for assay development, design, and analysis and for instrumentation training. Access to microplate based liquid handling equipment (SciClone ALH3000, Agilent Bravo and VPrep, Plate Washers, Reagent/Cells Dispensers), for plate replication, reformatting, reagent/cell dispensing and washing. Access to multi-mode microplate based detection equipment (AnalystGT, Flexstation and Tecan Infinite M1000 96-384-well plate readers) for fluorescence (FP, HTRF, FI, FLIPR, FRET), luminescence, and absorbance reads. Access to automated microplate imaging equipment with the ImageXpress Micro (epi-fluorescence, brightfield/phase contrast, environmental control options).
  • Location — Center for Clinical Sciences Research (CCSR) 0133
  • Questions — David Solow-Cordero  email, (650) 725-6002
  • Website
  • Selected References

    Small-molecule inhibitors reveal multiple strategies for Hedgehog pathway blockade. Hyman JM, Firestone AJ, Heine VM, Zhao Y, Ocasio CA, Han K, Sun M, Rack PG, Sinha S, Wu JJ, Solow-Cordero DE, Jiang J, Rowitch DH, Chen JK. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):14132-7. Epub 2009 Aug 5. PubMedID: 19666565; PMCID: PMC2721821

    A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Paulsen RD, Soni DV, Wollman R, Hahn AT, Yee MC, Guan A, Hesley JA, Miller SC, Cromwell EF, Solow-Cordero DE, Meyer T, Cimprich KA. Mol Cell. 2009 Jul 31; 35 (2): 228-39. PubMedID: 19647519; PMCID: PMC2772893

    The roles of cyclin A2, B1, and B2 in early and late mitotic events. Gong D, Ferrell JE Jr. Mol Biol Cell. 2010 Sep 15;21(18):3149-61. Epub 2010 Jul 21. PubMedID: 20660152; PMCID: PMC2938381

Protein & Nucleic Acid (PAN)
  • Description — The Protein and Nucleic Acid (PAN) Facility is a multifaceted biotechnology fee-for-service laboratory. In Molecular Genetics the services include Gene Expression and Genotypring (Affymetrix microarray), quantitative methylation and mutation analysis (PyroMark), qPCR, DNA sequencing and fragment analysis, Nucleic Acid QC (Agilent Bioanalyzer) and Oligonucleotide synthesis. For protein characterization the laboratory offers Protein Sequencing, Peptide Synthesis, Protein Identification (MALDI) and Biomolecular interaction analysis using Surface Plasmon Resonance (Biacore).
  • Location — Beckman Center B065/B017
  • Questions — Michael Eckart, PhD  email, (650) 723-1907
  • Website
  • Selected References

    Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP, Benayoun BA, Shi Y and Brunet A. Nature 2011; 479: 365–371. PubMedID: 22012258

    Antagonistic VEGF variants engineered to simultaneously bind to and inhibit VEGFR2 and αvβ3 integrin. Papo N, Silverman AP, Lahti JL, and Cochran JR. Proc Natl Acad Sci U S A. 2011 Aug 23; 108 (34): 14067-14072. PubMedID: 21825147; PMCID: PMC3161552

    Masking the 5′ terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex. Machlin ES, Sarnow P and Sagan SM. Proc Natl Acad Sci U S A. 2011 Feb 22; 108(8): 3193–3198. PubMedID: 21220300; PMCID: PMC3044371

Stanford Functional Genomics Facility (SFGF)
  • Description — The Stanford Functional Genomics Facility (SFGF) provides microarrays and microarray services to researchers within the Stanford community and beyond. The facility also provides 24/7 access to instruments, equipment and software utilized within the microarray field. We support all arrays based on a microscope slide format including Agilent, Illumina, Nimblegen, and arrays produced by SFGF. Besides printing cDNA and oligonucliotide microarrays, the facility can also print arrays of your material in a high throughput fashion, including proteins, peptides, antibodies, cell lysates, siRNAs, etc.
  • Location — Center for Clinical Sciences Research (CCSR), 0120
  • Questions — John Coller, PhD  email, (650) 736-2434
  • Website
  • Selected References

    The essential genome of a bacterium.  Christen B, Abeliuk E, Collier JM, Kalogeraki VS, Passarelli B, Coller JA, Fero MJ, McAdams HH, Shapiro L. Mol Syst Biol. 2011 Aug 30;7:528. PubMedID: 21878915.

    Single-molecule sequencing of an individual human genome.  Pushkarev D, Neff NF, Quake SR. Nat. Biotechnol. 2009 Sep;27(9):847-50. Epub 2009 Aug 10. PubMedID: 19668243.

    Direct lineage conversion of terminally differentiated hepatocytes to functional neurons.  Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M. Cell Stem Cell. 2011 Oct 4;9(4):374-82. PubMedID: 21962918.

Stanford University Mass Spectrometry (SUMS)
  • Description — Capabilities include routine analyses such as nanoLC-MS/MS protein identification; LC-MS based amino acid analysis; mass determination of small molecules, peptides, and proteins; accurate mass determinations; LC-MS, MSn, and high-resolution MS. Custom projects encompass diverse areas of proteomics, metabolomics, metabolite identification, non-covalent interactions, and targeted quantitation; examples include characterization of post-translational modifications, identification of protein binding partners, proteomic and metabolomic profiling, and biomarker verification.
  • Location — Mudd 175
  • Questions — Allis Chien, PhD  email, (650) 723-0710
  • Website
  • Selected References

    Activation of aldehyde dehydrogenase-2 reduces ischemic damage to the heart.  Chen CH, Budas GR, Churchill EN, Disatnik MH, Hurley TD, Mochly-Rosen D. Science. 2008 Sep 12;321(5895):1493-5. PubMedID: 18787169; PMCID: PMC2741612

    Neural Precursor Cell-expressed Developmentally Down-regulated Protein 4-2 (Nedd4-2) Regulation by 14-3-3 Protein Binding at Canonical Serum and Glucocorticoid Kinase 1 (SGK1) Phosphorylation Sites.  Chandran S, Li H, Dong W, Krasinska K, Adams C, Alexandrova L, Chien A, Hallows KR and Bhalla V. The Journal of Biological Chemistry. October 28, 2011; 286, (43): 37830–37840. PubMedID: 21900244.

    Colonic Contribution to Uremic Solutes.  Aronov PA, Luo F J-G, Plummer NS, Quan Z, Holmes S, Hostetter TH, and Meyer TW. JASN. September 1, 2011; 22 (9): 1769-1776. PubMedID: 21784895

    Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae.   Tsvetanova NG, Klass DM, Salzman J, Brown PO. PLoS ONE. Sep 10, 2010; 5(9): e12671. doi:10.1371/journal.pone.0012671 PubMedID: 20844764; PMCID: PMC2937035

Transgenic, Knockout and Tumor Model Center (TKTC)
  • Description — Mouse models for gene of interest: transgenic mouse production; targeted ES cell clone production; chimeric mouse production; sperm/embryo cryopreservation; strain rederivation; xenograft tumor models; drug dosing; toxicity studies.
  • Location — CCSR 0137
  • Questions — Hong Zeng, PhD  email, (650) 724-9556
  • Website
  • Selected References

    Site-specific recombinase strategy to create induced pluripotent stem cells efficiently with plasmid DNA.  Karow M, Chavez CL, Farruggio AP, Geisinger JM, Keravala A, Jung WE, Lan F, Wu JC, Chen-Tsai Y, Calos MP. Stem Cells. 2011 Nov;29(11):1696-704. PubMedID: 21898697.

    Cortical representations of olfactory input by trans-synaptic tracing.  Miyamichi K, Amat F, Moussavi F, Wang C, Wickersham I, Wall NR, Taniguchi H, Tasic B, Huang ZJ, He Z, Callaway EM, Horowitz MA, Luo L. Nature. 2011 Apr 14;472(7342):191-6. PubMedID: 21179085; PMCID: PMC3073090

    Embryonic stem cells require Wnt proteins to prevent differentiation to epiblast stem cells. ten Berge D, Kurek D, Blauwkamp T, Koole W, Maas A, Eroglu E, Siu RK, Nusse R. Nat Cell Biol. 2011 Aug 14;13(9):1070-5. PubMedID: 21841791.