Merchant Lab Research Resources
Merchant Lab Research Resources
- Antibodies vs 27March08.xls - updated March 2008 (requires password) - UNDER CONSTRUCTION -
Archived Protocols
- Chlamy Chloroplast DNA Protocol
- Chloroplast DNA Prep Protocol
- DNA Preparation from Chlamydomonas Reinhardtii
- Pronase Method for Making DNA From C.r.  
Biosciences Core Facilities at UCLA
Chemical Inventory - see computer in 5069
Computing Services (For security reasons link active on-campus only)
Counseling Services
- Students & Staff

Digital Imagery
- Digital Expert Web Site (Resources & Tutorials)
- Preparing Digital Images for Publication in Scientific Journals

- Color Choices for Figures - Color Choices for Figures 2

- Alphabetical List of NEB Enzymes
- Cleavage Near End of Linear DNA
- Double Digests Buffer Compatibility
- Heat Inactivation
- NEBcutter
- Restriction Enzymes Available

- Setting up a Reaction
- Survival in a Reaction

Facilities Management - report a UCLA facilities problem

Freezer Contents
- Inventory for Chest Freezer - November 2007 -UNDER CONSTRUCTION-
- Template for Inventory

Genetic Nomenclature
- Maize
- Microbes
- Plants

Group Meetings Schedule - updated January 2010
Journal Club
- Merchant Lab Journal Club group on Mendeley

Articles of Interest
- Mineral Nutrition from Lambers et al. (requires password)
  Large file: To download Mineral Nutrition right click on link and select "Save Target As" (PC) or press Ctrl + Click and select "Download Linked File" (Mac)
- Problems with Scientific Research: How Science Goes Wrong | Trouble at the Lab
- Data Visualization Points of View

- Points of Significance: Let’s give statistics the attention it deserves
- Algal of the year 2014: Chlamydomonas reinhardtii - a fast swimmer serves as a model organism
- Trends in Place Science: Why measure enzyme activities in the era of systems biology?
- The Economist: How Science Goes Wrong

Lab Manual
- 137c Strain Reference
- Add database to Mascot server
- Agencourt Instructions Generic
- Amino acid analysis at UC Davis
- arg2 vs. arg7 - Courtesy of Lib Harris
- Argon for ICP-MS
- Balancing Tubes in a Microfuge
- Bioanalyzer
    - Analysis of Small RNAs Application Note
    - Bioanalyzer Brochure
    - Quality Control of Protein Samples Prior to MS-analysis
- Brij lysis plasmid prep purified by CsCl gradients
- Calbiochem Buffers (requires password)
- Calbiochem-Behring Buffers (requires password)
- Cell and size counts by Coulter counter
- Chlamy Growth Medium
    - Chemical Inventory for Hutner's Trace Element
- Special K Traces
- Chlamy Center QC Practices 2009
- Chlamy Sourcebook, Chapter 1 (requires password)
    Large file: To download the Chlamy Sourcebook, Chapter 1 , right click on link & select "Save Target As" (PC) or press Ctrl + Click & select "Download Linked File" (Mac)
- Chlamy strains storage protocol by liquid N2 freezing (from Paris group via Olivier)
Chlamydomonas Freezing protocol (from Umen Lab)
- Chlamydomonas DNA Midiprep
- Chlorophyll assay
     - Porra et al 2002
     - Porra et al 1989

- Chlorophyll Measurement of Cells in a Culture
- Counting Chlamydomonas Cells
- CW Determination
- Cytochrome c nomenclature
- Deb Berthold's suggestions for protein expression in E. coli
Determining quality of Chlamydomonas reinhardtii RNA
- Dialysis Tubing, Preparation of
- Dynamics of Microbial Growth
    Large file: To download Dynamics of Microbial Growth right click on link & select "Save Target As" (PC) or press Ctrl + Click & select "Download Linked File" (Mac)
- ECL Reagents, Home Made
- EMBO Course Protocols
- Endnote X1
- Formaldehyde Gel Electrophoresis of RNA & RNA Blot Hybridization
- Heat Map Generator
- HiSeq2000 request form for Stem Cell Institute
- How to Cross Chlamydomonas
- Image Processing: Manipulation and Misconduct in the Handling of Image Data
- Iron-Deficient Medium, Preparation of
- JOVE Tetrad Dissection
- Laemmli Gel Stocks
- Lipid Sample Preparation
- Lowry Assay
- Metal content of chlamy cells and chlamy medium
- Methods of Molecular Biology
- Methods of Possible Interest
    - Chl and carotenoids
- Native Gel "Angel" Stock Solutions
- NBS Universal Platform, Optimum use of
- Oligolabelling Procedure
    - Info on oligolabelling
    - Optimization
    - Optimization - template concentration & size
    - Protocol
Radiochemical Degradation of Nucleic Acids by 32-Phosphorus
    - Schematic
- Operations Manuals
    - O2 Electrode Preparation and Maintenance
- Ordering Guide (requires password)
- Ordering Tax-Free Items (Services)
- Phytozome Tutorial from David Goodstein
- Pigment Analysis: Instructions to send samples to Niyogi Lab
- Plasmid Mini-Prep Protocol
- pJD100
    - pJD100 Schematic
    - pJD100 Sequence
    - pJD100GW Schematic
    - pJD100GW Sequence

- Product Technical Information
   -Promega Online
- Protein Detection Methods on Blots
- Protein Stain, Negative
- Purification of Taq (requires password)
- Pipette Washing Instructions
- Radiation Safety Protocols and Procedures (requires password)
- Rapid Isolation of Plasmid DNA - Midi Prep
- Real Time PCR Protocols
    - Eleven Golden Rules of Quantitative RT-PCR
    - Merchant Lab qPCR Protocol (requires password)
    - MIQE Guidelines & MIQE Checklist
    - Rieu & Powers Article
    - Remans et al Article
    - The PCR Song
    - CFX96 RT-PCR Instrument
CFXM 1.6 Installation Program Download Note: this is a compressed zip file. (requires password)
        - Pfaffl 2001
        - Vandesompele et al 2002
        - UCLA CFX96 PowerPoint Presentation
- Refractometer
        - Instruction for Refractometer
        - Abbe Refractometer, Step by Step Instructions
        - Sucrose Gradient Refractive Index

- Reporter Gene Assays
        - YFP
        - Arylsulfatase

RNA Extraction
        - Freezing Cells in Lysis Buffer
        - RNA Isolation from Chlamydomonas reinhardtii - from cells frozen in lysis buffer
- RNA isolation from Chlamydomonas
- Scaled Venn Tools
        - Venn Diagram Plotter
        - Drawing Area-Proportional Euler and Venn Diagrams Using Ellipses
        - Venny
- Silver Gel
- Standard Operating Procedures (SOPs)
    - Compressed Gas Cylinders
    - Handling Specific Chemicals

- SOD activity gel

- Southern Blot
- Springer Protocols
- TAP medium preparation from SM files (original from Togasaki)
- Trypsin in gel digestion

- What is Microbiology?
    Large file
: To download What is Microbiology? right click on link & select "Save Target As" (PC) or press Ctrl + Click & select "Download Linked File" (Mac)
- Zygote DNA Prep (from Jim Umen)

Educating Scientists
- HHMI Making the Right Moves: A Practical Guide to Scientific Management for Post Docs and New Faculty
- HHMI Training Scientists to Make the Right Moves
- Entering Mentoring
- Career Advice for Life Scientists
Lab Responsibilities - updated January 2017
Managing Your Notebook (Courtesy of Vessela Ensberg, UCLA Biomed library)
Molecular Weight Markers (requires password)
 - Protein ladders
 - DNA ladders
 - RNA ladders
Homologies, Orthologs and Paralogs
- Orthologs and paralogs - we need to get it right
- Homology - a personal view on some of the problems
- “Homology” in proteins and nucleic acids: A terminology muddle and a way out of it
- How confident can we be that orthologs are similar, but paralogs differ?
- Phylogeny for the faint of heart: a tutorial
Online Courses
- Animal Subjects
- EH&S Online Safety Training
- Sexual Harrassmment
- Workplace Ethics

Personnel (requires password)

Recycling Locations
Purchase Order List
Replicates & Statistics
- Basic Statistical Considerations in Virological Experiments
- Collection on statistics
- How Robust is Your Data? (Nature Cell Biology)
    - Additional Guidelines (see further editorial information)
- Error Bars
- Experimental Design for Yeast Genomic Expression Analyses
- Sample Size
- Significant Figures
- Statistical analysis of real time PCR data
- Statistics & Errors: Errors in Biology
- The Power of Replicates
- Raising Standards
- Ten Simple Rules for Reproducible Computational Research
Research Responsibility
- Accurately Reporting Research
Research Projects
Room Reservation Calendar

- Chem & Biochem Department Safety Web Site
- Departmental Policy

     - Chair's Memo on Safety (February 8th, 2009)

     - EH&S Online Safety Training
     - Radiation Safety Protocols and Procedures (requires password)
Enviromental Health and Safety and UCLA

- Formaldehyde
- How to Prepare for a Power Failure in the Lab (November 26, 2014)
- Material Safety Date Sheets (MSDS)
- "Spot The Mistakes" [YouTube Video]

- UCLA guidelines on the PI's responsibilities for laboratory safety

- UCLA guidelines on the PI's responsibilities for radiation safety, see page 1-2

- NIH Guidelines on the PI's Responsibilities for Research Involving Recombinant or Synthetic Nucleic Acid Molecules

- NIH Guidelines on the PI's Responsibilities for Animal Research

Shipping & Mailing Information
- Mailing Instructions updated Sept. 2014
- International Mail/Customs Information
Strain List
- Bacteria
- Yeast
- Chlamydomonas
ESTs - 06/07/11 (requires password) - UNDER CONSTRUCTION -
Trace Metal Analysis Guide
University of California Traveler Insurance Coverage

Updated 12/01/14