Haynes:Protocols

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(Bioinformatics)
 
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[[Image:Hayneslab3.gif|link=Haynes_Lab]] [[Image:Asu_logo_3.gif|right|link=http://engineering.asu.edu/]]<br>
[[Image:Hayneslab3.gif|link=Haynes_Lab]] [[Image:Asu_logo_3.gif|right|link=http://engineering.asu.edu/]]<br>
&nbsp;&nbsp;[[Haynes_Lab | <font face="trebuchet ms" style="color:#000000"> '''Home''' </font>]] &nbsp;&nbsp;&nbsp;
&nbsp;&nbsp;[[Haynes_Lab | <font face="trebuchet ms" style="color:#000000"> '''Home''' </font>]] &nbsp;&nbsp;&nbsp;
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[[Haynes:Research | <font face="trebuchet ms" style="color:#000000"> '''Research''' </font>]] &nbsp;&nbsp;&nbsp;
 
[[Haynes:Publications | <font face="trebuchet ms" style="color:#000000"> '''Publications''' </font>]] &nbsp;&nbsp;&nbsp;
[[Haynes:Publications | <font face="trebuchet ms" style="color:#000000"> '''Publications''' </font>]] &nbsp;&nbsp;&nbsp;
[[Haynes:Lab Members | <font face="trebuchet ms" style="color:#000000"> '''People''' </font>]] &nbsp;&nbsp;&nbsp;
[[Haynes:Lab Members | <font face="trebuchet ms" style="color:#000000"> '''People''' </font>]] &nbsp;&nbsp;&nbsp;
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[[Haynes:Protocols | <font face="trebuchet ms" style="color:#000000"> '''Protocols''' </font>]] &nbsp;&nbsp;&nbsp;
[[Haynes:Protocols | <font face="trebuchet ms" style="color:#000000"> '''Protocols''' </font>]] &nbsp;&nbsp;&nbsp;
[[Haynes:TechResources | <font face="trebuchet ms" style="color:#000000"> '''Lab Resources''' </font>]] &nbsp;&nbsp;&nbsp;
[[Haynes:TechResources | <font face="trebuchet ms" style="color:#000000"> '''Lab Resources''' </font>]] &nbsp;&nbsp;&nbsp;
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[[Haynes:Internal | <font face="trebuchet ms" style="color:#000000"> '''Personnel Info''' </font>]]
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[[Haynes:Internal | <font face="trebuchet ms" style="color:#000000"> '''Personnel''' </font>]] &nbsp;&nbsp;&nbsp;
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</div>
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[[Haynes:Calendar | <font face="trebuchet ms" style="color:#000000"> '''Calendar''' </font>]]
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* [[Haynes:Gibson_Assembly | Gibson Assembly]]
* [[Haynes:Gibson_Assembly | Gibson Assembly]]
* [[Haynes:TypeIIS_Assembly | Type IIS Assembly]] - similar to Golden Gate, Golden Braid, and Moclo
* [[Haynes:TypeIIS_Assembly | Type IIS Assembly]] - similar to Golden Gate, Golden Braid, and Moclo
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<br>
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==Bioinformatics==
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* [[Haynes:GalaxyChiP | ChIP in GALAXY]] - How to use GALAXY and a large BED file from your hard drive to create a track for the UCSC browser. Useful for data that is too large to create a custom track directly on the UCSC website.
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* [[Haynes:ChIPDataMining1 | ChIP on Promoters]] - How to find chromatin protein enrichment at gene promoters of interest for small sets of genes or all 23,000 human genes, using public ChIP data
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'''LB (Lennox) Agar plates''' {{hide|  
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'''[http://openwetware.org/wiki/Haynes:LBagarAmp LB (Lennox) Agar plates]''' {{hide|  
Volume: 1 L
Volume: 1 L
* Bacto-agar, 15 g
* Bacto-agar, 15 g
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'''LB Broth (Lennox)''' {{hide|  
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'''[http://openwetware.org/wiki/Haynes:LB_liquid_media#LB_Liquid_Media LB Broth (Lennox)]''' {{hide|  
Volume: 1 L
Volume: 1 L
* Caesin tryptone, 10 g
* Caesin tryptone, 10 g

Current revision

link=Haynes_Lab
link=http://engineering.asu.edu/

   Home     Publications     People     Contact     Protocols     Lab Resources     Personnel     Calendar


Contents

Protocols

DNA Assembly


Bioinformatics

  • ChIP in GALAXY - How to use GALAXY and a large BED file from your hard drive to create a track for the UCSC browser. Useful for data that is too large to create a custom track directly on the UCSC website.
  • ChIP on Promoters - How to find chromatin protein enrichment at gene promoters of interest for small sets of genes or all 23,000 human genes, using public ChIP data



Cell Culture: Bacteria


Cell Culture: Mammalian


Imaging: Mammalian

Flow Cytometry

Microscopy

Protein & Enzyme Assays

  • Bradford assay - measure protein concentration
  • ELISA assay - specific antibody-based quantification of protein; simpler than Western, but no protein size data
  • Luciferase assay - Measuring firefly luciferase reporter activity with D-luciferin substrate

Real Time Quantitative PCR


RNA & cDNA protocols


Other Resources - OpenWetWare

  • E. coli Strains
  • Materials: buffer formulas; specific information on commonly used reagents (e.g., LB broth, ampicillin, restriction enzymes, etc.)


Software Guides



Recipes

Click "show" to expand each recipe, and "hide" to, well, hide it.

Bromo-Blue/X-cyanol Loading Buffer, 20X

Formula: [60% glycerol; 12.5 mg/mL bromophenol blue; 12.5 mg/mL xylene cyanol]
Volume: 20 mL

  • 100% glycerol, 12 mL
  • Bromophenol blue, 250 mg
  • Xylene cyanol, 250 mg

Start with 18 mL dH2O. Add in glycerol 6 mL at a time and mix by pipetting up and down several times (it is very viscous). Add dyes.

Chromatin Prep Buffer A

Formula: [10 mM HEPES (pH 7.9); 10 mM KCl, 1.5 mM MgCl2; 0.34 M sucrose; 10% glycerol; 1 mM dithiothreitol; 1x protease inhibitor cocktail]
Volume: 100 mL

  • 1 M HEPES pH 7.9, 1 mL
  • 1 M KCl, 1 mL
  • 1 M MgCl2, 150 μL
  • Sucrose, 11.6 g
  • 50% Glycerol, 20 mL
  • 1 M Dithiotreitol (DTT), 100 μL

Bring up to total volume with dH2O. Store at 4°C. Add 100x protease inhibitor cocktail* (1:100) immediately before use.

DNA Ladder mix, Gene Ruler 1 kb Plus

Formula: [0.5 ng/ 10 μL Fermentas Gene Ruler 1 kb Plus; 1x loading dye]
Volume: 1000 μL

  • Gene Ruler plus (0.5 ng/μL), 100 μL
  • 20x loading dye, 50 μL
  • dH2O, 850 μL

Add dH2O directly to the supplier's tube (containing 100 μL of ladder). Add the 20x loading dye. Mix. Aliquot 200 μL portions into five 1.5 mL tubes. Store at -20°C.

LB (Lennox) Agar plates

Volume: 1 L

  • Bacto-agar, 15 g
  • Caesin tryptone, 10 g
  • Yeast extract, 5 g
  • NaCl, 5 g
  • 1 N NaOH, 1 mL

Dissolve in 1000 mL dH2O. Autoclave to sterilize. Cool to ~50°C (warm to touch) before adding antibiotics. Add antibiotic(s) and pour into sterile petri dishes. 1L should yield about 40 plates. Shortcut: Use 25 g Acros LB Broth, Lennox (BP9722-500) granules instead of caesin tryptone, yeast extract, and NaCl.

LB Broth (Lennox)

Volume: 1 L

  • Caesin tryptone, 10 g
  • Yeast extract, 5 g
  • NaCl, 5 g
  • 1 N NaOH, 1 mL

Dissolve in 1000 mL dH2O. Autoclave to sterilize. Cool to room temperature before adding antibiotics. Shortcut: Use 25 g Acros LB Broth, Lennox (BP9722-500) granules instead of caesin tryptone, yeast extract, and NaCl.

Mammalian Cell Media

Volume: 500 mL

Add FBS and pen-strep directly to the incomplete medium in the original stock bottle. Cap and invert to mix. Filter sterilize using a vacuum filtration unit.

Oligo Annealing Buffer, 10x

Formula: [1M NaCl; 100 mM Tris-HCl pH 7.4]
Volume: 1000 μL

  • 5M NaCl, 200 μL
  • 1M Tris-HCl, 100 μL
  • dH2O, 700 μL

Keep frozen at -20°C.



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