Friday 04/12/13

Web Notebook Updates

• Switched to Markdown-on-Save plugin instead of WP markdown
• supports Markdown Plus features like tables etc.
• Saves original and markdown separately, no corrupting the original entry format because the markdown compiler doesn’t recognize things as a list.
• Reorganizing Protcols

OligoPaint Probes

Qubit Quantification of samples

• See results

Restriction Digest

• Heated lid FAILED on PCR block 3A (arbitrarily went to -20C instead of 100C). Dramatic evaporation/condensation issues. White percipitate visible in both 10mL scale samples.
• save 1 uL of sample for QuBit
• extract sample using cleanup kit
• take 1 uL of sample for QuBit

Diagnostic Denaturing Gel

• Using new casting trays for small denaturing gels
• 300 uL of APS is too much! turns solid in less than 1 min. Only managed to pour 3 of 4 gels. Probably < 15 mL per gel.
• Might not have mixed well enough — beaker turned solid but poured gels seem slower to polymerize. Lets wait.
• New gel protocol. Today’s miniPAGE BioRad Protocol.

Try 2 at T7 digestion

• Y-PPT and Y-PPT control are both at 100 ug/mL. in 10 uL that’s 1 ug, or 0.0131 nmols/10 uL or 1.300 mM (nmols/L). Dilute 1:10.
• Reaction Mix = 5 uL of 1.3 mM DNA + 5 uL Buffer 4 + 39 uL ddH2O + 1 uL T7
• Take 1 uL of ‘original sample’ prior to adding T7 for quantification.
• React at 37C 1 hr
• Take 1 uL of each sample for quantification, store samples at 4C or on ice.
• React at 37C for a further 1 hr
• Take 1 uL of each sample for quantification, store samples at 4C or on ice.

Computing clean & concentrate efficiency

• Before elution: YP control 67.3 ug/mL in 250 uL = 16.8 ug. After elution: YP cont = 97.0 ug/mL in 150 uL (14.5 ug).

First round elution

• y asym = 57.1 ug (in ~ 1mL). After elution = 3.42 ug (in 150 uL)
• B asym 37 ug. After elution = 7.65 ug
• (N ug)/(116660)10^3 = N nmol dsDNA 116 bp probe. = 0.75 nmol (added 1 nmol primer) [510 ng/uL]
• b asym = 37 ug/mL –> 0.48 nmol probe [506 ng/uL]

Markdown plus tables

• Outer pipes on tables are optional
• Colon used for alignment (right versus left)

Markdown plus definition lists

Bottled water

$ 1.25

$ 1.55 (Large)