Noi/NOTES/2014-4-14

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gDNA extraction of cell cultures (Song' samples)[edit]

Sample info.
- Three vials for day 0 ESCs (ESCd0.1, ESCd0.2,ESCd0.3)
- Three vials for definitive endoderm cells (DEd3.1,DEd3.2,DEd3.3)
- Two vials for naive cells. (naiveESC.1, naiveESC.2)
- Extract gDNA using DNeasy Blood & Tissue Kit (QIAGEN) with RNaseA treatment and followed the instruction of the kit
- Elute DNA with 200ul AE buffer (single elution)
- Measure concentration with Nanodrop (ND) and Qubit dsDNA HS assay

Qubit dsDNA HS assay and Nanodrop (ND) quantification[edit]

Sample Conc. in the Qubit Unit uL used Dilution Sample conc. (ng/ul) Yields in 200ul (ug) conc. By ND (ng/ul) 260/280 260/230
ESCd0.1 201 ng/mL 1 200 40.30 8.06 53.15 1.92 1.88
ESCd0.2 280 ng/mL 1 200 56.00 11.20 76.53 1.88 1.81
ESCd0.3 430 ng/mL 1 200 86.00 17.20 107.13 1.91 1.94
DEd3.1 170 ng/mL 1 200 34.00 6.80 44.91 1.91 2.07
DEd3.2 188 ng/mL 1 200 37.70 7.54 47.82 1.91 2.02
DEd3.3 129 ng/mL 1 200 25.70 5.14 34.79 1.84 1.85
naiveESC.1 132 ng/mL 1 200 26.30 5.26 39.75 1.86 1.55
naiveESC.2 150 ng/mL 1 200 30.00 6.00 44.82 1.86 1.52
- For accuracy, the concentration will be based on Qubit measurement

Amplified DNA samples form Illumina[edit]

4-14-2014

  • Received 8 additional amplified DNA samples from Xuyu Cai
  • No information of sample was provide only 5ul for each one and concentration ~200ng/ul
  • I added more H2O to bring volume to 12ul, transfered samples to 8-tube strip with individual cap, and re-quantified concentration with Qubit ssDNA HS assay

Qubit dsDNA assay HS results[edit]

Sample Conc. in the Qubit Unit uL used Dilution Sample conc. (ng/ul) Total volume Total amount (ng)
#1 173 ng/mL 1 200 34.6 12 415.2
#2 152 ng/mL 1 200 30.4 12 364.8
#3 199 ng/mL 1 200 39.9 12 478.8
#4 207 ng/mL 1 200 41.4 12 496.8
#5 108 ng/mL 1 200 21.6 12 259.2
#6 154 ng/mL 1 200 30.9 12 370.8
#7 181 ng/mL 1 200 36.1 12 433.2
#8 172 ng/mL 1 200 34.4 12 412.8

5-06-2014

  • Received ~30ul of polymerase with property similar to Amplitaq Stoffel fragment. Conc. 3U/ul. She is not allowed to provide any further info. of this enzyme.