Noi/NOTES/2011-9-16

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Revision as of 17:55, 17 September 2011 by >Noi
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BSPP DMR330k capture of samples from Sergio, two largest pedigrees from HAPMAPPT01, ten replicates, HFF somatic lines, repeat UPenn samples, and comparing DNA methylation kit from Zymoresearch and Sigma

  • Total number of reactions = 39 reactions
    • 9 samples from Sergio
      • 1. H9 P43 mTeSR
      • 2. H9 p43+Activin 100ng/mL 5days
      • 3. H9 p43+BMP4 50ng/mL 5days
      • 4. HUViPS4F1 p19
      • 5. HUViPS4F1 p19+Activin 100ng/mL 5days
      • 6. HUViPS4F1 p19+BMP4 50ng/mL 5days
      • 7. HUViPS4F3
      • 8. HUViPS4F3+Activin 100ng/mL 5days
      • 9. HUViPS4F3+BMP4 50ng/mL 5days
    • 12 samples from 2 largest pedigrees of HAPMAPPT01
      • Note: wellID = wellID from original HAPMAPPT01 plate
      • Family 1362
        • GM11995 (wellID G7)
        • GM11993 (wellID F2)
        • GM10861 (wellID A9)
        • GM11992 (wellID C2 )
        • GM11994 (wellID G9 )
        • GM10860 (wellID F10)
      • Family 1454
        • GM12813 (wellID E8)
        • GM12802 (wellID E7)
        • GM12815 (wellID G12)
        • GM12812 (wellID F11)
        • GM12814 (wellID A7)
        • GM12801 (wellID D9)
    • 10 replicates
      • NA12156 (HAPMAPPT01, wellID B3)
    • 2 somatic lines
      • 2HFF P6
      • 218 HFF P7
    • 4 samples from Penn (repeat the low QC value samples from the first batch)
    • 2 reactions to compare bis-cvt gDNA quality processed by two different DNA methylation kits, Zymoresearch (DNA methylation gold kit) and Sigma (Imprint DNA modification kit)
      • PGP1iPS
  • Note: For the gDNA of HAPMAPPT01, aliquot 10 ug to each of two working plates and save the original plate

Plate layout

Plate layout 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00
A Sergio1 Sergio9 GM12802 (wellID E7) NA12156 (wellID B3)-4 218 HFF P7 PGP1iPS
B Sergio2 GM11995 (wellID G7) GM12815 (wellID G12) NA12156 (wellID B3)-5 KEBR028A (B4-plate2)-1 KEBR028A (B4-plate2)-2
C Sergio3 GM11993 (wellID F2) GM12812 (wellID F11) NA12156 (wellID B3)-6 KEBR028A (tube)-1 KEBR028A (tube)-2
D Sergio4 GM10861 (wellID A9) GM12814 (wellID A7) NA12156 (wellID B3)-7 KEBR040 (D4-plate1) KEBR040 (D4-plate2)
E Sergio5 GM11992 (wellID C2 ) GM12801 (wellID D9) NA12156 (wellID B3)-8 TZHZ018 (F1-plate1) TZHZ018 (F1-plate2)
F Sergio6 GM11994 (wellID G9 ) NA12156 (wellID B3)-1 NA12156 (wellID B3)-9 TZHZ031A (tube)-1 TZHZ031A (tube)-2
G Sergio7 GM10860 (wellID F10) NA12156 (wellID B3)-2 NA12156 (wellID B3)-10 TZHZ041A (tube)-1 TZHZ041A (tube)-2
H Sergio8 GM12813 (wellID E8) NA12156 (wellID B3)-3 2HFF P6 TZHZ075 (H01-plate2)-1 TZHZ075 (H01-plate2)-1