Noi/NOTES/2013-1-31: Difference between revisions
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>Noi mNo edit summary |
>Noi mNo edit summary |
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= Skin Microbiom Project = | = Skin Microbiom Project = | ||
# To do list | # To do list | ||
## Transfer amplicons from '''AC-777-384-well''' to '''4 of 96-well plates'''; plan & plate arrangement [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-11]] | ## Transfer amplicons from '''AC-777-384-well''' to '''4 of 96-well plates'''; plan & plate arrangement [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-11]]. Since the total volume of samples in 384-well plate is very small ~8ul, I will add 12ul of H2O or TE buffer in the 96-well plate to bring the total volume to ~20ul. | ||
## Picked 67 samples from the 96-well plate to 96-well shearing plate. Arrange well ID of original 384-well plate, new 96-well plate, and location in 96-well shearing plate. | ## Picked 67 samples from the 96-well plate to 96-well shearing plate. Arrange well ID of original 384-well plate, new 96-well plate, and location in 96-well shearing plate. | ||
## Plus 5 samples from '''AC-718-96-well_plate1''' (A2-E2, sample info. [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-11]]), total of samples will be processed is 72 samples | ## Plus 5 samples from '''AC-718-96-well_plate1''' (A2-E2, sample info. [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-11]]), total of samples will be processed is 72 samples | ||
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{| class="wikitable" style="text-align:center; | {| class="wikitable" style="text-align:center; | ||
| align="center" style="background:#f0f0f0;"|'''Plate_ID''' | | align="center" style="background:#f0f0f0;"|'''Plate_ID''' | ||
| align="center" style="background:#f0f0f0;"|'''Location.in.AC- | | align="center" style="background:#f0f0f0;"|'''Location.in.AC-718-384-well''' | ||
| align="center" style="background:#f0f0f0;"|'''Note_Cp''' | | align="center" style="background:#f0f0f0;"|'''Note_Cp''' | ||
| align="center" style="background:#f0f0f0;"|'''New_96-well-plate_ID''' | | align="center" style="background:#f0f0f0;"|'''New_96-well-plate_ID''' | ||
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| AC-718||K06||b_6.47||AC-718-96-well_plate1||e2||h11 | | AC-718||K06||b_6.47||AC-718-96-well_plate1||e2||h11 | ||
|} | |} | ||
'''CSV input file:''' | |||
'''Step:1''' | |||
[[Media:AC-777_plate1_A1-H12_e.csv| AC-777_plate1_A1-H12_e.csv]] | |||
[[Media:AC-777_plate2_I1-P12_e.csv| AC-777_plate2_I1-P12_e.csv]] | |||
[[Media:AC-777_plate3_A13-H24_e.csv| AC-777_plate3_A13-H24_e.csv]] | |||
[[Media:AC-777_plate4_I13-P24_e.csv| AC-777_plate4_I13-P24_e.csv]] | |||
'''Step:2&3''' | |||
[[Media:2013.01.31_SkinMB.sample-transfer-2-shearing-plate.csv| 2013.01.31_SkinMB.sample-transfer-2-shearing-plate.csv]] | |||
'''Note:''' | |||
Rack (Source) 1 = AC-777_plate1_A1-H12 | |||
Rack (Source) 2 = AC-777_plate3_A13-H24 | |||
Rack (Source) 3 = AC-718-96-well_plate1 | |||
Rack (Destination) 1 = 96-well shearing plate |
Revision as of 04:21, 31 January 2013
Skin Microbiom Project
- To do list
- Transfer amplicons from AC-777-384-well to 4 of 96-well plates; plan & plate arrangement [[1]]. Since the total volume of samples in 384-well plate is very small ~8ul, I will add 12ul of H2O or TE buffer in the 96-well plate to bring the total volume to ~20ul.
- Picked 67 samples from the 96-well plate to 96-well shearing plate. Arrange well ID of original 384-well plate, new 96-well plate, and location in 96-well shearing plate.
- Plus 5 samples from AC-718-96-well_plate1 (A2-E2, sample info. [[2]]), total of samples will be processed is 72 samples
- Shear DNA by Covaris shearing to get ~400bp fragments
Sample pick up and well ID arrangement
Plate_ID | Location.in.AC-777-384-well | Note_Cp | New_96-well-plate_ID | Location.in.96-well-plate | Location.in.96-well-shearing_plate |
AC-777 | a4 | b13 | AC-777_plate1_A1-H12 | a4 | a3 |
AC-777 | a8 | b13 | AC-777_plate1_A1-H12 | a8 | b3 |
AC-777 | a9 | 13.12 | AC-777_plate1_A1-H12 | a9 | c3 |
AC-777 | a16 | b13 | AC-777_plate3_A13-H24 | a4 | d3 |
AC-777 | a17 | b13 | AC-777_plate3_A13-H24 | a5 | e3 |
AC-777 | a19 | b13 | AC-777_plate3_A13-H24 | a7 | f3 |
AC-777 | a20 | b13 | AC-777_plate3_A13-H24 | a8 | g3 |
AC-777 | a23 | b13 | AC-777_plate3_A13-H24 | a11 | h3 |
AC-777 | b4 | 13.11 | AC-777_plate1_A1-H12 | b4 | a4 |
AC-777 | b9 | 13.03 | AC-777_plate1_A1-H12 | b9 | b4 |
AC-777 | b17 | b13 | AC-777_plate3_A13-H24 | b5 | c4 |
AC-777 | b18 | b13 | AC-777_plate3_A13-H24 | b6 | d4 |
AC-777 | b21 | 13.5 | AC-777_plate3_A13-H24 | b9 | e4 |
AC-777 | b23 | b13 | AC-777_plate3_A13-H24 | b11 | f4 |
AC-777 | c2 | 13.46 | AC-777_plate1_A1-H12 | c2 | g4 |
AC-777 | c4 | 13.41 | AC-777_plate1_A1-H12 | c4 | h4 |
AC-777 | c7 | 13.22 | AC-777_plate1_A1-H12 | c7 | a5 |
AC-777 | c9 | 13.05 | AC-777_plate1_A1-H12 | c9 | b5 |
AC-777 | c10 | 13.15 | AC-777_plate1_A1-H12 | c10 | c5 |
AC-777 | c16 | 13.11 | AC-777_plate3_A13-H24 | c4 | d5 |
AC-777 | c17 | b13 | AC-777_plate3_A13-H24 | c5 | e5 |
AC-777 | c18 | b13 | AC-777_plate3_A13-H24 | c6 | f5 |
AC-777 | c21 | 13.18 | AC-777_plate3_A13-H24 | c9 | g5 |
AC-777 | c23 | b13 | AC-777_plate3_A13-H24 | c11 | h5 |
AC-777 | d3 | 13.44 | AC-777_plate1_A1-H12 | d3 | a6 |
AC-777 | d6 | b13 | AC-777_plate1_A1-H12 | d6 | b6 |
AC-777 | d8 | b13 | AC-777_plate1_A1-H12 | d8 | c6 |
AC-777 | d10 | 13.39 | AC-777_plate1_A1-H12 | d10 | d6 |
AC-777 | d11 | b13 | AC-777_plate1_A1-H12 | d11 | e6 |
AC-777 | d15 | b13 | AC-777_plate3_A13-H24 | d3 | f6 |
AC-777 | d16 | b13 | AC-777_plate3_A13-H24 | d4 | g6 |
AC-777 | d19 | 13.19 | AC-777_plate3_A13-H24 | d7 | h6 |
AC-777 | d20 | 13.19 | AC-777_plate3_A13-H24 | d8 | a7 |
AC-777 | e2 | b13 | AC-777_plate1_A1-H12 | e2 | b7 |
AC-777 | e5 | b13 | AC-777_plate1_A1-H12 | e5 | c7 |
AC-777 | e9 | 13.52 | AC-777_plate1_A1-H12 | e9 | d7 |
AC-777 | e10 | 13.09 | AC-777_plate1_A1-H12 | e10 | e7 |
AC-777 | e13 | 13.43 | AC-777_plate3_A13-H24 | e1 | f7 |
AC-777 | e14 | 13.4 | AC-777_plate3_A13-H24 | e2 | g7 |
AC-777 | e15 | 13.22 | AC-777_plate3_A13-H24 | e3 | h7 |
AC-777 | e17 | 13.04 | AC-777_plate3_A13-H24 | e5 | a8 |
AC-777 | e18 | b13 | AC-777_plate3_A13-H24 | e6 | b8 |
AC-777 | e20 | 13.06 | AC-777_plate3_A13-H24 | e8 | c8 |
AC-777 | f2 | b13 | AC-777_plate1_A1-H12 | f2 | d8 |
AC-777 | f5 | 13.04 | AC-777_plate1_A1-H12 | f5 | e8 |
AC-777 | f6 | b13 | AC-777_plate1_A1-H12 | f6 | f8 |
AC-777 | f7 | 13.34 | AC-777_plate1_A1-H12 | f7 | g8 |
AC-777 | f9 | 13.33 | AC-777_plate1_A1-H12 | f9 | h8 |
AC-777 | f10 | 13.05 | AC-777_plate1_A1-H12 | f10 | a9 |
AC-777 | f14 | b13 | AC-777_plate3_A13-H24 | f2 | b9 |
AC-777 | f15 | b13 | AC-777_plate3_A13-H24 | f3 | c9 |
AC-777 | f16 | 13 | AC-777_plate3_A13-H24 | f4 | d9 |
AC-777 | f17 | b13 | AC-777_plate3_A13-H24 | f5 | e9 |
AC-777 | f20 | 13.01 | AC-777_plate3_A13-H24 | f8 | f9 |
AC-777 | f23 | b13 | AC-777_plate3_A13-H24 | f11 | g9 |
AC-777 | g2 | b13 | AC-777_plate1_A1-H12 | g2 | h9 |
AC-777 | g4 | b13 | AC-777_plate1_A1-H12 | g4 | a10 |
AC-777 | g5 | 13.12 | AC-777_plate1_A1-H12 | g5 | b10 |
AC-777 | g6 | 13.01 | AC-777_plate1_A1-H12 | g6 | c10 |
AC-777 | g7 | b13 | AC-777_plate1_A1-H12 | g7 | d10 |
AC-777 | g8 | 13.35 | AC-777_plate1_A1-H12 | g8 | e10 |
AC-777 | g9 | b13 | AC-777_plate1_A1-H12 | g9 | f10 |
AC-777 | g10 | b13 | AC-777_plate1_A1-H12 | g10 | g10 |
AC-777 | g13 | 13.36 | AC-777_plate3_A13-H24 | g1 | h10 |
AC-777 | g14 | b13 | AC-777_plate3_A13-H24 | g2 | a11 |
AC-777 | g18 | 13.25 | AC-777_plate3_A13-H24 | g6 | b11 |
AC-777 | g19 | b13 | AC-777_plate3_A13-H24 | g7 | c11 |
- Note
- b13 = Cp value < 13 cycles (between 10<Cp<13)
- Because I list the sample based on the order in the original plate (AC-777-384-well), the order of samples from the New_96-well-plate to 96-well-shearing_plate might be not in the order of plate 1 and plate3. However, this will not be confusing when I program epMotion to transfer the sample.
- Arrangement of other 5 samples from AC-718-384-well (Note: these 5 samples were already transferred from 384-well to 96-well plate. The table below just for keep track of the location of samples in original 384-well plate, the new 96-well plate, and the 96-well shearing plate
Plate_ID | Location.in.AC-718-384-well | Note_Cp | New_96-well-plate_ID | Location.in.96-well-plate | Location.in.96-well-shearing_plate |
AC-718 | P07 | b_10.15 | AC-718-96-well_plate1 | a2 | d11 |
AC-718 | N17 | c_8.07 | AC-718-96-well_plate1 | b2 | e11 |
AC-718 | A21 | c_8.54 | AC-718-96-well_plate1 | c2 | f11 |
AC-718 | J04 | b_7.45 | AC-718-96-well_plate1 | d2 | g11 |
AC-718 | K06 | b_6.47 | AC-718-96-well_plate1 | e2 | h11 |
CSV input file: Step:1 AC-777_plate1_A1-H12_e.csv AC-777_plate2_I1-P12_e.csv AC-777_plate3_A13-H24_e.csv AC-777_plate4_I13-P24_e.csv Step:2&3 2013.01.31_SkinMB.sample-transfer-2-shearing-plate.csv Note: Rack (Source) 1 = AC-777_plate1_A1-H12 Rack (Source) 2 = AC-777_plate3_A13-H24 Rack (Source) 3 = AC-718-96-well_plate1 Rack (Destination) 1 = 96-well shearing plate