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>Noi (Created page with "* http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''' = Skin Microbiom Project = # To do list ## Transfer amplicons from AC-777-384-...") |
>Noi mNo edit summary |
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* [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']] | * [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']] | ||
* Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-15 | |||
= Skin Microbiom Project = | = Skin Microbiom Project = | ||
# To do list | # To do list | ||
## Transfer amplicons from AC-777-384-well to 4 of 96-well plate | ## 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 (take 6ul for library construction). | ||
## Picked 67 samples from the 96-well 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 | ||
## Shear DNA by Covaris shearing to get ~400bp fragments | ## Shear DNA by Covaris shearing to get ~400bp fragments | ||
== Sample pick up and well ID arrangement == | |||
{| class="wikitable" style="text-align:center; | |||
| align="center" style="background:#f0f0f0;"|'''Plate_ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Location.in.AC-777-384-well''' | |||
| align="center" style="background:#f0f0f0;"|'''Note_Cp''' | |||
| align="center" style="background:#f0f0f0;"|'''New_96-well-plate_ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Location.in.96-well-plate''' | |||
| align="center" style="background:#f0f0f0;"|'''Location.in.96-well-shearing_plate''' | |||
|- style="text-align: center;" | |||
| AC-777||a4||b13||AC-777_plate1_A1-H12||a4||a3 | |||
|- style="text-align: center;" | |||
| AC-777||a8||b13||AC-777_plate1_A1-H12||a8||b3 | |||
|- style="text-align: center;" | |||
| AC-777||a9||13.12||AC-777_plate1_A1-H12||a9||c3 | |||
|- style="text-align: center;" | |||
| AC-777||a16||b13||AC-777_plate3_A13-H24||a4||d3 | |||
|- style="text-align: center;" | |||
| AC-777||a17||b13||AC-777_plate3_A13-H24||a5||e3 | |||
|- style="text-align: center;" | |||
| AC-777||a19||b13||AC-777_plate3_A13-H24||a7||f3 | |||
|- style="text-align: center;" | |||
| AC-777||a20||b13||AC-777_plate3_A13-H24||a8||g3 | |||
|- style="text-align: center;" | |||
| AC-777||a23||b13||AC-777_plate3_A13-H24||a11||h3 | |||
|- style="text-align: center;" | |||
| AC-777||b4||13.11||AC-777_plate1_A1-H12||b4||a4 | |||
|- style="text-align: center;" | |||
| AC-777||b9||13.03||AC-777_plate1_A1-H12||b9||b4 | |||
|- style="text-align: center;" | |||
| AC-777||b17||b13||AC-777_plate3_A13-H24||b5||c4 | |||
|- style="text-align: center;" | |||
| AC-777||b18||b13||AC-777_plate3_A13-H24||b6||d4 | |||
|- style="text-align: center;" | |||
| AC-777||b21||13.5||AC-777_plate3_A13-H24||b9||e4 | |||
|- style="text-align: center;" | |||
| AC-777||b23||b13||AC-777_plate3_A13-H24||b11||f4 | |||
|- style="text-align: center;" | |||
| AC-777||c2||13.46||AC-777_plate1_A1-H12||c2||g4 | |||
|- style="text-align: center;" | |||
| AC-777||c4||13.41||AC-777_plate1_A1-H12||c4||h4 | |||
|- style="text-align: center;" | |||
| AC-777||c7||13.22||AC-777_plate1_A1-H12||c7||a5 | |||
|- style="text-align: center;" | |||
| AC-777||c9||13.05||AC-777_plate1_A1-H12||c9||b5 | |||
|- style="text-align: center;" | |||
| AC-777||c10||13.15||AC-777_plate1_A1-H12||c10||c5 | |||
|- style="text-align: center;" | |||
| AC-777||c16||13.11||AC-777_plate3_A13-H24||c4||d5 | |||
|- style="text-align: center;" | |||
| AC-777||c17||b13||AC-777_plate3_A13-H24||c5||e5 | |||
|- style="text-align: center;" | |||
| AC-777||c18||b13||AC-777_plate3_A13-H24||c6||f5 | |||
|- style="text-align: center;" | |||
| AC-777||c21||13.18||AC-777_plate3_A13-H24||c9||g5 | |||
|- style="text-align: center;" | |||
| AC-777||c23||b13||AC-777_plate3_A13-H24||c11||h5 | |||
|- style="text-align: center;" | |||
| AC-777||d3||13.44||AC-777_plate1_A1-H12||d3||a6 | |||
|- style="text-align: center;" | |||
| AC-777||d6||b13||AC-777_plate1_A1-H12||d6||b6 | |||
|- style="text-align: center;" | |||
| AC-777||d8||b13||AC-777_plate1_A1-H12||d8||c6 | |||
|- style="text-align: center;" | |||
| AC-777||d10||13.39||AC-777_plate1_A1-H12||d10||d6 | |||
|- style="text-align: center;" | |||
| AC-777||d11||b13||AC-777_plate1_A1-H12||d11||e6 | |||
|- style="text-align: center;" | |||
| AC-777||d15||b13||AC-777_plate3_A13-H24||d3||f6 | |||
|- style="text-align: center;" | |||
| AC-777||d16||b13||AC-777_plate3_A13-H24||d4||g6 | |||
|- style="text-align: center;" | |||
| AC-777||d19||13.19||AC-777_plate3_A13-H24||d7||h6 | |||
|- style="text-align: center;" | |||
| AC-777||d20||13.19||AC-777_plate3_A13-H24||d8||a7 | |||
|- style="text-align: center;" | |||
| AC-777||e2||b13||AC-777_plate1_A1-H12||e2||b7 | |||
|- style="text-align: center;" | |||
| AC-777||e5||b13||AC-777_plate1_A1-H12||e5||c7 | |||
|- style="text-align: center;" | |||
| AC-777||e9||13.52||AC-777_plate1_A1-H12||e9||d7 | |||
|- style="text-align: center;" | |||
| AC-777||e10||13.09||AC-777_plate1_A1-H12||e10||e7 | |||
|- style="text-align: center;" | |||
| AC-777||e13||13.43||AC-777_plate3_A13-H24||e1||f7 | |||
|- style="text-align: center;" | |||
| AC-777||e14||13.4||AC-777_plate3_A13-H24||e2||g7 | |||
|- style="text-align: center;" | |||
| AC-777||e15||13.22||AC-777_plate3_A13-H24||e3||h7 | |||
|- style="text-align: center;" | |||
| AC-777||e17||13.04||AC-777_plate3_A13-H24||e5||a8 | |||
|- style="text-align: center;" | |||
| AC-777||e18||b13||AC-777_plate3_A13-H24||e6||b8 | |||
|- style="text-align: center;" | |||
| AC-777||e20||13.06||AC-777_plate3_A13-H24||e8||c8 | |||
|- style="text-align: center;" | |||
| AC-777||f2||b13||AC-777_plate1_A1-H12||f2||d8 | |||
|- style="text-align: center;" | |||
| AC-777||f5||13.04||AC-777_plate1_A1-H12||f5||e8 | |||
|- style="text-align: center;" | |||
| AC-777||f6||b13||AC-777_plate1_A1-H12||f6||f8 | |||
|- style="text-align: center;" | |||
| AC-777||f7||13.34||AC-777_plate1_A1-H12||f7||g8 | |||
|- style="text-align: center;" | |||
| AC-777||f9||13.33||AC-777_plate1_A1-H12||f9||h8 | |||
|- style="text-align: center;" | |||
| AC-777||f10||13.05||AC-777_plate1_A1-H12||f10||a9 | |||
|- style="text-align: center;" | |||
| AC-777||f14||b13||AC-777_plate3_A13-H24||f2||b9 | |||
|- style="text-align: center;" | |||
| AC-777||f15||b13||AC-777_plate3_A13-H24||f3||c9 | |||
|- style="text-align: center;" | |||
| AC-777||f16||13||AC-777_plate3_A13-H24||f4||d9 | |||
|- style="text-align: center;" | |||
| AC-777||f17||b13||AC-777_plate3_A13-H24||f5||e9 | |||
|- style="text-align: center;" | |||
| AC-777||f20||13.01||AC-777_plate3_A13-H24||f8||f9 | |||
|- style="text-align: center;" | |||
| AC-777||f23||b13||AC-777_plate3_A13-H24||f11||g9 | |||
|- style="text-align: center;" | |||
| AC-777||g2||b13||AC-777_plate1_A1-H12||g2||h9 | |||
|- style="text-align: center;" | |||
| AC-777||g4||b13||AC-777_plate1_A1-H12||g4||a10 | |||
|- style="text-align: center;" | |||
| AC-777||g5||13.12||AC-777_plate1_A1-H12||g5||b10 | |||
|- style="text-align: center;" | |||
| AC-777||g6||13.01||AC-777_plate1_A1-H12||g6||c10 | |||
|- style="text-align: center;" | |||
| AC-777||g7||b13||AC-777_plate1_A1-H12||g7||d10 | |||
|- style="text-align: center;" | |||
| AC-777||g8||13.35||AC-777_plate1_A1-H12||g8||e10 | |||
|- style="text-align: center;" | |||
| AC-777||g9||b13||AC-777_plate1_A1-H12||g9||f10 | |||
|- style="text-align: center;" | |||
| AC-777||g10||b13||AC-777_plate1_A1-H12||g10||g10 | |||
|- style="text-align: center;" | |||
| AC-777||g13||13.36||AC-777_plate3_A13-H24||g1||h10 | |||
|- style="text-align: center;" | |||
| AC-777||g14||b13||AC-777_plate3_A13-H24||g2||a11 | |||
|- style="text-align: center;" | |||
| AC-777||g18||13.25||AC-777_plate3_A13-H24||g6||b11 | |||
|- style="text-align: center;" | |||
| 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 to plate3. However, this will not be confusing when I program epMotion to transfer the sample (see the sample transfer order in the CSV input file below). | |||
* 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 | |||
{| class="wikitable" style="text-align:center; | |||
| align="center" style="background:#f0f0f0;"|'''Plate_ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Location.in.AC-718-384-well''' | |||
| align="center" style="background:#f0f0f0;"|'''Note_Cp''' | |||
| align="center" style="background:#f0f0f0;"|'''New_96-well-plate_ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Location.in.96-well-plate''' | |||
| align="center" style="background:#f0f0f0;"|'''Location.in.96-well-shearing_plate''' | |||
|- style="text-align: center;" | |||
| AC-718||P07||b_10.15||AC-718-96-well_plate1||a2||d11 | |||
|- style="text-align: center;" | |||
| AC-718||N17||c_8.07||AC-718-96-well_plate1||b2||e11 | |||
|- style="text-align: center;" | |||
| AC-718||A21||c_8.54||AC-718-96-well_plate1||c2||f11 | |||
|- style="text-align: center;" | |||
| AC-718||J04||b_7.45||AC-718-96-well_plate1||d2||g11 | |||
|- style="text-align: center;" | |||
| AC-718||K06||b_6.47||AC-718-96-well_plate1||e2||h11 | |||
|} | |||
* Note | |||
** C = 1 cell Lysozyme | |||
'''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 | |||
* Continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-2-7 |
Latest revision as of 21:58, 7 February 2013
- [Link to calendar]
- Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-1-15
Skin Microbiom Project[edit]
- 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 (take 6ul for library construction).
- 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[edit]
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 to plate3. However, this will not be confusing when I program epMotion to transfer the sample (see the sample transfer order in the CSV input file below).
- 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 |
- Note
- C = 1 cell Lysozyme
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