Noi/NOTES/2013-1-31: Difference between revisions

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>Noi
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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 (original '''AC-777-384-well'''). 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
## 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

Skin Microbiom Project[edit]

  1. To do list
    1. 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).
    2. 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.
    3. Plus 5 samples from AC-718-96-well_plate1 (A2-E2, sample info. [[2]]), total of samples will be processed is 72 samples
    4. 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