Andrew:Notebook/AR150702 C1: Difference between revisions
>Andrew (Created page with "==Sequential MDA on C1 with PEO1== * July 2, 2015 * Experiment ID: AR150702_C1 ===Results=== ====Gels==== 600px") |
>Andrew |
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(11 intermediate revisions by the same user not shown) | |||
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==Sequential MDA on C1 with PEO1 | ==Planning== | ||
* Sequential MDA on C1 with PEO1 | |||
* July 2, 2015 | * July 2, 2015 | ||
* Experiment ID: AR150702_C1 | * Experiment ID: AR150702_C1 | ||
===Results=== | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''(bases)''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
|- | |||
| haploid length|| 3,100,000,000 |||||| | |||
|- | |||
| diploid length|| 6,200,000,000 |||||| | |||
|- | |||
| denature length|| 12,400,000,000 |||||| | |||
|- | |||
| |||||||| | |||
|- | |||
| phi29 mean processivity|| 70,000 |||||| | |||
|- | |||
| N9 combinations|| 262,144 ||N6|||| | |||
|- | |||
| % annealed template at 30 C||98%||2%|||| | |||
|- | |||
| |||||||| | |||
|- | |||
| desired gain||100||1000|||| | |||
|- | |||
| space between primers|| 691 || 61 |||| | |||
|- | |||
| # N9s to cover every base|| 1,377,777,778 |||||| | |||
|- | |||
| # N9s for spacing|| 1,968,254 |||||| | |||
|- | |||
| mols of N9 desired||3.27E-18|||||| | |||
|- | |||
| |||||||| | |||
|- | |||
| volume of first MDA (nL)|| 31.5 |||||| | |||
|- | |||
| volume of first MDA (L)||3.15E-08|||||| | |||
|- | |||
| concentration of N9 (M)||1.038E-10|||||| | |||
|- | |||
| concentration of N9 (nM)|| 0.1038 ||1|||| | |||
|- | |||
| fold change vs 50 uM|| 481,721 |||||| | |||
|- | |||
| |||||||| | |||
|- | |||
| primers (uM)||50|||||| | |||
|- | |||
| primers (M)||0.00005|||||| | |||
|- | |||
| |||||||| | |||
|- | |||
| ||C1 31 nL||Microwell 12 nL||volume (L)||1.20E-08 | |||
|- | |||
| dNTPs (mM)||4.00E-01|||||| | |||
|- | |||
| dNTPs (M)||4.00E-04|||||| | |||
|- | |||
| mol dNTPs||1.26E-11|||||| | |||
|- | |||
| # dNTPs||7.59E+12|||||| | |||
|- | |||
| mass/dNTPS incorporated (g/mol)||3.30E+02|||||| | |||
|- | |||
| mass of dntps (g)||4.16E-09|||||| | |||
|- | |||
| mass of dntps (pg)||4.16E+03|||||| | |||
|- | |||
| mass of single genome (pg)||6.6|||||| | |||
|- | |||
| gain|| 630 || 240 |||| | |||
|- | |||
| | |||
|} | |||
===Protocol=== | |||
====C1 setup==== | |||
[[File:AR150702_reagents-page-001.jpg|600px]] | |||
[[File:Protocol Worksheet AR150702_C1 v1-page-001.jpg|600px]] | |||
[[File:Protocol Worksheet AR150702_C1 v1-page-002.jpg|600px]] | |||
[[File:Protocol Worksheet AR150702_C1 v1-page-003.jpg|600px]] | |||
[[File:AR150702_thermalProfile.jpg|600px]] | |||
====Off chip==== | |||
Prep | |||
* Add 1.2 uL 50X SYBR Green I to 120 uL NPM | |||
Nextera XT | |||
*Same as standard protocol, but add 15.5 uL NPM/SYBR Green I mix and run on qPCR machine (final volume 50.5 uL) | |||
0.1X Tn5-059 | |||
*5 uL total | |||
**3 ul template | |||
**1 ul SSB | |||
**1 ul 1X Tn5-059 | |||
*Incubate 55 C for 5 min, transfer to cold block | |||
*Add 1 ul 0.2 mg/ml Qiagen Protease | |||
*Incubate 50 C for 15 min, followed by heat inactivation at 70 C for 20 min | |||
*Add 19 uL H2O to bring volume up from 6 uL to 25 uL | |||
*Add 5 uL each index (N7xx/S5xx) | |||
*Add 15.5 uL NPM/SYBR Green I mix | |||
qPCR protocol | |||
*72 C for 3 min | |||
*95 C for 1 min | |||
*25 cycles (but prepare to stop early) | |||
**95 C for 15 sec | |||
**55 C for 30 sec | |||
**72 C for 30 sec, acquisition | |||
**72 C for 15 sec | |||
*72 C for 5 min | |||
==Results== | |||
===C1 capture=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Chamber''' | |||
| align="center" style="background:#f0f0f0;"|'''Well''' | |||
| align="center" style="background:#f0f0f0;"|'''Number''' | |||
| align="center" style="background:#f0f0f0;"|'''LiveOrDead''' | |||
| align="center" style="background:#f0f0f0;"|'''Notes''' | |||
|- | |||
| Ch01||A03||0||na||na | |||
|- | |||
| Ch02||A02||0||na||na | |||
|- | |||
| Ch13||C03||1||both||na | |||
|- | |||
| Ch04||A09||0||na||na | |||
|- | |||
| Ch05||A08||0||na||na | |||
|- | |||
| Ch06||A07||0||na||na | |||
|- | |||
| Ch07||B03||0||na||na | |||
|- | |||
| Ch08||B02||0||na||na | |||
|- | |||
| Ch14||C02||1||both||na | |||
|- | |||
| Ch10||B09||0||na||na | |||
|- | |||
| Ch11||B08||0||na||na | |||
|- | |||
| Ch12||B07||0||na||na | |||
|- | |||
| Ch18||C07||1||both||na | |||
|- | |||
| Ch24||D07||1||both||na | |||
|- | |||
| Ch15||C01||0||na||na | |||
|- | |||
| Ch16||C09||0||na||na | |||
|- | |||
| Ch25||E01||1||both||na | |||
|- | |||
| Ch26||E02||1||both||na | |||
|- | |||
| Ch19||D03||0||na||na | |||
|- | |||
| Ch20||D02||0||na||na | |||
|- | |||
| Ch29||E08||1||both||na | |||
|- | |||
| Ch30||E09||1||both||na | |||
|- | |||
| Ch23||Ch||0||na||na | |||
|- | |||
| Ch31||F01||1||both||na | |||
|- | |||
| Ch34||F07||3||both||na | |||
|- | |||
| Ch35||F08||1||both||na | |||
|- | |||
| Ch27||E03||0||na||na | |||
|- | |||
| Ch28||E07||0||na||na | |||
|- | |||
| Ch36||F09||1||both||na | |||
|- | |||
| Ch40||G07||1||both||na | |||
|- | |||
| Ch45||H03||1||both||extravasating | |||
|- | |||
| Ch32||F02||0||na||na | |||
|- | |||
| Ch33||F03||0||na||na | |||
|- | |||
| Ch48||H09||1||both||extravasating | |||
|- | |||
| Ch17||C08||2||dead||na | |||
|- | |||
| Ch21||D01||1||dead||na | |||
|- | |||
| Ch37||G01||1||dead||na | |||
|- | |||
| Ch38||G02||0||na||na | |||
|- | |||
| Ch39||G03||0||na||na | |||
|- | |||
| Ch44||H02||1||dead||na | |||
|- | |||
| Ch46||H07||1||dead||na | |||
|- | |||
| Ch42||G09||0||na||na | |||
|- | |||
| Ch43||H01||0||na||na | |||
|- | |||
| Ch47||H08||1||dead||na | |||
|- | |||
| Ch03||A01||1||live||na | |||
|- | |||
| Ch09||B01||1||live||na | |||
|- | |||
| Ch22||D09||1||live||weak | |||
|- | |||
| Ch41||G08||1||live||na | |||
|- | |||
| Ch49||A04||0||na||na | |||
|- | |||
| Ch50||A05||0||na||na | |||
|- | |||
| Ch51||A06||0||na||na | |||
|- | |||
| Ch52||A10||0||na||na | |||
|- | |||
| Ch53||A11||0||na||na | |||
|- | |||
| Ch54||A12||0||na||na | |||
|- | |||
| Ch55||B04||0||na||na | |||
|- | |||
| Ch56||B05||0||na||na | |||
|- | |||
| Ch57||B06||0||na||na | |||
|- | |||
| Ch58||B10||0||na||na | |||
|- | |||
| Ch59||B11||0||na||na | |||
|- | |||
| Ch60||B12||0||na||na | |||
|- | |||
| Ch61||C04||0||na||na | |||
|- | |||
| Ch62||C05||0||na||na | |||
|- | |||
| Ch63||C06||0||na||na | |||
|- | |||
| Ch64||C10||0||na||na | |||
|- | |||
| Ch65||C11||0||na||na | |||
|- | |||
| Ch66||C12||0||na||na | |||
|- | |||
| Ch67||D04||0||na||na | |||
|- | |||
| Ch68||D05||0||na||na | |||
|- | |||
| Ch69||D06||0||na||na | |||
|- | |||
| Ch70||D10||0||na||na | |||
|- | |||
| Ch71||D11||0||na||na | |||
|- | |||
| Ch72||D12||0||na||na | |||
|- | |||
| Ch73||E06||0||na||na | |||
|- | |||
| Ch74||E05||0||na||na | |||
|- | |||
| Ch75||E04||0||na||na | |||
|- | |||
| Ch76||E12||0||na||na | |||
|- | |||
| Ch77||E11||0||na||na | |||
|- | |||
| Ch78||E10||0||na||na | |||
|- | |||
| Ch79||F06||0||na||na | |||
|- | |||
| Ch80||F05||0||na||na | |||
|- | |||
| Ch81||F04||0||na||na | |||
|- | |||
| Ch82||F12||0||na||na | |||
|- | |||
| Ch83||F11||0||na||na | |||
|- | |||
| Ch84||F10||0||na||na | |||
|- | |||
| Ch85||G06||0||na||na | |||
|- | |||
| Ch86||G05||0||na||na | |||
|- | |||
| Ch87||G04||0||na||na | |||
|- | |||
| Ch88||G12||0||na||na | |||
|- | |||
| Ch89||G11||0||na||na | |||
|- | |||
| Ch90||G10||0||na||na | |||
|- | |||
| Ch91||H06||0||na||na | |||
|- | |||
| Ch92||H05||0||na||na | |||
|- | |||
| Ch93||H04||0||na||na | |||
|- | |||
| Ch94||H12||0||na||na | |||
|- | |||
| Ch95||H11||0||na||na | |||
|- | |||
| Ch96||H10||0||na||debris (clog) | |||
|- | |||
| | |||
|} | |||
===Gels=== | |||
[[File:AR150702_C1_gelsSlide1.png|600px]] | |||
[[File:AR150702_C1_gelsSlide2.png|600px]] | |||
[[File:AR150702_C1_gelsSlide3.png|600px]] | |||
[[File:AR150702_C1_gelsSlide4.png|600px]] | |||
===Sequencing=== | |||
First round of sequencing | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Index Sequence''' | |||
| align="center" style="background:#f0f0f0;"|'''# of Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''Run Type, Minmum BP''' | |||
| align="center" style="background:#f0f0f0;"|'''Library Size''' | |||
| align="center" style="background:#f0f0f0;"|'''Read 1 Sequencing Primer''' | |||
| align="center" style="background:#f0f0f0;"|'''Index Primer''' | |||
| align="center" style="background:#f0f0f0;"|'''Read 2 Sequencing Primer''' | |||
| align="center" style="background:#f0f0f0;"|'''Notes''' | |||
|- | |||
| INITIAL-PROJECT-SAMPLE-DATE-Index||CGTGCA||Million||SE/PE, 36+6+36||SIZE RANGE (BP)||Name||Name||Name|| | |||
|- | |||
| AR-150702-D01-NxtXT-N702-S502||CGTACTAG-CTCTCTAT||1.5||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-E01-NxtXT-N702-S503||CGTACTAG-TATCCTCT||1.5||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-G01-NxtXT-N702-S505||CGTACTAG-GTAAGGAG||1.5||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-D01-CoRE-NEBNext25||TACTGC||1.5||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-E01-CoRE-NEBNext26||TCGTGA||1.5||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-G01-CoRE-NEBNext27||TACGCG||1.5||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-D01-Tn5059-N701-S506||TAAGGCGA-ACTGCATA||3||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 New | |||
|- | |||
| AR-150702-E01-Tn5059-N701-S507||TAAGGCGA-AAGGAGTA||3||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 New | |||
|- | |||
| AR-150702-G01-Tn5059-N701-S508||TAAGGCGA-CTAAGCCT||3||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 New | |||
|- | |||
| | |||
|} | |||
2nd Round of sequencing | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''SampleID''' | |||
| align="center" style="background:#f0f0f0;"|'''Index Sequence''' | |||
| align="center" style="background:#f0f0f0;"|'''# of Reads (M)''' | |||
| align="center" style="background:#f0f0f0;"|'''Run Type, Minmum BP''' | |||
| align="center" style="background:#f0f0f0;"|'''Size range (bp)''' | |||
| align="center" style="background:#f0f0f0;"|'''Read 1 Primer''' | |||
| align="center" style="background:#f0f0f0;"|'''Index 1 Primer''' | |||
| align="center" style="background:#f0f0f0;"|'''Read 2 Primer''' | |||
| align="center" style="background:#f0f0f0;"|'''Tube labeled''' | |||
|- | |||
| AR-150702-Ch03-A01-N703-S502||AGGCAGAA-CTCTCTAT||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool1 | |||
|- | |||
| AR-150702-Ch09-B01-N703-S503||AGGCAGAA-TATCCTCT||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool1 | |||
|- | |||
| AR-150702-Ch22-D09-N703-S505||AGGCAGAA-GTAAGGAG||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool1 | |||
|- | |||
| AR-150702-Ch44-H02-N703-S506||AGGCAGAA-ACTGCATA||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool1 | |||
|- | |||
| AR-150702-Ch45-H03-N703-S507||AGGCAGAA-AAGGAGTA||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool2 | |||
|- | |||
| AR-150702-Ch46-H07-N703-S508||AGGCAGAA-CTAAGCCT||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool2 | |||
|- | |||
| AR-150702-Ch47-H08-N703-S504||AGGCAGAA-AGAGTAGA||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool2 | |||
|- | |||
| AR-150702-Ch48-H09-N703-S517||AGGCAGAA-GCGTAAGA||2||SE50+8+8||200-800||HP10||HP12||NA||AR150714_Pool2 | |||
|- | |||
| AR-150702-D01-NxtXT-N702-S502||CGTACTAG-CTCTCTAT||0.67||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-E01-NxtXT-N702-S503||CGTACTAG-TATCCTCT||0.67||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-G01-NxtXT-N702-S505||CGTACTAG-GTAAGGAG||0.67||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-D01-CoRE-NEBNext25||TACTGC||0.67||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-E01-CoRE-NEBNext26||TCGTGA||0.67||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| AR-150702-G01-CoRE-NEBNext27||TACGCG||0.67||SE50+8+8||200-800||HP10||HP12||NA||DT Tn5 Old | |||
|- | |||
| | |||
|} | |||
===Screening=== | |||
[[File:AR150702_libraryComplexities.jpg|600px]] | |||
===CNV profiling=== | |||
[[File:AR-150702-Ch02ntc-A02-N702-S502.all.png|600px]] | |||
[[File:AR-150702-Ch03wklve-A01-N703-S502.all.png|600px]] | |||
[[File:AR-150702-Ch09wklve-B01-N703-S503.all.png|600px]] | |||
[[File:AR-150702-Ch21dea-D01-N702-S502.all.png|600px]] | |||
[[File:AR-150702-Ch22wklve-D09-N703-S505.all.png|600px]] | |||
[[File:AR-150702-Ch25bth-E01-N702-S503.all.png|600px]] | |||
[[File:AR-150702-Ch35bth-F08-N706-S517.all.png|600px]] | |||
[[File:AR-150702-Ch37dea-G01-N702-S505.all.png|600px]] | |||
[[File:AR-150702-Ch44dea-H02-N703-S506.all.png|600px]] | |||
[[File:AR-150702-Ch45lve-H03-N703-S507.all.png|600px]] | |||
[[File:AR-150702-Ch46dea-H07-N703-S508.all.png|600px]] | |||
[[File:AR-150702-Ch47dea-H08-N703-S504.all.png|600px]] | |||
[[File:AR-150702-Ch48bth-H09-N703-S517.all.png|600px]] | |||
[[File:DT-150701-bulk-PEO1-N704-S502.all.png|600px]] | |||
[[File:DT-150701-bulk-PEO4-N703-S517.all.png|600px]] | |||
===MAPD profiling=== |
Latest revision as of 20:41, 10 September 2015
Planning[edit]
- Sequential MDA on C1 with PEO1
- July 2, 2015
- Experiment ID: AR150702_C1
' | (bases) | ' | ' | ' |
haploid length | 3,100,000,000 | |||
diploid length | 6,200,000,000 | |||
denature length | 12,400,000,000 | |||
phi29 mean processivity | 70,000 | |||
N9 combinations | 262,144 | N6 | ||
% annealed template at 30 C | 98% | 2% | ||
desired gain | 100 | 1000 | ||
space between primers | 691 | 61 | ||
# N9s to cover every base | 1,377,777,778 | |||
# N9s for spacing | 1,968,254 | |||
mols of N9 desired | 3.27E-18 | |||
volume of first MDA (nL) | 31.5 | |||
volume of first MDA (L) | 3.15E-08 | |||
concentration of N9 (M) | 1.038E-10 | |||
concentration of N9 (nM) | 0.1038 | 1 | ||
fold change vs 50 uM | 481,721 | |||
primers (uM) | 50 | |||
primers (M) | 0.00005 | |||
C1 31 nL | Microwell 12 nL | volume (L) | 1.20E-08 | |
dNTPs (mM) | 4.00E-01 | |||
dNTPs (M) | 4.00E-04 | |||
mol dNTPs | 1.26E-11 | |||
# dNTPs | 7.59E+12 | |||
mass/dNTPS incorporated (g/mol) | 3.30E+02 | |||
mass of dntps (g) | 4.16E-09 | |||
mass of dntps (pg) | 4.16E+03 | |||
mass of single genome (pg) | 6.6 | |||
gain | 630 | 240 | ||
Protocol[edit]
C1 setup[edit]
File:AR150702 reagents-page-001.jpg File:Protocol Worksheet AR150702 C1 v1-page-001.jpg File:Protocol Worksheet AR150702 C1 v1-page-002.jpg File:Protocol Worksheet AR150702 C1 v1-page-003.jpg File:AR150702 thermalProfile.jpg
Off chip[edit]
Prep
- Add 1.2 uL 50X SYBR Green I to 120 uL NPM
Nextera XT
- Same as standard protocol, but add 15.5 uL NPM/SYBR Green I mix and run on qPCR machine (final volume 50.5 uL)
0.1X Tn5-059
- 5 uL total
- 3 ul template
- 1 ul SSB
- 1 ul 1X Tn5-059
- Incubate 55 C for 5 min, transfer to cold block
- Add 1 ul 0.2 mg/ml Qiagen Protease
- Incubate 50 C for 15 min, followed by heat inactivation at 70 C for 20 min
- Add 19 uL H2O to bring volume up from 6 uL to 25 uL
- Add 5 uL each index (N7xx/S5xx)
- Add 15.5 uL NPM/SYBR Green I mix
qPCR protocol
- 72 C for 3 min
- 95 C for 1 min
- 25 cycles (but prepare to stop early)
- 95 C for 15 sec
- 55 C for 30 sec
- 72 C for 30 sec, acquisition
- 72 C for 15 sec
- 72 C for 5 min
Results[edit]
C1 capture[edit]
Chamber | Well | Number | LiveOrDead | Notes |
Ch01 | A03 | 0 | na | na |
Ch02 | A02 | 0 | na | na |
Ch13 | C03 | 1 | both | na |
Ch04 | A09 | 0 | na | na |
Ch05 | A08 | 0 | na | na |
Ch06 | A07 | 0 | na | na |
Ch07 | B03 | 0 | na | na |
Ch08 | B02 | 0 | na | na |
Ch14 | C02 | 1 | both | na |
Ch10 | B09 | 0 | na | na |
Ch11 | B08 | 0 | na | na |
Ch12 | B07 | 0 | na | na |
Ch18 | C07 | 1 | both | na |
Ch24 | D07 | 1 | both | na |
Ch15 | C01 | 0 | na | na |
Ch16 | C09 | 0 | na | na |
Ch25 | E01 | 1 | both | na |
Ch26 | E02 | 1 | both | na |
Ch19 | D03 | 0 | na | na |
Ch20 | D02 | 0 | na | na |
Ch29 | E08 | 1 | both | na |
Ch30 | E09 | 1 | both | na |
Ch23 | Ch | 0 | na | na |
Ch31 | F01 | 1 | both | na |
Ch34 | F07 | 3 | both | na |
Ch35 | F08 | 1 | both | na |
Ch27 | E03 | 0 | na | na |
Ch28 | E07 | 0 | na | na |
Ch36 | F09 | 1 | both | na |
Ch40 | G07 | 1 | both | na |
Ch45 | H03 | 1 | both | extravasating |
Ch32 | F02 | 0 | na | na |
Ch33 | F03 | 0 | na | na |
Ch48 | H09 | 1 | both | extravasating |
Ch17 | C08 | 2 | dead | na |
Ch21 | D01 | 1 | dead | na |
Ch37 | G01 | 1 | dead | na |
Ch38 | G02 | 0 | na | na |
Ch39 | G03 | 0 | na | na |
Ch44 | H02 | 1 | dead | na |
Ch46 | H07 | 1 | dead | na |
Ch42 | G09 | 0 | na | na |
Ch43 | H01 | 0 | na | na |
Ch47 | H08 | 1 | dead | na |
Ch03 | A01 | 1 | live | na |
Ch09 | B01 | 1 | live | na |
Ch22 | D09 | 1 | live | weak |
Ch41 | G08 | 1 | live | na |
Ch49 | A04 | 0 | na | na |
Ch50 | A05 | 0 | na | na |
Ch51 | A06 | 0 | na | na |
Ch52 | A10 | 0 | na | na |
Ch53 | A11 | 0 | na | na |
Ch54 | A12 | 0 | na | na |
Ch55 | B04 | 0 | na | na |
Ch56 | B05 | 0 | na | na |
Ch57 | B06 | 0 | na | na |
Ch58 | B10 | 0 | na | na |
Ch59 | B11 | 0 | na | na |
Ch60 | B12 | 0 | na | na |
Ch61 | C04 | 0 | na | na |
Ch62 | C05 | 0 | na | na |
Ch63 | C06 | 0 | na | na |
Ch64 | C10 | 0 | na | na |
Ch65 | C11 | 0 | na | na |
Ch66 | C12 | 0 | na | na |
Ch67 | D04 | 0 | na | na |
Ch68 | D05 | 0 | na | na |
Ch69 | D06 | 0 | na | na |
Ch70 | D10 | 0 | na | na |
Ch71 | D11 | 0 | na | na |
Ch72 | D12 | 0 | na | na |
Ch73 | E06 | 0 | na | na |
Ch74 | E05 | 0 | na | na |
Ch75 | E04 | 0 | na | na |
Ch76 | E12 | 0 | na | na |
Ch77 | E11 | 0 | na | na |
Ch78 | E10 | 0 | na | na |
Ch79 | F06 | 0 | na | na |
Ch80 | F05 | 0 | na | na |
Ch81 | F04 | 0 | na | na |
Ch82 | F12 | 0 | na | na |
Ch83 | F11 | 0 | na | na |
Ch84 | F10 | 0 | na | na |
Ch85 | G06 | 0 | na | na |
Ch86 | G05 | 0 | na | na |
Ch87 | G04 | 0 | na | na |
Ch88 | G12 | 0 | na | na |
Ch89 | G11 | 0 | na | na |
Ch90 | G10 | 0 | na | na |
Ch91 | H06 | 0 | na | na |
Ch92 | H05 | 0 | na | na |
Ch93 | H04 | 0 | na | na |
Ch94 | H12 | 0 | na | na |
Ch95 | H11 | 0 | na | na |
Ch96 | H10 | 0 | na | debris (clog) |
Gels[edit]
File:AR150702 C1 gelsSlide1.png
File:AR150702 C1 gelsSlide2.png
File:AR150702 C1 gelsSlide3.png
File:AR150702 C1 gelsSlide4.png
Sequencing[edit]
First round of sequencing
Sample ID | Index Sequence | # of Reads | Run Type, Minmum BP | Library Size | Read 1 Sequencing Primer | Index Primer | Read 2 Sequencing Primer | Notes |
INITIAL-PROJECT-SAMPLE-DATE-Index | CGTGCA | Million | SE/PE, 36+6+36 | SIZE RANGE (BP) | Name | Name | Name | |
AR-150702-D01-NxtXT-N702-S502 | CGTACTAG-CTCTCTAT | 1.5 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-E01-NxtXT-N702-S503 | CGTACTAG-TATCCTCT | 1.5 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-G01-NxtXT-N702-S505 | CGTACTAG-GTAAGGAG | 1.5 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-D01-CoRE-NEBNext25 | TACTGC | 1.5 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-E01-CoRE-NEBNext26 | TCGTGA | 1.5 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-G01-CoRE-NEBNext27 | TACGCG | 1.5 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-D01-Tn5059-N701-S506 | TAAGGCGA-ACTGCATA | 3 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 New |
AR-150702-E01-Tn5059-N701-S507 | TAAGGCGA-AAGGAGTA | 3 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 New |
AR-150702-G01-Tn5059-N701-S508 | TAAGGCGA-CTAAGCCT | 3 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 New |
2nd Round of sequencing
SampleID | Index Sequence | # of Reads (M) | Run Type, Minmum BP | Size range (bp) | Read 1 Primer | Index 1 Primer | Read 2 Primer | Tube labeled |
AR-150702-Ch03-A01-N703-S502 | AGGCAGAA-CTCTCTAT | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool1 |
AR-150702-Ch09-B01-N703-S503 | AGGCAGAA-TATCCTCT | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool1 |
AR-150702-Ch22-D09-N703-S505 | AGGCAGAA-GTAAGGAG | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool1 |
AR-150702-Ch44-H02-N703-S506 | AGGCAGAA-ACTGCATA | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool1 |
AR-150702-Ch45-H03-N703-S507 | AGGCAGAA-AAGGAGTA | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool2 |
AR-150702-Ch46-H07-N703-S508 | AGGCAGAA-CTAAGCCT | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool2 |
AR-150702-Ch47-H08-N703-S504 | AGGCAGAA-AGAGTAGA | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool2 |
AR-150702-Ch48-H09-N703-S517 | AGGCAGAA-GCGTAAGA | 2 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | AR150714_Pool2 |
AR-150702-D01-NxtXT-N702-S502 | CGTACTAG-CTCTCTAT | 0.67 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-E01-NxtXT-N702-S503 | CGTACTAG-TATCCTCT | 0.67 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-G01-NxtXT-N702-S505 | CGTACTAG-GTAAGGAG | 0.67 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-D01-CoRE-NEBNext25 | TACTGC | 0.67 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-E01-CoRE-NEBNext26 | TCGTGA | 0.67 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
AR-150702-G01-CoRE-NEBNext27 | TACGCG | 0.67 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | DT Tn5 Old |
Screening[edit]
File:AR150702 libraryComplexities.jpg
CNV profiling[edit]
File:AR-150702-Ch02ntc-A02-N702-S502.all.png File:AR-150702-Ch03wklve-A01-N703-S502.all.png File:AR-150702-Ch09wklve-B01-N703-S503.all.png File:AR-150702-Ch21dea-D01-N702-S502.all.png File:AR-150702-Ch22wklve-D09-N703-S505.all.png File:AR-150702-Ch25bth-E01-N702-S503.all.png File:AR-150702-Ch35bth-F08-N706-S517.all.png File:AR-150702-Ch37dea-G01-N702-S505.all.png File:AR-150702-Ch44dea-H02-N703-S506.all.png File:AR-150702-Ch45lve-H03-N703-S507.all.png File:AR-150702-Ch46dea-H07-N703-S508.all.png File:AR-150702-Ch47dea-H08-N703-S504.all.png File:AR-150702-Ch48bth-H09-N703-S517.all.png File:DT-150701-bulk-PEO1-N704-S502.all.png File:DT-150701-bulk-PEO4-N703-S517.all.png