Andrew Richards: Difference between revisions
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==Notebook== | ==Notebook (Old)== | ||
[[Arichard:Notebook/2012|2012]] | [[Arichard:Notebook/2012|2012]] | ||
[[Arichard:Notebook/2013|2013]] | |||
[[Arichard:Notebook/2014|2014]] | |||
[[Arichard:Notebook/biasPlots|Bias Plots]] | |||
[http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140911 MagVigen DNA Select Focus 300/600 beads, October 1, 2014] | |||
==Experiments by project== | |||
===Gel Micro Droplets (GMDs)=== | |||
[[Arichard:Notebook/AR151201|December 1, 2015]] | |||
[[Arichard:Notebook/AR151202|December 2, 2015]] | |||
[[Arichard:Notebook/AR151203|December 3, 2015]] | |||
===Bulk Nextera libraries=== | |||
[[Arichard:Notebook/bulkNxt2014Jul30|July 30, 2014]] | |||
[[Arichard:Notebook/bulk150122|January 22, 2015 (SW480)]] | |||
[[Arichard:Notebook/bulk150125|January 25, 2015 (SW480 and lymphocyte)]] | |||
[[Arichard:Notebook/bulk150210|February 10, 2015 (1-02 and 25-01)]] | |||
===Bulk GM12878 libraries to create copy number z-distributions=== | |||
[[Arichard:Notebook/AR150914|10 libraries analyzed 9/14/2015]] | |||
===MIDAS=== | |||
[[Arichard:Notebook/midas2013Jul03|July 03, 2013]] | |||
[[Arichard:Notebook/midas2013Jul17And24|July 17 and 24, 2013]] | |||
[[Arichard:Notebook/midas2013Sep30|September 30, 2013]] | |||
[[Arichard:Notebook/midas2013Oct11|October 11, 2013]] | |||
[[Arichard:Notebook/midas2014Feb27|February 27, 2014]] | |||
[[Arichard:Notebook/midas2014Mar24|March 24, 2014]] | |||
[[Arichard:Notebook/midas2014Apr08|April 08, 2014]] | |||
[[Arichard:Notebook/midas2014Apr08Ecoli|April 08 Ecoli, 2014]] | |||
[[Arichard:Notebook/midas2014May13|May 13, 2014]] | |||
[[Arichard:Notebook/midas2014May28|May 28, 2014]] | |||
[[Arichard:Notebook/midas2014Jun27|June 27, 2014]] | |||
[[Arichard:Notebook/midas2014Jun30|June 30, 2014]] | |||
[[Arichard:Notebook/midas2014Aug28|August 28, 2014]] | |||
[[Arichard:Notebook/midas140911|September 11, 2014]] | |||
[[Arichard:Notebook/midas140917|September 17, 2014]] | |||
[[Arichard:Notebook/midas140924|September 24, 2014]] | |||
[[Arichard:Notebook/midas150109|January 09, 2015]] | |||
[[Arichard:Notebook/midas150130|January 30, 2015]] | |||
===C1 DNA Experiments=== | |||
[[Chris:LabNotes/FateMapping/Calendar/2014/2014-7-30| C1 DNA 5-10 um Chip on July 30, 2014]] | |||
[[Andrew:Notebook/directTn5150301 | In tube validation of ALS/Direct Tn5 3/3/2015]] | |||
[[Andrew:Notebook/directTn5150303 | Direct Tn5 with 1-02 NeuN+ Ctx on C1 3/3/2015]] | |||
[[Andrew:Notebook/C1_InTube_31nL_MDA_150320 | In tube validation for 31 nL MDA protocol 3/20/2015]] | |||
[[Andrew:Notebook/C1_InTube_23nL_MDA_150324 | In tube validation for 23 nL MDA protocol 3/24/2015]] | |||
[[Andrew:Notebook/C1_InTube_ALS_150330 | In tube validation for ALS protocol 3/30/2015]] | |||
[[Andrew:Notebook/C1_InTube_HLS_150333 | In tube validation for HLS protocol 3/33/2015]] | |||
[[Andrew:Notebook/C1_HLS_150409 | C1 OpenApp HLS protocol with NeuN+ cortex from AD patient 1-02 4/9/2015]] | |||
[[Andrew:Notebook/C1Tube_HLS_150420 | In tube validation for HLS protocol with NPM PCR on NeuN+ cortex from AD patient 1-02 4/20/2015]] | |||
[[Andrew:Notebook/C1_OpenApp_150421 | C1 OpenApp on NeuN+ cortex from AD patient 18-99 4/21/2015]] | |||
[[Andrew:Notebook/C1_OpenApp_150429 | C1 OpenApp Tn5-059 vs. EZ-Tn5 on GM12878 4/29/2015]] | |||
* Includes in-tube trouble-shooting experiments from May | |||
[[Andrew:Notebook/C1_InTube_150525 | Troubleshooting HLS-Tn5 protocol on GM12878 5/25/2015]] | |||
[[Andrew:Notebook/AR150602_Tn5Titrate_C1 | Tn5 titration on C1 with GM12878 6/02/2015]] | |||
* Loaded too much mouse DNA, repeated 6/05 with correct dilution | |||
[[Andrew:Notebook/AR150605_Tn5Titrate_C1 | Tn5 titration on C1 with GM12878 6/05/2015]] | |||
* Library prep failed | |||
[[Andrew:Notebook/AR150612_Tn5Titrate_inTube | Tn5 titration in tube with GM12878 6/12/2015]] | |||
* Library prep failed. Last attempt at titrating Tn5 on-chip | |||
[[Andrew:Notebook/AR150618_C1 | 31 nL MDA on C1 with GM12878 6/18/2015]] | |||
* Very noisy, high MDA bias suspected | |||
[[Andrew:Notebook/AR150625_C1 | 31 nL MDA on C1 with GM12878 and PEO1 6/25/2015]] | |||
* This experiment was performed before seeing the results of 31 nL MDA on GM12878. The amplification bias looked bad, and the CNV profiles were very noisy | |||
[[Andrew:Notebook/AR150701_bulk | Bulk Nextera XT with PEO1 and PEO4 7/1/2015]] | |||
[[Andrew:Notebook/AR150702_C1 | Sequential MDA on C1 with PEO1 7/2/2015]] | |||
* First promising results in several months! | |||
[[Andrew:Notebook/AR150720_C1 | Sequential MDA on C1 with PEO1/GM12878 7/20/2015]] | |||
* Modification of 7/2 protocol, unsuccessful due to excessive amplification bias | |||
[[Andrew:Notebook/AR150729_inTube | Sequential MDA in tube with GM12878 7/29/2015]] | |||
[[Andrew:Notebook/AR150809_C1 | Sequential MDA on C1 with GM12878 and PEO1 8/9/2015]] | |||
[[Andrew:Notebook/AR150817_C1 | Sequential MDA on C1 with PEO4 8/17/2015]] | |||
[[Andrew:Notebook/AR150921_C1 | Sequential MDA on C1 with 2N GM12878 nuclei 9/21/2015]] | |||
[[Andrew:Notebook/AR151006_C1_sMDA | C1-sMDA on 2N sorted GM12878 nuclei 10/01/2015 and 10/06/2015]] | |||
===Direct Tn5=== | |||
[[Arichard:Notebook/superMut150217| Tn5059 (super mutant) test, February 17, 2015]] | |||
[[Arichard:Notebook/DirectTn5_InTube| In tube validation of Direct Tn5 C1 protocol]] | |||
===Feng Lab liver cancer=== | |||
[[Arichard:Notebook/XL151216_ExomeCNVs_AR | CNV calling on Feng lab exome data from 12/16/2015]] | |||
* Exome capture by Xiaolin Luo | |||
* Sequenced at IGM | |||
[[Arichard:Notebook/JL160222_ExomeCNVs_AR | CNV calling on Feng lab exome data from 2/22/2016]] | |||
* Exome capture by Jin Lee | |||
* Sequenced at IGM | |||
[[Arichards:Notebook/MeetingWithKota160317 | Meeting with Kota Kaneko 3/17/2016]] | |||
===Misc=== | |||
[[Arichard:Notebook/AR150908_mycoTest | PCR test for Mycoplasma contamination 9/8/2015]] | |||
[[Arichard:Notebook/BZ150825_tubeMDA | In tube MDA with hLINE qPCR to test Phi29 yield 8/25/2015]] | |||
* Performed by BZ. Showed possible contamination. Yield inconsistent with hypothesis, with N9 having higher yield than N9* or N9** | |||
[[Arichard:Notebook/BZ150826_tubeMDA | In tube MDA with hLINE qPCR to test Phi29 yield 8/26/2015]] | |||
* Performed by BZ. This time, amplification efficiency appeared to be zero. NEC had highest quantification, possibly due to lack of exonuclease activity. | |||
[[Arichard:Notebook/QJ150910_mycoTest | In tube MDA with hLINE qPCR to test Phi29 activity 9/10/2015]] | |||
* Performed by QJ | |||
[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-7-13 Dr. Zhang's gel-MDA experiment #1] | |||
[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-5-12 Dr. Zhang's gel-MDA experiment #2] | |||
==Protocols== | ==Protocols== | ||
Line 11: | Line 176: | ||
[[Arichard:Protocols/MDA_on_microarray|MDA on microarray]] | [[Arichard:Protocols/MDA_on_microarray|MDA on microarray]] | ||
[[Arichard:Protocols/ | [[Arichard:Protocols/MDA_on_microarray_2013_09_05|MDA on microarray as of September 5, 2013]] | ||
[[Arichard:Protocols/MDA_amplicon_extraction_and_processing|MDA amplicon extraction and processing]] | |||
[[Arichard:Protocols/MDA_amplicon_extraction_and_processing_2013_09_05|MDA amplicon extraction and processing as of September 5, 2013]] | |||
[[Arichard:Protocols/MDA_amplicon_tagmentation_and_amplification|MDA amplicon tagmentation and PCR]] | |||
[[Arichard:Protocols/MDA_amplicon_tagmentation_and_amplification_2013_09_05|MDA amplicon tagmentation and PCR as of September 5, 2013]] | |||
[[Arichard:Protocols/MDA_amplicon_size_selection|MDA amplicon size selection]] | |||
[[Arichard:Protocols/size_selection_150402|Size selection, 4/2/2015]] | |||
[[Arichard:Protocols/CEL_Seq|CEL-Seq]] | |||
[[Arichard:Protocols/Microscope_bulb_change|Microscope bulb change]] | |||
[[Arichard:Protocols/Technics_PEIIB|Technics PEIIB Planar Etcher for PDMS surface activation]] | |||
[[Arichard:Protocols/neuronalnucleiisolation20131203|Neuronal nuclei isolation as of December 3, 2013]] | |||
[http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2014-11-18 Brandon's protocol for DNA purification after guanidine HCl] | |||
[[Arichard:Protocols/tn5059|Tn5059 protocol (supermutant)]] | |||
[[Arichard:Protocols/thawing_mammalian_cells_from_LN2|Thawing mammalian cells from LN2]] | |||
==Computational stuff== | |||
[[Arichard:Computational/CNV_workflow|CNV workflow]] | |||
[[File:mapdata.sh|mapdata.sh]] | |||
[[File:fastq2CNV.txt|fastq2CNV perl.pl]] | |||
[[File:callCNVs.sh|callCNVs.sh]] | |||
[[File:getCNVdata.sh|getCNVdata.sh]] | |||
[[Arichard:Computational/email_from_jeff|Email from Jeff with tips on CNV calling]] | |||
==Sorts and samples== | |||
[[Arichard:Samples/sort140520 | 25-00 AD and 7-03 Control sorted May 20, 2014]] | |||
[[Arichard:Samples/sort141009 | 1-02 AD and 25-01 Control sorted October 9, 2014]] | |||
[[Arichard:Samples/sort141021 | SW480 and lymphocytes sorted October 21, 2014]] | |||
[[Arichard:Samples/sort150408 | 18-99 AD Cortex +/- Full PI sorted April 8, 2015]] | |||
[[Arichard:Samples/cells150514 | GM12878 from Brandon, frozen down on May 14, 2015]] | |||
==Samples== | ==Samples== | ||
[https://docs.google.com/spreadsheet/ccc?key=0Amo99lqQqQEYdDI2RDMwRDRjMWdRY3JTX2VzeV9ySHc#gid=0 Samples for CNV analysis] | |||
[https://docs.google.com/spreadsheet/ccc?key=0Amo99lqQqQEYdHUyWkUwT1p4YTB2UTZHUVRfV0NsRUE&usp=drive_web#gid=0 Sequenced libraries for CNV analysis] | |||
[[Arichard:Samples/MDA_microarray_samples|MDA microarray samples]] | [[Arichard:Samples/MDA_microarray_samples|MDA microarray samples]] | ||
* This is old. See [https://docs.google.com/spreadsheet/ccc?key=0Amo99lqQqQEYdDI2RDMwRDRjMWdRY3JTX2VzeV9ySHc#gid=0 Samples] for full information | |||
[[Arichard:Samples/Sequencing_samples|Sequencing samples]] | |||
* This is also old. See [https://docs.google.com/spreadsheet/ccc?key=0Amo99lqQqQEYdHUyWkUwT1p4YTB2UTZHUVRfV0NsRUE&usp=drive_web#gid=0 Sequenced libraries] | |||
==Reagents== | ==Reagents== | ||
[[Arichard:Reagents/ | [[Arichard:Reagents/celseq primers|CEL-Seq primers]] | ||
[[Arichard:Reagents/hmw_buffer|High molecular weight (HMW) buffer recipe]] | |||
* From Rui's wiki | |||
[[Arichard:Reagents/nexteraDilution|Nextera dilution]] | |||
[[Arichard:Reagents/als|Alkaline lysis solution (ALS)]] | |||
[[Arichard:Reagents/ns|Neutralization solution (NS)]] | |||
[[Arichard:Reagents/hls|Hypotonic lysis solution (HLS)]] | |||
[[Arichard:Reagents/nexteraXTv2|Nextera XT v2 primers (8 x 12)]] | |||
==Slides== | |||
[[File: 20130226ProgressReport.pptx| Progress report for February 26, 2013]] | |||
[[File: 20130226ProgressReportRevised.pptx| Progress report for February 26, 2013 REVISED]] | |||
[[File: 20130425ProgressReport.pptx| Progress report for April 25, 2013]] | |||
[[File: 20130605ProgressReport.pptx| Progress report for June 5, 2013]] | |||
[[File: 20130904ProgressReport.pptx| Progress report for September 04, 2013]] | |||
[[File: 20131205ProgressReport.pptx| Progress report for December 5, 2013]] | |||
[[File: 20140113ProgressReport.pptx| Progress report for January 13, 2014]] |
Latest revision as of 21:05, 21 July 2016
Notebook (Old)[edit]
MagVigen DNA Select Focus 300/600 beads, October 1, 2014
Experiments by project[edit]
Gel Micro Droplets (GMDs)[edit]
Bulk Nextera libraries[edit]
January 25, 2015 (SW480 and lymphocyte)
February 10, 2015 (1-02 and 25-01)
Bulk GM12878 libraries to create copy number z-distributions[edit]
10 libraries analyzed 9/14/2015
MIDAS[edit]
C1 DNA Experiments[edit]
C1 DNA 5-10 um Chip on July 30, 2014
In tube validation of ALS/Direct Tn5 3/3/2015
Direct Tn5 with 1-02 NeuN+ Ctx on C1 3/3/2015
In tube validation for 31 nL MDA protocol 3/20/2015
In tube validation for 23 nL MDA protocol 3/24/2015
In tube validation for ALS protocol 3/30/2015
In tube validation for HLS protocol 3/33/2015
C1 OpenApp HLS protocol with NeuN+ cortex from AD patient 1-02 4/9/2015
In tube validation for HLS protocol with NPM PCR on NeuN+ cortex from AD patient 1-02 4/20/2015
C1 OpenApp on NeuN+ cortex from AD patient 18-99 4/21/2015
C1 OpenApp Tn5-059 vs. EZ-Tn5 on GM12878 4/29/2015
- Includes in-tube trouble-shooting experiments from May
Troubleshooting HLS-Tn5 protocol on GM12878 5/25/2015
Tn5 titration on C1 with GM12878 6/02/2015
- Loaded too much mouse DNA, repeated 6/05 with correct dilution
Tn5 titration on C1 with GM12878 6/05/2015
- Library prep failed
Tn5 titration in tube with GM12878 6/12/2015
- Library prep failed. Last attempt at titrating Tn5 on-chip
31 nL MDA on C1 with GM12878 6/18/2015
- Very noisy, high MDA bias suspected
31 nL MDA on C1 with GM12878 and PEO1 6/25/2015
- This experiment was performed before seeing the results of 31 nL MDA on GM12878. The amplification bias looked bad, and the CNV profiles were very noisy
Bulk Nextera XT with PEO1 and PEO4 7/1/2015
Sequential MDA on C1 with PEO1 7/2/2015
- First promising results in several months!
Sequential MDA on C1 with PEO1/GM12878 7/20/2015
- Modification of 7/2 protocol, unsuccessful due to excessive amplification bias
Sequential MDA in tube with GM12878 7/29/2015
Sequential MDA on C1 with GM12878 and PEO1 8/9/2015
Sequential MDA on C1 with PEO4 8/17/2015
Sequential MDA on C1 with 2N GM12878 nuclei 9/21/2015
C1-sMDA on 2N sorted GM12878 nuclei 10/01/2015 and 10/06/2015
Direct Tn5[edit]
Tn5059 (super mutant) test, February 17, 2015
In tube validation of Direct Tn5 C1 protocol
Feng Lab liver cancer[edit]
CNV calling on Feng lab exome data from 12/16/2015
- Exome capture by Xiaolin Luo
- Sequenced at IGM
CNV calling on Feng lab exome data from 2/22/2016
- Exome capture by Jin Lee
- Sequenced at IGM
Meeting with Kota Kaneko 3/17/2016
Misc[edit]
PCR test for Mycoplasma contamination 9/8/2015
In tube MDA with hLINE qPCR to test Phi29 yield 8/25/2015
- Performed by BZ. Showed possible contamination. Yield inconsistent with hypothesis, with N9 having higher yield than N9* or N9**
In tube MDA with hLINE qPCR to test Phi29 yield 8/26/2015
- Performed by BZ. This time, amplification efficiency appeared to be zero. NEC had highest quantification, possibly due to lack of exonuclease activity.
In tube MDA with hLINE qPCR to test Phi29 activity 9/10/2015
- Performed by QJ
Dr. Zhang's gel-MDA experiment #1
Dr. Zhang's gel-MDA experiment #2
Protocols[edit]
Glass micropipette fabrication
MDA on microarray as of September 5, 2013
MDA amplicon extraction and processing
MDA amplicon extraction and processing as of September 5, 2013
MDA amplicon tagmentation and PCR
MDA amplicon tagmentation and PCR as of September 5, 2013
Technics PEIIB Planar Etcher for PDMS surface activation
Neuronal nuclei isolation as of December 3, 2013
Brandon's protocol for DNA purification after guanidine HCl
Thawing mammalian cells from LN2
Computational stuff[edit]
Email from Jeff with tips on CNV calling
Sorts and samples[edit]
25-00 AD and 7-03 Control sorted May 20, 2014
1-02 AD and 25-01 Control sorted October 9, 2014
SW480 and lymphocytes sorted October 21, 2014
18-99 AD Cortex +/- Full PI sorted April 8, 2015
GM12878 from Brandon, frozen down on May 14, 2015
Samples[edit]
Sequenced libraries for CNV analysis
- This is old. See Samples for full information
- This is also old. See Sequenced libraries
Reagents[edit]
High molecular weight (HMW) buffer recipe
- From Rui's wiki
Hypotonic lysis solution (HLS)
Nextera XT v2 primers (8 x 12)
Slides[edit]
Progress report for February 26, 2013
Progress report for February 26, 2013 REVISED
Progress report for April 25, 2013
Progress report for June 5, 2013
Progress report for September 04, 2013