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==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]
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