Andrew Richards

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Notebook (Old)[edit]

2012

2013

2014

Bias Plots

MagVigen DNA Select Focus 300/600 beads, October 1, 2014

Experiments by project[edit]

Gel Micro Droplets (GMDs)[edit]

December 1, 2015

December 2, 2015

December 3, 2015

Bulk Nextera libraries[edit]

July 30, 2014

January 22, 2015 (SW480)

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]

July 03, 2013

July 17 and 24, 2013

September 30, 2013

October 11, 2013

February 27, 2014

March 24, 2014

April 08, 2014

April 08 Ecoli, 2014

May 13, 2014

May 28, 2014

June 27, 2014

June 30, 2014

August 28, 2014

September 11, 2014

September 17, 2014

September 24, 2014

January 09, 2015

January 30, 2015

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

Microarray fabrication

MDA on microarray

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

MDA amplicon size selection

Size selection, 4/2/2015

CEL-Seq

Microscope bulb change

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

Tn5059 protocol (supermutant)

Thawing mammalian cells from LN2

Computational stuff[edit]

CNV workflow

mapdata.sh

fastq2CNV perl.pl

callCNVs.sh

getCNVdata.sh

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]

Samples for CNV analysis

Sequenced libraries for CNV analysis

MDA microarray samples

  • This is old. See Samples for full information

Sequencing samples

Reagents[edit]

CEL-Seq primers

High molecular weight (HMW) buffer recipe

  • From Rui's wiki

Nextera dilution

Alkaline lysis solution (ALS)

Neutralization solution (NS)

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

Progress report for December 5, 2013

Progress report for January 13, 2014