Andrew Richards

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Revision as of 19:08, 11 September 2015 by >Andrew
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Notebook (Old)

2012

2013

2014

Bias Plots

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

Experiments by project

Bulk Nextera libraries

July 30, 2014

January 22, 2015 (SW480)

January 25, 2015 (SW480 and lymphocyte)

February 10, 2015 (1-02 and 25-01)

MIDAS

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

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

Sequential MDA in tube with GM12878 7/29/2015

Direct Tn5

Tn5059 (super mutant) test, February 17, 2015

In tube validation of Direct Tn5 C1 protocol

Misc

PCR test for Mycoplasma contamination 9/8/2015

Protocols

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)

Computational stuff

CNV workflow

mapdata.sh

fastq2CNV perl.pl

callCNVs.sh

getCNVdata.sh

Email from Jeff with tips on CNV calling

Sorts and samples

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

Samples for CNV analysis

Sequenced libraries for CNV analysis

MDA microarray samples

  • This is old. See Samples for full information

Sequencing samples

Reagents

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

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