Goto: Data generated with tag sequence, and adenine homopolymer, DNA speed calc from intervals of tag; showed 100bp/sec data #AGBT17
8:42pm February 14th 2017 via Hootsuite
Goto: Motion-control at nm-scale: piezo actuator using laser doppler inferometry, showed 34nm/s speed or 100bp/sec #AGBT17
Goto: Looking at spatial resolution: five A's and a C, then 5 A's and a C. Showing signal histogram, four-mer resolution #AGBT17
8:41pm February 14th 2017 via Hootsuite
Goto: Shows homopolymeric signals, and blockade current's ability to discriminate between the four bases. #AGBT17
Goto: Showed 1.5nm, 2.4nm and 3.1nm pored via TEM images. #AGBT17
Goto: Use dielectric breakdown for nanopore fabrication. Can tune to target molecular size; accuracy of +/- 0.3nm (300pm!) #AGBT17
8:40pm February 14th 2017 via Hootsuite
Goto: Will talk mainly about sensing and motion control system (on the nanometer scale). Showed photos of LSI on wafer, and membrane #AGBT17
Goto: Using both modes - forward and reverse reads. Shows system concept, w/arrayed nanopore device on top of LSI circuit #AGBT17
Goto: Can do direct motion control - piezo actuator wtih mechanical (!) control. Can pull-down, and reverse to pull-up (!) #AGBT17
8:39pm February 14th 2017 via Hootsuite
Goto: Precise control of speed is impt for this method to work. They have developed SiN, 2.6nm thin membrane, on an 8-inch wafers #AGBT17
Goto: Points out Hitachi's development of ABi's 3730. Shows blockade current through solid-state, w/discrete signal pattern #AGBT17
8:38pm February 14th 2017 via Hootsuite
Goto: Shows short tandem repeats: ACACAC, ATCATC, AGTCAGTC: shows different blockage signals that can discriminate between 3 types #AGBT16
8:37pm February 14th 2017 via Hootsuite
Goto: Data generated with tag sequence, and adenine homopolymer, DNA speed calc from intervals of tag; showed 100bp/sec data #AGBT16
8:36pm February 14th 2017 via Hootsuite
Goto: Motion-control at nm-scale: piezo actuator using laser doppler inferometry, showed 34nm/s speed or 100bp/sec #AGBT16
8:35pm February 14th 2017 via Hootsuite
Goto: Looking at spatial resolution: five A's and a C, then 5 A's and a C. Showing signal histogram, four-mer resolution #AGBT16
8:34pm February 14th 2017 via Hootsuite
.@shgoodwin1 This talk is off the hook! Wild stuff!
8:33pm February 14th 2017 via Hootsuite in reply to shgoodwin1
Goto: Shows homopolymeric signals, and blockade current's ability to discriminate between the four bases. #AGBT16
8:33pm February 14th 2017 via Hootsuite
Goto: Showed 1.5nm, 2.4nm and 3.1nm pored via TEM images. #AGBT16
8:32pm February 14th 2017 via Hootsuite
Goto: Use dielectric breakdown for nanopore fabrication. Can tune to target molecular size; accuracy of +/- 0.3nm (300pm!) #AGBT16
8:31pm February 14th 2017 via Hootsuite
Goto: Will talk mainly about sensing and motion control system (on the nanometer scale). Showed photos of LSI on wafer, and membrane #AGBT16
8:30pm February 14th 2017 via Hootsuite
Goto: Using both modes - forward and reverse reads. Shows system concept, w/arrayed nanopore device on top of LSI circuit #AGBT16
8:29pm February 14th 2017 via Hootsuite
Goto: Can do direct motion control - piezo actuator wtih mechanical (!) control. Can pull-down, and reverse to pull-up (!) #AGBT16
8:28pm February 14th 2017 via Hootsuite
Goto: Precise control of speed is impt for this method to work. They have developed SiN, 2.6nm thin membrane, on an 8-inch wafers #AGBT16
8:27pm February 14th 2017 via Hootsuite
Goto: Points out Hitachi's development of ABi's 3730. Shows blockade current through solid-state, w/discrete signal pattern #AGBT16
8:26pm February 14th 2017 via Hootsuite
Yusuke Goto (Hitachi Ltd Japan) Solid state nanopore DNA sequencing: single-nucleotide discrimination and bidir. DNA translocation #AGBT17
8:24pm February 14th 2017 via Hootsuite
Can it be accessed now? Weile: Last stages of writing a paper and db to make it available #AGBT16
8:23pm February 14th 2017 via Hootsuite
Weile: Predict may be able to get to 57% of human disease genes with all these approaches. Est cost for a 500aa protein $5K #AGBT16
8:21pm February 14th 2017 via Hootsuite
Weile: How far can they go? 3970 disease genes, 5% have gene in yeast. 29% of disease genes in human cell culture. Also Y2H assay #AGBT16
8:20pm February 14th 2017 via Hootsuite
Weile: Working with @Invitae looked at their VUS to test, cp their DMS call to indication. 2/2 damaging; 5/5 benign 1 FN, 2 unk #AGBT16
8:19pm February 14th 2017 via Hootsuite
Weile: Describes deep mutational scanning (DMS), mutant ORFs plus barcodes, selection via complementation, then doing the genotyping #AGBT16
8:13pm February 14th 2017 via Hootsuite
Weile: Functional complementation assay - rescuing function by complementation. 'Surprising to see how well it works' #AGBT16
8:10pm February 14th 2017 via Hootsuite
Weile: PolyPhen-2 is popular but to base a clinical decision, precision vs recall curve, only 20% of disease assays would be called #AGBT16
8:09pm February 14th 2017 via Hootsuite
Weile: The problem of VUS: happening fairly often. Everyone has 100-400 rare missense variants never seen before. #AGBT16
8:08pm February 14th 2017 via Hootsuite
Jochen Weile (Uni Toronto CA) Building a functional atlas of all possible mutations in human disease genes. #AGBT16
Adey: sciATAC-Seq, SCI-seq (WGS), sciHiC (C-5), sciRNA-Seq for transcription. (Four papers.) BTW he's looking for a post-doc... #AGBT17
8:05pm February 14th 2017 via Hootsuite
Adey: However even though Li was more complex library, greater bias, impacting copy-number calls. #AGBT17
8:02pm February 14th 2017 via Hootsuite
Adey: Dev model to predict how many unique reads to expect/cell as a function of depth. about 872K reads. Showed Li=more complex #AGBT17
8:01pm February 14th 2017 via Hootsuite
Adey: Two methods - Li salt for disrupt; another is to crosslink and SDS denature. Can get 1200-2200 libraries per PCR plate #AGBT17
7:59pm February 14th 2017 via Hootsuite
Adey: faced challenge of chromatin accessibility. Need to unbind nucleosomes from chromatin w/o disrupting nuclear integrity #AGBT17
7:58pm February 14th 2017 via Hootsuite
Adey: Single-cell barcoding w/o handling or equipment, just a flow cytometer. sciATAC-Seq #AGBT17
Adey: Isolate nuclei, use tranposase-based Index 1 at 96-plex, FACS or dilute to ~20/well. PCR w/index 2. #AGBT17
7:56pm February 14th 2017 via Hootsuite
Adey: Current single cell depends on physical compartments. Their '14 Nature Gen https://t.co/o8VSbsVyZt https://t.co/gJFBgTHJyU #AGBT17
7:55pm February 14th 2017 via Hootsuite
Adey: Application is to look at intra-tumoral heterogeneity. Then tease out drug resistance, metastatic potential etc #AGBT17
7:53pm February 14th 2017 via Hootsuite
Andrew Adey (Oregan Health & Science Univ OR) Sequencing thousands of single-cell genomes with combinatorial indexing #AGBT17
7:51pm February 14th 2017 via Hootsuite
Q: Overcoming RNA degradation from kidney tissue? Bhalla: Most useful to cp groups to groups. 14 types ID'd #AGBT17
7:50pm February 14th 2017 via Hootsuite
Q: 1/10 population, 10K-20K cells/expt? Bhalla: Yes, only did 1,200 cells. #AGBT17
7:48pm February 14th 2017 via Hootsuite
Bhalla: Also could ID a novel cell type (could be transdifferentiation due to Rx, or perhaps new cell types) #AGBT17
7:46pm February 14th 2017 via Hootsuite
Bhalla: Specialized organs with many cell types - can scale to 100's of cells per cell type. Likes the agnostic nature (spp etc) #AGBT17
7:45pm February 14th 2017 via Hootsuite
Bhalla: Fourteen segment kidney, doing PCA, looked at gene expression patterns - very clean separation by PCA #AGBT17
7:42pm February 14th 2017 via Hootsuite
Bhalla: Shows data from '15 paper https://t.co/oozktjQKgN terribly labor-intensive, to look at diuretics, common Rx #AGBT17
7:40pm February 14th 2017 via Hootsuite
