Q: Barrier to real-time analysis? Wiley #AGBT19 Areas are unsafe, not wanting to disrupt diagnostic labs. (Space is precious.)
9:10pm March 1st 2019 via Twitter Web Client
Wiley #AGBT19 Shows primer/probes for Cepheid GeneXpert cartridge. Concl able to train local scientist to go from s… https://t.co/msh97qxcI3
9:05pm March 1st 2019 via Twitter Web Client
Wiley #AGBT19 Clear that the two outbreaks (on opposite sides of the Congo) were not related to each other.
9:01pm March 1st 2019 via Twitter Web Client
Wiley #AGBT19 Timeline - time from the samples to arrive from the field took time. FedEx equipment got stuck in customs.
9:00pm March 1st 2019 via Twitter Web Client
Wiley #AGBT19 Had a pan-viral probe set, synthesized by Twist, 600K probes from over 1000 RefSeq viral segments.
Wiley #AGBT19 Supply chain - +4 or -20C using 120h shippers. Other groups were using ONT, so they chose iSeq. They… https://t.co/UCiZFlpnsv
8:55pm March 1st 2019 via Twitter Web Client
Wiley #AGBT19 Can synthesize for vaccine or therapy development. Congo has an Ebola outbreak 2018-2019, 54 in Bikoro; >800 in Nord-Kivu.
8:52pm March 1st 2019 via Twitter Web Client
Wiley #AGBT19 Why WGS for outbreak response? Dx will give yes/no answer. WGS can get appropriate countermeasures. C… https://t.co/qwBnWfg4GY
8:51pm March 1st 2019 via Twitter Web Client
Michael Wiley (Univ Nebraska) #AGBT19 “Rapid deployment of an Illumina iSeq100 for accurate whole viral genome sequ… https://t.co/n1U7PxYGTJ
8:50pm March 1st 2019 via Twitter Web Client
Van Dorpe #AGBT19 Conclude - sensitive at single molecule, can distinguish bases, but not sequence yet.
8:44pm March 1st 2019 via Twitter Web Client
Van Dorpe #AGBT19 Now measuring adjacent bases. Poly-A end with CG. Also epigenetic modifications, shows different Raman shift.
8:43pm March 1st 2019 via Twitter Web Client
RT @DCGenomics: Manolis Kellis shows disease relevance of cell type specific epigenomics! #AGBT19 https://t.co/PozJUAgQCT
8:42pm March 1st 2019 via Hootsuite Inc.
Van Dorpe #AGBT19 Adenine isotopes at single molecule limit, data from '18 Nature Comm https://t.co/86Vdibvgul Asyn… https://t.co/ijd8Ahk3j2
8:41pm March 1st 2019 via Twitter Web Client
Van Dorpe #AGBT19 Like a guitar string, has to resonate at right frequency. A few nm gap between gold slits. Mfg in… https://t.co/PS53j6hImA
8:39pm March 1st 2019 via Twitter Web Client
Van Dorpe #AGBT19 Surface Raman - many orders of magnitude (7) better signal. '18 ref https://t.co/5r02Famzi9 Thei… https://t.co/k7vIhyKCfr
8:36pm March 1st 2019 via Twitter Web Client
Van Dorpe #AGBT19 Raman needs at least a Billion molecules, inelastic scattering of light by molecules through exci… https://t.co/vTvZe9lAai
8:35pm March 1st 2019 via Twitter Web Client
Van Dorpe #AGBT19 The methods they are working on - today focus on last one. https://t.co/BctOdATubY
8:34pm March 1st 2019 via Twitter for iPhone
Van Dorpe #AGBT19 Nanopore sensing mainly current-based. Measure current through pore. Solid-state, or biological.… https://t.co/dxYK7fbk14
8:33pm March 1st 2019 via Twitter Web Client
Can Dorpe #AGBT19 Photo of their capabilities - extensive. https://t.co/zPU3DNPAnM
8:32pm March 1st 2019 via Twitter for iPhone
Van Dorpe #AGBT19 Warning: physics ahead! IMEC is world-leading Belgian R&D in nano-electronics and digital technol… https://t.co/sbZrbu
8:31pm March 1st 2019 via Twitter Web Client
Pol Van Dorpe, IMEC #AGBT19 “Label-free identification of single nucleobases in a DNA strand using surface enhanced… https://t.co/r1zy7KHAJb
8:29pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 Applied to V(D)J pairing, have started to generate a kit, and send to collaborators. Q: Ligation effic? A: Haven't measured.
8:27pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 Concl: Most scalable, >100K cells, multiplex samples, stored and frozen cells, choice of fixatives.
8:26pm March 1st 2019 via Hootsuite Inc.
Seelig #AGBT19 Re-embed lineage cells in a second tSNE, organize genes early to late, and look at how the expressio… https://t.co/NkuVB1pOUm
8:21pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 How to make sense of clusters? Use the analysis and automate annotation. tSNE plots, and mouse brain… https://t.co/83nOV5KSKK
8:19pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 Sample multiplexing. iPSC to cardiomyocyte differentiation. Many months cells collected, and fixed.… https://t.co/uUZdJ4OwDp
8:16pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 Also works with nuclei. Iterated, compared with 10x and smartseq (another method) Genes/cell is higher with splitseq.
8:14pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 What doublet rate? 1% means 100K cells. Used species mixing 888 mouse cells 868 human and 2 mixed ce… https://t.co/UndEMFt5q0
8:12pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 Then perform RT in the well, with 1000 cells. Collect, and mix, and then re-distribute. A second rou… https://t.co/b77ZxRII16
Seelig #AGBT19 They treat the cell as a compartment. First fix, then permeabilize and deliver reagents to the fixed… https://t.co/NLNvhCFxpG
8:10pm March 1st 2019 via Twitter Web Client
Seelig #AGBT19 One cell, into one compartment, with a barcode of RT primers. Then lysed, converted to cDNA, then ba… https://t.co/xnWpQVeRLK
Georg Seelig (Univ Washington) #AGBT19 “Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding”
8:09pm March 1st 2019 via Twitter Web Client
Q: Modified bases? Hunkapillar #AGBT19 Easier with CCS method.
8:08pm March 1st 2019 via Hootsuite Inc.
Hunkapillar #AGBT19 - Can you do centromeres? One 4.2 Mb contig with Hyperscaffold - highly repetitive, region.
Hunkapillar #AGBT19 Is this a centromere? Tantalizing. https://t.co/AnxwY2gNDj
8:08pm March 1st 2019 via Twitter for iPhone
Hunkapillar #AGBT19 CCS reads have high accuracy and long readlength. Showed some Sequel II system data. Inserts up… https://t.co/KUcW9PujdK
8:05pm March 1st 2019 via Hootsuite Inc.
Hunkapillar #AGBT19 Using Google DeepVariant increased accuracy doing this calling a different way. https://t.co/Ck5Ok1d0u6
8:00pm March 1st 2019 via Twitter for iPhone
Hunkapiller #AGBT19 Error profiles between short and long reads can be quite different. '18 ref https://t.co/goDlC7WbvX
7:59pm March 1st 2019 via Hootsuite Inc.
Hunkapiller #AGBT19 CCS reads - can get 1,733 bp deletion (cp to short reads which of course are missed). Showed pr… https://t.co/EkH23Kn6Hy
7:57pm March 1st 2019 via Hootsuite Inc.
Hunkapillar #AGBT19 Accuracy of de novo assembly. https://t.co/QspwPeBltk
7:56pm March 1st 2019 via Twitter for iPhone
Hunkapiller #AGBT19 De novo assembly of CCS (twice) and CLR, all about 3GB apiece. N50 15-18 MB; concordance (Phred) 48, 47, 40.
7:56pm March 1st 2019 via Hootsuite Inc.
Hunkapiller #AGBT19 Chose to demonstrate this: HG002 (Askkenazim son), RM8391. '16 ref Sci Data https://t.co/cdyhZViODR
7:54pm March 1st 2019 via Hootsuite Inc.
Hunkapiller#AGBT19 CLR now >20kb, accuracy 89.0%. Linear dsDNA with hairpin adapters is now a circle, can go around… https://t.co/iP1fsfX
7:52pm March 1st 2019 via Hootsuite Inc.
Mike Hunkapiller Pacific Biosciences #AGBT19 “High fidelity long reads for comprehensive genomic analysis”
7:50pm March 1st 2019 via Hootsuite Inc.
@OmicsOmicsBlog No mention at all, sorry. Nice to hear from you Keith!
7:49pm March 1st 2019 via Hootsuite Inc. in reply to OmicsOmicsBlog
Rodriques #AGBT19 Onto neuronal activity. Built now with c-fos, active when neurons fire. KCl causes neurons to fir… https://t.co/JAKOnqdzuK
7:47pm March 1st 2019 via Twitter Web Client
Rodriques #AGBT19 Single-cell measurements, and bulks at 100K each. Single cells recapitulate the bulk signal well.
7:45pm March 1st 2019 via Hootsuite Inc.
Rodriques #AGBT19 Now the pulses gets complicated and additive. https://t.co/hPlEs1IBeL
7:44pm March 1st 2019 via Twitter for iPhone
RT @OmicsOmicsBlog: Now here’s a badass choice of a model system! #AGBT19 https://t.co/8Yp9pzDuOD
7:42pm March 1st 2019 via Hootsuite Inc.
Rodriques #AGBT19 The edits per transcript moves over time. Infer promoter activation time-point. https://t.co/DwMFEWxcVo
7:40pm March 1st 2019 via Twitter for iPhone
