Nolan: Shows replicate data, CD44 x TCRbeta. 50K cells 'by sequencing' the Ab tags, 30 markers at a time. #AGBT17
3:21pm February 16th 2017 via Hootsuite
Nolan: Additive splints, combinatorial, then you can do a flow standard and look for co-expression patterns #AGBT17
Nolan: Able to get cells tagged with individual DNA sequences. Split pool synthesis - each cell goes through from plate to plate... #AGBT17
3:19pm February 16th 2017 via Hootsuite
Nolan: Ab panels have problems, fluorescence is 'contaminated', instruments are variable. Have DNA tags on Abs #AGBT17
3:18pm February 16th 2017 via Hootsuite
Nolan: '17 Cell https://t.co/XhWwW45SMM shows feature of cells ordered by connectivity of 'only 50 parameters' via CyTOF #AGBT17
3:17pm February 16th 2017 via Hootsuite
Gary Nolan (Stanford Univ CA) Sequencers as flow cytometers: ultra-high throughput single cell analysis by split-pool synthesis #AGBT17
3:15pm February 16th 2017 via Hootsuite
Q: Pipette tis? Mason: Individually wrapped! #AGBT17
2:53pm February 16th 2017 via Hootsuite
Mason: Journey to Mars? Space-Seq open as a NASA resource in late '17. >200K isoforms observed from space travel #AGBT17
2:52pm February 16th 2017 via Hootsuite
Mason: Finishes with the need for standards, SEQC2. Deep sequencing of the GIAB samples, putting base mods out, and ABRF studies #AGBT17
2:51pm February 16th 2017 via Hootsuite
Mason: Looking at m6A calling, mCaller Github repo: https://t.co/T8KssEnBsY #AGBT17
2:50pm February 16th 2017 via Hootsuite
RT @jaredtsimpson: Slides from my #AGBT17 talk: https://t.co/UgmjkWXPwZ
2:48pm February 16th 2017 via Hootsuite
Mason: 2D reads 89-92%; 1D reads 76-7%. About 1-2% better than ground-data. De-novo on Amazon. Perhaps do assy in space? #AGBT17
2:47pm February 16th 2017 via Hootsuite
Mason: v7 flow-cells, loaded library, shows video of data coming off, great photo https://t.co/dPiSzvety7 #AGBT17
2:45pm February 16th 2017 via Hootsuite
Mason: Photos of @Astro_Kate7 and rocket blows up, gets a nice letter 'saying your supply ship blew up'. Kate gets up there in Aug #AGBT17
Mason: Nanopore in Antarctica, Africa. What about space? Cool patch shown. $10K/kg upmass cost. Preprint https://t.co/VL70HHtldj #AGBT17
2:44pm February 16th 2017 via Hootsuite
Mason: continuing with urban metagenomics, https://t.co/HL2K8Of6bD looking at ubiquitous sequencing https://t.co/p94W4CT1PV #AGBT17
2:42pm February 16th 2017 via Hootsuite
Mason: ...some allele-spec switching of gravity response genes in RNA-seq data #AGBT17
2:41pm February 16th 2017 via Hootsuite
Mason: Cells were alive but 'not happy' due to handling / landing of spacecraft. Looking at allele-spec expression (ASE) shows... #AGBT17
2:40pm February 16th 2017 via Hootsuite
Mason: Terrestrial vs ISS RNA-Seq; mtDNA reads map when there are many dying cells. Blood drawn in space and sent back via Soyuz #AGBT17
Mason: #AGBT17 Suggested that this approach https://t.co/lgCsYcK6rO could be used in combination with ONT, some data so far.
2:39pm February 16th 2017 via Hootsuite
Mason: Nature News piece https://t.co/2jH0BgtTKU Looked at telomere length; RFI ovia FISH of T-cells; no easy way to validate #AGBT17
2:37pm February 16th 2017 via Hootsuite
Mason: #AGBT17 (Is trying to talk as fast as he can about the two-year NASA twin study.) NGS can 'confirm they are identical'.
2:36pm February 16th 2017 via Hootsuite
Mason: 'Whoever guesses the number of slides wins a patch'. (Worthy effort, the patch is really cool looking.) #AGBT17
2:35pm February 16th 2017 via Hootsuite
Mason: #AGBT17 shows chart from '13 ref https://t.co/56f6LMwKSM about the 'inevitable march' of epigenetic change and eventual death
2:34pm February 16th 2017 via Hootsuite
Mason: Epigenetic evolution - EPM '16 ref https://t.co/1BwtwuPQJn Shows figure from '05 of epigenetic marks shift in twins #AGBT17
2:33pm February 16th 2017 via Hootsuite
Chris Mason (Weill Cornell NY): DNA sequencing, genome assembly, and epigenetics on the international space station #AGBT17
2:31pm February 16th 2017 via Hootsuite
Q: Repetitive sequence improvements? Simpson: Trinucleotides easier than homopolymers, but it is HPs where the work is. #AGBT17
2:29pm February 16th 2017 via Hootsuite
Simpson: A2: there will be more work coming out with new motifs for modified bases soon. #AGBT17
2:28pm February 16th 2017 via Hootsuite
Q: Ability for novel bases? Simpson: Paper on Bioarxiv can pull out motif (via t-test) looking at raw data. They work model-based #AGBT17
2:27pm February 16th 2017 via Hootsuite
Q: For 1D^2 how often it gets to other side? Simpson: Has only seen data he's been given. #AGBT17
2:26pm February 16th 2017 via Hootsuite
Simpson: Concludes that scrappie basecaller is promising; as well as looking at long-range methylation patterns #AGBT17
2:25pm February 16th 2017 via Hootsuite
Simpson: Working on single-read, single-base methylation calling (haplotype-phased) with nanopolish tool #AGBT17
2:23pm February 16th 2017 via Hootsuite
Simpson: 5meC change signal in a detectable way. Did an experiment modeling C vs 5meC via Gaussian distribution #AGBT17
2:22pm February 16th 2017 via Hootsuite
1D^2 illustrated (too hard to capture!) RT @coregenomics: #agbt17 https://t.co/icAjHF79sr
2:20pm February 16th 2017 via Hootsuite
Simpson: New method of generating 2D reads, 1D^2: being able to pull in opposite strand without hairpin. Shows accuracy comparison #AGBT17
2:19pm February 16th 2017 via Hootsuite
RT @coregenomics: Variability in @nanopore yield by JS at #agbt17 https://t.co/dPZ11nicaN
2:17pm February 16th 2017 via Hootsuite
Simpson: Latest basecaller ("scrappie") estimates length based upon time measurement takes for sequence #AGBT17
Simpson: Homopolymers (HP) 'main source of residual errors in consensus sequences'. Early basecallers collapse HP's to 6-mers #AGBT17
2:16pm February 16th 2017 via Hootsuite
Simpson: Coming up with better human assembly, 'very much a work in progress' with a fraction of the data. https://t.co/CXSIOOlYAq #AGBT17
2:14pm February 16th 2017 via Hootsuite
Simpson: Accuracy of 1D reads was 82-83%. Canu assembly, NG50 3.0MB. 50-10 contigs across each chromosome #AGBT17
2:13pm February 16th 2017 via Hootsuite
Simpson: Ave readlength across sites, from 6.6kb, rapid library now have longer lengths #AGBT17
2:12pm February 16th 2017 via Hootsuite
Simpson: Optimize draft genome seq with HMM constraints; used for mobile Ebola using toookit called Nanopolish #AGBT17
2:11pm February 16th 2017 via Hootsuite
Simpson: RNN=recurrent neural network, shown improvement. They are interested in groups of nanopore reads, generating consensus #AGBT17
2:09pm February 16th 2017 via Hootsuite
Simpson: Uses speech recognition algorithms following similar path, from HMM to neural networks. R9 metrichor, nanonet, deepnano #AGBT17
2:08pm February 16th 2017 via Hootsuite
Simpson:Hidden Markov models were first-gen basecallers. Latest ones: moved to recurrent neural networks. #AGBT17
2:07pm February 16th 2017 via Hootsuite
Simpson: Signal-level analysis: what bases are registered by what current events? Existing tries to use 5- or 6-base calls #AGBT17
2:06pm February 16th 2017 via Hootsuite
Simpson: 0.5s, 60 picoA of current. Sees the next base, signal drops to 40 pA, then up to 50 etc. Stepwise changes #AGBT17
2:05pm February 16th 2017 via Hootsuite
Simpson: 4k samplings per second, as current is disrupted there are characteristics of the DNA as it passes thru #AGBT17
2:04pm February 16th 2017 via Hootsuite
Simpson: Shows a drawing of the protein pore, the charge differential across the membrane, and ssDNA able to pass through the pore #AGBT17
Simpson: Will intro nanopore, signal-level analysis, initial results, and direct detection of 5-meC #AGBT17
2:03pm February 16th 2017 via Hootsuite
