Tweets from Hootsuite

SG: De novo assembly of ONT reads as a hybrid assembly; genomic elements >1300bp. Full-length isoforms: human cDNA 80K reads. #AGBT15

8:44pm February 27th 2015 via Hootsuite

SG: % of aligned reads - from 8% to 21% to top at 61%. #AGBT15

8:43pm February 27th 2015 via Hootsuite

SG:Analysis of 1024 types of 5-mers - GC% x fold difference graph some slope #AGBT15

8:40pm February 27th 2015 via Hootsuite

SG: The right aligner isn't a solved issue - lots of active research. She uses Blast for now. Reports some bias via G-C #AGBT15

8:39pm February 27th 2015 via Hootsuite

SG: Longest 2D read was 5.7kb. Shearing: unsheared DNA seems prone to breakage. 10Kb or 20Kb best sizes #AGBT15

8:37pm February 27th 2015 via Hootsuite

SG: Number of pores used directly impacts perf; 400 pores = >100MB data. Largest 191,145 bp long. "But not that useful' - no mapping #AGB

8:36pm February 27th 2015 via Hootsuite

SG:Yields range from 40MB, 200MB, 40MB, <<10MB (by library-prep type). Using his-tag protein for selection of hairpin adapters (!) #AG

8:34pm February 27th 2015 via Hootsuite

SG: 3 library formats - leader/leader adapter, hairpin/hairpin, leader + hairpin. "Flow cell yield has been highly variable" #AGBT15

8:32pm February 27th 2015 via Hootsuite

SG:Describes the MAP program for @nanopore and have had R6, R7 and R7.3 iterations to-date. Yeast W303 strain of S288C, some hum DNA #AGBT15

8:30pm February 27th 2015 via Hootsuite

Sara Goodwin Cold Spring Harbor: An in Depth Evaluation and Optimization of the Oxford MinION Device for de novo and cDNA Sequencing #AGBT15

8:29pm February 27th 2015 via Hootsuite

AK:Does RNA editing have a role in learning and memory? Hint at some evidence of cells in their circuits and behavior #AGBT15

8:24pm February 27th 2015 via Hootsuite

AK: 5HT induces synaptic genes in sensory neurons. Nascent RNAs are largely transcribed from demethylated genes #AGBT15

8:23pm February 27th 2015 via Hootsuite

AK: "Nothing in neuroscience makes sense except in the light of circuits" #AGBT15

8:20pm February 27th 2015 via Hootsuite

AK: Ratio of mC/C is similar across promoter elements; polyploid neruons are methylated the same way as diploid cells #AGBT15

8:19pm February 27th 2015 via Hootsuite

AK: ...have low gene-body and promoter methylation #AGBT15

8:18pm February 27th 2015 via Hootsuite

AK: Now looking at methylation (CG or CHG) across cell types. Saw mosaic pattern. But highly expressed neuron-spec genes... #AGBT15

8:18pm February 27th 2015 via Hootsuite

AK: Three types of neurons examined: Glutamatergic sensory, serotonergic interneuron, cholinergic motor. Grow in Uracil-biotinylated #AGBT15

8:17pm February 27th 2015 via Hootsuite

AK: Following growth cones, look at up/down regulated genes. 5HT = serotonin, 'feel good' molecule; induces 5-mC down 5-hmC up #AGBT15

8:14pm February 27th 2015 via Hootsuite

AK: Long-term depression w/ FMRF. Further simplified - single sensory neuron, then motorneuron, look at behavior #AGBT15

8:13pm February 27th 2015 via Hootsuite

AK: Tail, gill still attached, can follow nerve, can condense from sensory neuron to motoneuron. Interneron 5-HT/NO (long-term sens) #AGBT15

8:12pm February 27th 2015 via Hootsuite

AK: Aplysia neurons as large as 1.1mm; like a bouquet of flowers, 10K neurons in brain, accessible, identifiable, same location #AGBT15

8:11pm February 27th 2015 via Hootsuite

AK: Roadmap Epigenomics Consortium: 'we still lack a systematic understanding' about cellular circuitry & differentiation #AGBT15

8:10pm February 27th 2015 via Hootsuite

AK: (Collaborator w/Leonid Moroz, highlighted here: http://t.co/oIzIo3yVuQ @iontorrent ) #AGBT15

8:09pm February 27th 2015 via Hootsuite

Andrea Kohn Univ FL Single-Cell Methylome Profiling: Integration of a Transcriptome and Methylome From Individual Identified Neurons #AGBT15

8:08pm February 27th 2015 via Hootsuite

AM: Now sequence activity map: fn of CD36 by aa position. Collapse to 3D structure from '08 Nature ref http://t.co/hqoXhLmL8N #AGBT15

8:06pm February 27th 2015 via Hootsuite

AM: Now: test in advance every mutation of PPAR-gamma. 9,576 var's, one var/pre-adipocyte cell. CD36 cell surface marker for assay #AGBT15

8:04pm February 27th 2015 via Hootsuite

AM: Of 16 indivs w/var: T2D 7x increased risk #AGBT15

8:03pm February 27th 2015 via Hootsuite

AM:PPAR-gamma from 20K T2D cases/controls: 2014 PNAS ref http://t.co/8k6YsRHBh2 Most var's fn as WT; 9 novel PPARg cause loss-of-fn #AGBT15

8:02pm February 27th 2015 via Hootsuite

AM: Now application of MITE-Seq ot PPARg in human fat cells: a master reglator of adipocyte diff and antidiabetic drug target #AGBT15

8:01pm February 27th 2015 via Hootsuite

AM: Engineered synthetic var's found 2000x difference in specificities to antibiotics #AGBT15

8:00pm February 27th 2015 via Hootsuite

AM:ID of spec-determining residues. Positions tolerated or depleted under paromycin selection #AGBT15

7:59pm February 27th 2015 via Hootsuite

AM: (These tweets dedicated to Keith R of @omicsomicsblog) #AGBT15

7:58pm February 27th 2015 via Hootsuite

AM: Dec [kana] -> fewer mutations. Showed structure of predicted changes. More tolerance for mut's outside the core #AGBT15

7:58pm February 27th 2015 via Hootsuite

AM: MITE library, selection in liquid carbinicellin w/diff conc of aminoglycoside. Showed map of kanamycin conc-dep sequence act map #AGBT15

7:57pm February 27th 2015 via Hootsuite

AM: APH(3')II bacterial enzyme; 6 aminoglycoside antibiotics w/diff structures / potencies. Synth 4997 single aa subst across enz #AGBT15

7:56pm February 27th 2015 via Hootsuite

AM:Deep mut scanning; 1000's of mutated protein-coding var's; select for fn via cell-based assay; char seq http://t.co/ElLnEvEJ6i #AGBT14

7:55pm February 27th 2015 via Hootsuite

#AGBT15: Ion AmpliSeq Transcriptome poster interview (Video) http://t.co/9VbYPk0KTy Behind the Bench Blog

7:55pm February 27th 2015 via Hootsuite

Alexandre Melnikov, The Broad Inst "Comprehensive Mutational Scanning of Bacterial and Human Proteins Using MITE-Seq” #AGBT15

7:53pm February 27th 2015 via Hootsuite

#AGBT15: Ion AmpliSeq Automation (Video) http://t.co/h2uN5ABHrT Behind the Bench blog

7:50pm February 27th 2015 via Hootsuite

#AGBT15: The Avalanche of NGS Data http://t.co/lYJNyGiAuu Behind the Bench blog

7:39pm February 27th 2015 via Hootsuite

Nice work on Single Cell sequencing - too bad tweeps!

7:38pm February 27th 2015 via Hootsuite

While discussing natural human knockouts w/a new friend at #ASHG15 I was told to thank my paralogues. So there it is.

5:41pm February 27th 2015 via Hootsuite

Worth a look! MT @gsaldanha: Here's the @10xgenomics video #AGBT15 http://t.co/gsvkHNx2P0

5:01pm February 27th 2015 via Hootsuite

BH:Announces instrument - $75K cost, $500/sample, Q2 availability #AGBT15

5:00pm February 27th 2015 via Hootsuite

BH: Quotes Jay Shendure (UW Mendelian genetics center), "high quality exomes from 1ng!" #AGBT15

4:59pm February 27th 2015 via Hootsuite

BH: Showed slide from David Jaffe's talk last night - 'behaves like 100kb accurate read'. #AGBT15

4:58pm February 27th 2015 via Hootsuite

BH: Shows strong PPV and sensitivity data with a fraction of input for WES. #AGBT15

4:57pm February 27th 2015 via Hootsuite

BH: Large-scale structural rearrangements LUMPY ref: http://t.co/A6oSyLqPnN showed nice reduction of errors #AGBT15

4:56pm February 27th 2015 via Hootsuite