EM: ID's known markers of spec amacrine subpopulations. Specs: 10K libraries/day; 12h from cell to sequencer; $0.06/cell. #AGBT15
2:59pm February 28th 2015 via Hootsuite
EM: Separation in 2D is from PCA relative weight. ID 39 retinal types; able to generate dendrogram easily from literature #AGBT15
2:57pm February 28th 2015 via Hootsuite
EM: 570 cells, 10's of thousands of genes detected. Moving to 44.8K retina cells. Found 32 PCA's. Generated movie of a 2D plot #AGBT15
2:56pm February 28th 2015 via Hootsuite
EM: Use a version of SMART (template switch PCR). Used species mixing expts to guarantee each droplet had one cell only in it. #AGBT15
2:53pm February 28th 2015 via Hootsuite
EM:(Reminiscent of RainDance). Movie of droplet generation (nL volumes) Library generation in a single tube of 10K cells #AGBT15
2:52pm February 28th 2015 via Hootsuite
EM: 12 rounds -> 16M barcodes. Several million primers on each bead. Then: generate droplets. Simplest design: oil pinching off #AGBT15
2:51pm February 28th 2015 via Hootsuite
EM: Needed to barcode beads w/PCR barcode, cell barcode, UMI. Did split-and-pool oligo synthesis #AGBT15
2:50pm February 28th 2015 via Hootsuite
EM:Describes emulsions - shows monodisperse droplets. Concept: lyse in emulsion, beads bind to RNA in bubble #AGBT15
2:49pm February 28th 2015 via Hootsuite
EM: Wish list for single-cell: scale (10^4-10^5 cells); flexible #'s (10 or 10K); sizes (2um - 50um); easy to use #AGBT15
2:48pm February 28th 2015 via Hootsuite
EM: Summary chart of # cells vs # of genes. CYTOF on far right, ISH toward 1/1, C1 / plate scRNA-Seq. Chart of cost for 500 cells #AGBT15
2:47pm February 28th 2015 via Hootsuite
EM: In the brain an est >1K cell subtypes. Study cell types & states in complex tissues? Illus bulk with smoothie / fruit salad #AGBT
2:46pm February 28th 2015 via Hootsuite
Evan Macosko, Harvard Med. DropSeq: A Droplet-Based Technology for Single-Cell mRNA-Seq Analysis on a Massive Scale #AGBT15
2:45pm February 28th 2015 via Hootsuite
RT @bioinformer: 600bp reads on Ion314 chip and with Isothermal amplification in 1/2 the time #AGBT15 http://t.co/tYdfmRCpEc
2:44pm February 28th 2015 via Twitter Web Client
RT @bioinformer: PII Chip data @iontorrent Proton #AGBT15 http://t.co/6FsMwbZ5CK
2:43pm February 28th 2015 via Twitter Web Client
.@CLCbio Many thanks! I did stop by last night! :) #AGBT15
2:42pm February 28th 2015 via Hootsuite in reply to
MT: CRISPR/Cas9 in human cells 'highly spec'; vary by gRNA design; full spectrum of var is inducible; NAHR-med disorders modeled #AGBT15
2:41pm February 28th 2015 via Hootsuite
MT: Designed an RNA-seq experiment to validate; data shows dups increased; deletion decreased. #AGBT15
2:40pm February 28th 2015 via Hootsuite
MT: Separated single iPSC via isolation by FACS; iPS cells. Method made both microdels and seg duplications. #AGBT15
2:38pm February 28th 2015 via Hootsuite
MT: Designed unique single gRNAs that can target each 16p segmented duplication. Ended up w/one copy of gene #AGBT15
2:37pm February 28th 2015 via Hootsuite
MT: Now engineering NAHR-mediated segmented microdeletion / duplication syndrome #AGBT15
2:35pm February 28th 2015 via Hootsuite
MT: Dual gRNA - could induce inversions at a couple of sites. '14 Cell Stem Cell ref http://t.co/IyuvqjaJbJ #AGBT15
2:34pm February 28th 2015 via Hootsuite
MT: Only 1/172 off-target sites enriched for mutations. Targeted CCR5 but CCR2 paralog could influence result #AGBT15
2:33pm February 28th 2015 via Hootsuite
MT: Looked for mut freq. On-target eff: 4-13%, gRNA-dep. Dual gRNA - up to 48% efficient deletion of region of interest #AGBT15
2:32pm February 28th 2015 via Hootsuite
MT: Mimic via CD34+ HPSCs (used for HIV co-inf). Used both single and dual gRNA. 1kb tiling probe capture, then deep seq #AGBT15
2:31pm February 28th 2015 via Hootsuite
MT: CRISPR brief intro, Nature 14 paper: http://t.co/hRXUCzgZDV single guide RNA; 2 guides can cause larger rearrangements #AGBT15
2:29pm February 28th 2015 via Hootsuite
MT: Looking at tissue spec in ASD now: between Mouse CTX, Human LCL and Human NPS models, Venn diagram of overlaps #AGBT15
2:28pm February 28th 2015 via Hootsuite
MT: Showed figure from this '14 Nature paper http://t.co/ukvXjLSZO2 #AGBT15
2:27pm February 28th 2015 via Hootsuite
MT: Now overlappiong with Hi-C peaks - suggests 16p interactions. The CNV's affects nuclear positioning in the genome #AGBT15
2:25pm February 28th 2015 via Hootsuite
MT: Showed Manhattan plot; positional effects in Cis; looking for significant bins (count vs. log(p-val)) Found distal CNV region #AGBT15
MT:16p11.2 recurr genomic disorder: classic example. Horev PNAS http://t.co/xStEOIsc3H Found limited dosage compensation #AGBT15
2:23pm February 28th 2015 via Hootsuite
MT:Neurodev disorders: does ASD/NDD converge on small # of shared final pathways? How to study pathogenesis of rare mut's w/N=1? #AGBT15
2:21pm February 28th 2015 via Hootsuite
MT: Will cover: xcr consequences of recurrent CNV; generation of CRISPR/Cas9 mutants #AGBT15
2:20pm February 28th 2015 via Hootsuite
Michael Talkowski Harvard Med Sch: Modeling Structural Variation and Genomic Disorders Using CRISPR/Cas9 and Integrative Genomics #AGBT15
2:19pm February 28th 2015 via Hootsuite
Here at #AGBT15 my laptop is only 30% power, and my body probably similar. Reminiscent of this cartoon. http://t.co/T5ubNEYLZW
2:15pm February 28th 2015 via Twitter Web Client
RT @TorontoGenomics: Mickey Williams: One of the key reasons for picking @iontorrent PGM was input material requirements #AGBT15
1:08pm February 28th 2015 via Hootsuite
LM:Q:Control animals for handling? A:3 groups - wild; 2nd all conditions w/gravity; 3rd to space. $3M missions; smpls kept #AGBT15
12:00pm February 28th 2015 via Hootsuite
LM: Sampling biodiversity; losing 1 species every 6h; "We cannot being these animals to the a lab" #AGBT15
11:59am February 28th 2015 via Hootsuite
LM: 'Neurons evolved more than once'; 9-12 ways to make a brain. 'Access 3.5B years of experiments already done by Nature' #AGBT15
11:56am February 28th 2015 via Hootsuite
LM: One of the fastest brain regeneration in the Animal Kingdom - 3-5d. 'Kings of regeneration' 2.5h wound regeneration #AGBT15
11:55am February 28th 2015 via Hootsuite
LM: No hox genes, no miRNAs, There is RNA editing in their development (!) 'There are many ways to make a neural system' #AGBT15
11:54am February 28th 2015 via Hootsuite
LM: 2014 Nature paper here: http://t.co/A70OnmnXlL Shows Centophoria, Porifera, Placozoa, Cnidaria, Bilateria: very diff 600MYa #AGBT15
11:53am February 28th 2015 via Hootsuite
LM:Shows EM photo of 'the aliens of the sea'. Blog post on ctenophores and @iontorrent PGM here http://t.co/ozI2xxPt8H #AGBT15
11:51am February 28th 2015 via Hootsuite
LM: Best astronauts are snail statocysts - 13 cells; 30/33 neuropeptides down regulated. #AGBT15
11:50am February 28th 2015 via Hootsuite
.@s_mccarroll After seeing that visual of 50%-80% affected by space sickness, um, count me out, thanks. #AGBT15
11:49am February 28th 2015 via Hootsuite in reply to
RT @s_mccarroll: The Moroz lab (U. Florida) is moving on from "Ship-Seq" to "Spaceship-Seq". Anyone up for a zero-G lab rotation? #agbt15
11:48am February 28th 2015 via Hootsuite
RT @TorontoGenomics: @CIgenomics Well Kirk and Spock Transported a whole whale so a fish is easy #AGBT15
LM: Also looked at microRNAs. Did indiv neurons; 'some of the most abundant neurons are ncRNAs' #AGBT15
11:47am February 28th 2015 via Hootsuite
LM: 1000's of up and down regulated genes: neuropeptide S largest up-reg. in space. 'Activates hyperactivity, hypersexuality' #AGBT15
11:46am February 28th 2015 via Hootsuite
LM: Many animal astronauts - geckos, mice, gerbils (died), snails. Genomic analysis of vestibular system. PCA analysis #AGBT15
11:45am February 28th 2015 via Hootsuite
LM: Talks about the Russian Bion-M1. Slideshow on http://t.co/UkipKukB5q here http://t.co/QOjHfg2uWI #AGBT15
11:43am February 28th 2015 via Hootsuite
