Park: Size-selection is done via columns; library input titration down to 50ng; good complexity data shown #RNASeq2014
11:06am June 18th 2014 via Hootsuite
Park: 1.5h hands-on, 4.5h TAT. Able to get strandedness easily, as there's no RT. Strand displacement can cause artifacts #RNASeq2014
11:02am June 18th 2014 via Hootsuite
Park: Sense uses polyA bound beads w/ pseudo-random probes with complementary regions; the probes then are ligated / processed #RNASeq2014
11:00am June 18th 2014 via Hootsuite
Park: Tech 'fragmentation-free library prep': Sense. PolyA + mag beads; 4.5h TAT to library (NB Ambion is 5-6h) #RNASeq2014
10:58am June 18th 2014 via Hootsuite
Park: Showed whisker plot of variation in RNA-Seq data (source?) indicating library prep and sample handling highest var #RNASeq2014
10:55am June 18th 2014 via Hootsuite
Park: Turnaround time (TAT) for 1 library prep hasn't improved like sequencing for 1GB #RNASeq2014
10:54am June 18th 2014 via Hootsuite
Park: Mentioned #ESHG14 and growth of hands-on time for NGS; growing to 25% of overall #RNASeq2014
10:53am June 18th 2014 via Hootsuite
Park: Showed Eagle Genomic's periodic table of bioinf. tools http://t.co/ptgMZyKb6S #RNASeq2014
10:52am June 18th 2014 via Hootsuite
Park: Put up @lexnederbragt slide of sequencing technologies / readlengths. (Didn't see attribution.) http://t.co/pyB3H5E5Zk #RNASeq2014
10:51am June 18th 2014 via Hootsuite
Park: Moore's law cp to NGS; pointed to 12 of McKinsey's disruptive technologies http://t.co/XS5SyIlyv9 #RNASeq2014
10:49am June 18th 2014 via Hootsuite
Park: Lexogen GmbH Vienna (Austria); Western Union: 'telephone is of no use to us'. "It's difficult to predict the future" #RNASeq2014
10:47am June 18th 2014 via Hootsuite
Jungsoo Park (Lexogen): "RNA-Seq Sample Prep does not need to be complicated" #RNASeq2014
10:43am June 18th 2014 via Hootsuite
Ge: RNA-Seq analysis has to control for Type I error; cut-off selection is data-driven. #RNASeq2014
10:35am June 18th 2014 via Hootsuite
Ge: Co-dev of drug with companion Dx: from PI thru PIII; proof of concept in PII. 2006 Vogelstein ed: http://t.co/osLhdKcUKQ #RNASeq2014
10:30am June 18th 2014 via Hootsuite
Ge: Cost per trial (200 subjects): as a % of $100M, from 0.1-1.2% ($400K for RNA-Seq). "My favorite slide to share at Gilead" #RNASeq2014
10:24am June 18th 2014 via Hootsuite
.@mnandita In brief, about 5% of transcripts are coming off of the >reverse< strand, and often have overlapping 5' exons (!)
10:16am June 18th 2014 via Hootsuite in reply to
Ge: Figure from this review 2004: http://t.co/EovxSqrpFW Only 24% patients receive medication with PGx info on label #RNASeq2014
10:14am June 18th 2014 via Hootsuite
Ge: Began with the Lucas Wartman story of a WashU pathologist who has ALL. Profiled in NYTimes 2012: http://t.co/EGLjkeYJFd #RNASeq2014
10:12am June 18th 2014 via Hootsuite
Dongliang Ge (Gilead): "RNA-Seq Strategies in Precision Medicine" #RNASeq2014
10:06am June 18th 2014 via Hootsuite
Comment on NuGEN: Why call everything 'Ovation' while InDA-C and selective priming are distinct tech? #MarketingFail #RNASeq2014
10:05am June 18th 2014 via Hootsuite
Kain: Showed r=0.975 linearity with ERCC spike-ins using their single-cell method #RNASeq2014
10:03am June 18th 2014 via Hootsuite
Kain: RNA-Seq results: <10% rRNA for HEK293, but 20-30% with MAQC HBRR and UHR RNA samples from 10pg total RNA. #RNASeq2014
10:01am June 18th 2014 via Hootsuite
Kain: Single-tube protocol without purification (until after ds cDNA generated). Lysis is simple freeze-thaws in buffer #RNASeq2014
9:59am June 18th 2014 via Hootsuite
Kain: Single-cell RNA-Seq is designed for higher vertebrate spp; minimizing rRNA. Enriched for coding, reg sequences #RNASeq2014
9:57am June 18th 2014 via Hootsuite
Kain: Single Cell RNA-Seq: NuGEN's method uses 'selective priming'; down to 10ng total RNA. #RNASeq2014
9:53am June 18th 2014 via Hootsuite
Kain: InDA-C can be iterative; example in grape, chloroplast rRNA's became a problem after rRNA reduction (second round) #RNASeq2014
9:51am June 18th 2014 via Hootsuite
Kain: Examples for human cardiac actin & myosin, goat casein RNAs; top 30 barley transcripts; etc. #RNASeq2014
9:49am June 18th 2014 via Hootsuite
Kain: 'Ovation Universal RNA-Seq System' commercial name for InDA-C; everything but InDA-C primers, custom design for spp's #RNASeq2014
9:48am June 18th 2014 via Hootsuite
Kain: Getting 80-90% aligned from 6 FFPE samples after rRNA InDA-C reduction. rRNA abundance 9-26% #RNASeq2014
9:47am June 18th 2014 via Hootsuite
Kain: From whole blood, reducing globin and rRNA to ~15-20% (hard to tell from pie charts) using InDA-C method. #RNASeq2014
9:45am June 18th 2014 via Hootsuite
Kain: Insert Dependent Adapter Cleavage (InDA-C) is a method for cleaving unwanted species after library construction #RNASeq2014
9:39am June 18th 2014 via Hootsuite
Steve Kain (NuGEN): "RNA-Seq sample prep solutions for challenging samples" #RNASeq2014
9:36am June 18th 2014 via Hootsuite
Levin: Q's: RNAseH oligo's? A: Not commercial but order-able #RNASeq2014
9:33am June 18th 2014 via Hootsuite
Levin: One spatial method called TIVA in Nat. Methods '14: http://t.co/8Ih2CbkZkx also Church's FISSEQ http://t.co/BYHrkDVaa3 #RNASeq2014
9:32am June 18th 2014 via Hootsuite
Levin: Notable RNA-Seq methods (specialized) listed: HITS-CLIP, ribosome profiling, long-read RNA-Seq for isoforms; spatial #RNASeq2014
9:30am June 18th 2014 via Hootsuite
Levin: Targeted RNA-Seq overview: 'RNA-Seq inherently uneven in coverage' Gave Genome Re ref http://t.co/RGOfWPocGf #RNASeq2014
9:29am June 18th 2014 via Hootsuite
Levin: Best at rRNA red, evenness, coverage. Ribozero 'second place if you can tolerate higher levels of rRNA' #RNASeq2014
9:26am June 18th 2014 via Hootsuite
Levin: Looked at QC parameters across these non-PolyA+ methods: RNAseH looks good across #RNASeq2014
Levin: DSN-lite; RNaseH, Ribo-Zero, NuGEN Ovation: listed by ease of use & cost; RNaseH both easy and inexpensive #RNASeq2014
9:23am June 18th 2014 via Hootsuite
Levin: non-PolyA+ RNA is impt: for genome annotation; for RNA splicing; for FFPE; listed 4 methods #RNASeq2014
9:22am June 18th 2014 via Hootsuite
Levin: Conclude that dUTP method performed well both 3' 5' evenness. Parchomchuk paper: http://t.co/2B9Fujzvu2 #RNASeq2014
9:21am June 18th 2014 via Hootsuite
Levin: Broad's RNA-SeQC pipeline for QC; measuring even-ness & strand specificity across 9 methods http://t.co/InTKVereOc #RNASeq2014
9:19am June 18th 2014 via Hootsuite
Levin: Reviewed importance of strand-specificity; 7 methods (!); they published this 2010 here: http://t.co/LKaKZZAiTo #RNASeq2014
9:16am June 18th 2014 via Hootsuite
Levin: Mentioned the importance of ERCC controls; Jiang et al 2011 Genome Res http://t.co/3ys9OO1kvY #RNASeq2014
9:14am June 18th 2014 via Hootsuite
Levin: Mentioned this Mortazavi et al 2007 paper http://t.co/mPe1RNy1yq Looked at read sensitivity to 30M reads for this sample #RNASeq2014
9:12am June 18th 2014 via Hootsuite
Levin: Broad's QC for RNA-Seq includes RIN score, qPCR for gDNA contam, rRNA measured to be <5% #RNASeq2014
9:09am June 18th 2014 via Hootsuite
Levin: Shows PubMed growth in the term RNA-Seq; uses include fusion xcr, SNP detection, allele-spec exp, RNA editing... #RNASeq2014
9:08am June 18th 2014 via Hootsuite
Joshua Levin (Broad): "An overview of the RNA-Seq field & a brief look at new technologies" #RNASeq2014
9:06am June 18th 2014 via Hootsuite
First day of #RNASeq2014 getting started. http://t.co/J4ROCzHQsJ http://t.co/wXdP0Ng2ef
9:02am June 18th 2014 via Hootsuite
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation - PubMed http://t.co/w3WV4sKRat
8:25am June 18th 2014 via Hootsuite
