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
Generation of DNA libraries for deep sequencing from picogram amounts of DNA - PubMed http://t.co/MfwPXN3XdR
7:45am June 18th 2014 via Hootsuite
MT @kirkenglehardt: Awesome paper title: 'Measuring mumbo jumbo: ...Quantification of the use of jargon in #scicomm' http://t.co/7xQ4OLp1So
6:10am June 18th 2014 via Hootsuite
RT @dgmacarthur: The danger of unsupported bioinformaticians in clinical labs: http://t.co/vdeJXWVWyV Spot on by @BioMickWatson
5:10am June 18th 2014 via Hootsuite
RT @iontorrent: Is triple negative a positive? Dr. Milan Radovich at Indiana University -- Behind the Bench http://t.co/0vFG6k7BwS
4:05am June 18th 2014 via Hootsuite
RT @wellcometrust: The Wellcome Trust's Liz Allen gives the economic case for medical research http://t.co/oegfuSpTsx
10:50pm June 17th 2014 via Hootsuite
Next Generation Sequencing (NGS) Market estimated 5y CAGR 16.7% | Markets and Markets report http://t.co/m7wl4VX60Q
9:15pm June 17th 2014 via Hootsuite
RT @9brandon: 2/2 + cavorting in Acadia Nat'l Park + sunset beers … for free! Schedule here http://t.co/S9bh3pGeQm @joycejax for details.
8:30pm June 17th 2014 via Hootsuite
RT @9brandon: 1/2 Attn #science writers: Fellowships for Jackson Lab short course. I.e., several days (or a week!) of great #genetics talks
8:25pm June 17th 2014 via Hootsuite
RT @infoecho: Great to show more understanding of the physics at nanopore scale. #NotJustAnimation http://t.co/MgRWoa9lix …
7:25pm June 17th 2014 via Hootsuite
Leerkes: High-throughput quantification of splicing isoforms. RNA 2010 PubMed http://t.co/EGZKyv2Nen
6:49pm June 17th 2014 via Hootsuite
RT @erikpelve: 10 Scientific Ideas That Scientists Wish You Would Stop Misusing http://t.co/yqaxMdlV88
6:25pm June 17th 2014 via Hootsuite
RT @CIPM_KAU: Training on new Ion Torrent PGM continue with PhD students taking lead @LIFECorporation @KACST http://t.co/dg4O3CpOVd
5:20pm June 17th 2014 via Hootsuite
RT @msclareryan: “When we invest in medical research, we win twice over” | @bmj_latest http://t.co/71yEfE35wD
4:20pm June 17th 2014 via Hootsuite in reply to
Leerkes: Fig 2 from: A beginner's guide to eukaryotic genome annotations Nat Rev Genet. 2012 PubMed http://t.co/il4nKpi6Ue
4:02pm June 17th 2014 via Hootsuite
