Wang: (Gary Schroth brings up the point that using SMARTer for miRNA isn't what that kit was designed for.) #RNASeq2014
3:28pm June 18th 2014 via Hootsuite
Wang: Concludes: method is 'the strongest confounding factor'; NEBNext appears best but missed large # lincRNA via random primer #RNASeq2014
3:22pm June 18th 2014 via Hootsuite
Wang: "Substantially different miRNA populations" between protocols, regardless of processing; informatics also makes difference #RNASeq2014
3:14pm June 18th 2014 via Hootsuite
Wang: Venn diagram: 4-13 common to all 3; dozens are specific to method for example samples shown #RNASeq2014
3:13pm June 18th 2014 via Hootsuite
Wang: In their analysis of 10M reads ea, NEBNext sRNA appears to be the best; but the methods cluster together; little overlap #RNASeq2014
3:12pm June 18th 2014 via Hootsuite
Wang: Analysis is by Genboree (Baylor: http://t.co/ylaEquyzUW) BOWTIE2 alignment and mirDeep2 #RNASeq2014
3:10pm June 18th 2014 via Hootsuite
Wang: Evaluated ProK, glycoblue add'n, DNAse as part of the process. Eval NEBNext sRNA, Epicentre Scripseq, Clontech SMARTer #RNASeq2014
3:06pm June 18th 2014 via Hootsuite
A few exosome resources from @LIFECorporation: http://t.co/T7r5cAcbpJ Online forum: http://t.co/0Vtc9aI2Mh #RNASeq2014
3:04pm June 18th 2014 via Hootsuite
Wang: Looking at extracellular RNAs (exosomes); but unknown distribution of types in these plasma samples #RNASeq2014
3:01pm June 18th 2014 via Hootsuite
Yaoyu Wang (Dana Farber Cancer Inst): "An unbiased comparison of RNA-Seq technologies" #RNASeq2014
2:52pm June 18th 2014 via Hootsuite
RT @atulbutte: An Annotated Online Bioinformatics / Computational Biology Curriculum http://t.co/Vicvfm5Utf
1:40pm June 18th 2014 via Hootsuite
ESHG14 Interview with Pfizer researcher: KRAS & cell free DNA detection using QuantStudio 3D digital PCR | YouTube http://t.co/Tep8T00dx
1:20pm June 18th 2014 via Hootsuite
Schroth:Q: Use of 2x75? A: 2x100 has lower mapping rate. Other applications though for longer reads. 2x50? Also fine #RNASeq2014
1:12pm June 18th 2014 via Hootsuite
Schroth: Q:BaseSpace for targeted? A: Cufflinks/TopHat view (implying - no, as it isn't for targeted RNA-Seq) #RNASeq2014
1:11pm June 18th 2014 via Hootsuite
Schroth: Showed browser view of captured RNA using exome capture - able to discover novel fusions in melanoma FFPE #RNASeq2014
1:07pm June 18th 2014 via Hootsuite
Schroth: Shows fold-change r2 values on the order of 0.96 from both FF and FFPE #RNASeq2014
1:03pm June 18th 2014 via Hootsuite
Schroth: Yield and DV200 quality highly correlated from FFPE RNA #RNASeq2014
Schroth: New metric DV200: amount of input 200nt long. Good is >70%, 20ng. Moderate 50-70%, 20-40ng. Poor 30-50%, 40ng #RNASeq2014
1:01pm June 18th 2014 via Hootsuite
Schroth: Showed loss of exons from FFPE RNA; but use exome capture from 10ng RNA #RNASeq2014
12:58pm June 18th 2014 via Hootsuite
Schroth: Reviewed TopHat / Cufflinks on BaseSpace (a commercial for @illumina - so it goes). #RNASeq2014
12:55pm June 18th 2014 via Hootsuite
Schroth: There is no 'one kit to use'; showed chart of 5 $ILMN kits; he has been working on BaseSpace analysis #RNASeq2014
12:48pm June 18th 2014 via Hootsuite
Schroth: Points to 2008 paper, done with only 20M reads http://t.co/FtUuJjMnXh pointing out there isn't any 'std' # reads to use #RNASeq2014
12:45pm June 18th 2014 via Hootsuite
MT @BioMickWatson: Phi X nanopore paper uses ref. quadromer map, and "aligns" raw data to the reference. Cp @nanopore's de novo base calling
Schroth: Biggest challenge of RNA-Seq: 'Enormous dynamic range', the genes at the low end #RNASeq2014
12:43pm June 18th 2014 via Hootsuite
Schroth: "I don't RNA-Seq should be as complicated as we make it out to be" #RNASeq2014
12:41pm June 18th 2014 via Hootsuite
RT @CompBiolPapers: Nanopore Sequencing of the phi X 174 genome. (arXiv:1406.4214v1 [q-bio.GN]) http://t.co/NG1vkje32c
12:40pm June 18th 2014 via Hootsuite
Gary Schroth (Illumina): "Total solutions for RNA-Seq within the Illumina ecosystem" #RNASeq2014
12:39pm June 18th 2014 via Hootsuite
Tan: Q: Pre-capture pooling? A: Have seen people using 4-plex; higher possible but not tested (yet) #RNASeq2014
12:37pm June 18th 2014 via Hootsuite
RT @Forbes: .@MeredithLEaton East Coast cities like Boston are tough because the cost of living tends to outpace wage growth. #AskForbes
12:30pm June 18th 2014 via Hootsuite
Tan: Showed MAQC HBR data for rRNA depletion and 256 neuro RNAs. On-target ~90%; linearity with ERCC from 3M-140M reads #RNASeq2014
12:26pm June 18th 2014 via Hootsuite
Tan: Showed figure from this 2014 Nat Protocols Mercer et al http://t.co/nD8d3wVwmo called SeqCap RNA #RNASeq2014
12:17pm June 18th 2014 via Hootsuite
John Tan (Roche NimbleGen): "Increased visibility to low-abundance variants through a novel RNA-Seq target enrichment method" #RNASeq2014
12:16pm June 18th 2014 via Hootsuite
.@Becky_Kusko Lexogen was light on the technical validation side. Would like to see more data, worth following up #RNASeq2014
11:20am June 18th 2014 via Hootsuite in reply to
.@Becky_Kusko Only correlation data IIRC, several impt details were lacking.
11:18am June 18th 2014 via Hootsuite in reply to
Park: Q: end bias? A: They claim similar performance, no data #RNASeq2014
11:15am June 18th 2014 via Hootsuite
Park: Sense 'very economical'; one PolyA+, soon-to-be-launched one will do total RNA. Has @illumina, @iontorrent and SOLiD #RNASeq2014
11:11am June 18th 2014 via Hootsuite
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
