Certa: Can determine pathway-based direct responses of novel cmpds to determine mech. of action. Timepoints, concentrations... #IWT14
8:03am September 15th 2014 via Hootsuite
Certa: Feels that 1K genes can be interrogated with AmpliSeq RNA at 100 samples per PI run #IWT14
7:58am September 15th 2014 via Hootsuite
Certa: Indicates modulated pathways as a short-hand for the genome-wide work #IWT14
7:57am September 15th 2014 via Hootsuite
Certa: Some examples of pathway development in hepato-toxicity, up & down regulation of genes on a microarray-wide scale... #IWT14
7:56am September 15th 2014 via Hootsuite
Certa: Instead of 48K genes on a microarray, same result from 917 AmpliSeq RNA genes #IWT14
7:52am September 15th 2014 via Hootsuite
Certa: Calculated 96 pathways for their model, and determined from AmpliSeq RNA data exactly 96 pathways from PCA analysis #IWT14
Certa: Key pathway reporter genes shown: TNF, Wnt, Nitric Oxide, TGF - comparing microarray vs. AmpliSeq RNA signals #IWT14
7:51am September 15th 2014 via Hootsuite
Certa: (Work published recently here in BMC Genomics http://t.co/QRIPsBF3dT using AmpliSeq RNA) #IWT14
7:50am September 15th 2014 via Hootsuite
Certa: Showing 50 low-expressors completely missed on the microarray. Moderate- or high-expressors very linear #IWT14
7:49am September 15th 2014 via Hootsuite
Certa: Signal intensities (microarray) - sigmoid curves are similar, r=0.78 RNA-Seq: r=0.87 (likely due to mapping of RNA-Seq) #IWT14
7:48am September 15th 2014 via Hootsuite
Certa: No mis-matches - b/c the amplicons are matched. One read corresponds to one molecule, RPKM values shown #IWT14
7:47am September 15th 2014 via Hootsuite
Certa: We like the speed - 30 minutes later we have an excel sheet for analysis" #IWT14
7:46am September 15th 2014 via Hootsuite
Certa: Reverse transcription to DNA - still use PolyA primed, kit for making full-length cDNA, 96 samples per Proton PI run #IWT14
7:45am September 15th 2014 via Hootsuite
Certa: 917 target transcripts with 4 species: human, mouse, Cynomolgus monkey (pharma important), minipig (custom) #IWT14
7:44am September 15th 2014 via Hootsuite
Certa: Pathways include everything - immune responses, toxicology, etc. Will publish soon in silico database - 917 'response genres' #IWT14
7:42am September 15th 2014 via Hootsuite
Certa: Can use different activators / compounds to look at primary molecular response based upon gene exp signatures #IWT14
7:41am September 15th 2014 via Hootsuite
Certa: Pathway diagram with reporter gene readouts; cover spectrum of cell types and cover each with all reporter genes #IWT14
7:40am September 15th 2014 via Hootsuite
Certa: Molecular phenotyping: 152 signalling pathways ID'd, 917 response genres; modularized signalling cascades in diff cell types #IWT14
7:38am September 15th 2014 via Hootsuite
Certa: Applied AmpliSeq RNA and compared to microarray as well as RNA-Seq on Ion Proton #IWT14
7:37am September 15th 2014 via Hootsuite
Certa: SC-specific, switch genes (Yamanaka factors), cardiomyocyte-spec gene regulation: model well-characterized #IWT14
7:36am September 15th 2014 via Hootsuite
Certa: They monitor diff. to the molecular level. First work on microarray gene expression; stem cell to myocytes big change #IWT14
7:35am September 15th 2014 via Hootsuite
Certa: Reviewed iPS cell differentiation; most popular starting point is cardiomyocytes as you can visualize them #IWT14
7:34am September 15th 2014 via Hootsuite
Next: Ulrich Certa (Roche): "Highly sensitive amplicon-based transcript quantification by Ion Proton™ sequencing" #IWT14
7:32am September 15th 2014 via Hootsuite
Affourtit: AmpliSeq transcriptome accessing FFPE - much simpler analysis compared to regular RNA-Seq #IWT14
6:26am September 15th 2014 via Hootsuite
Affourtit: Highlights custom panel made available to anyone, first one on hearing loss http://t.co/5XOcMBO3Og #IWT14
6:22am September 15th 2014 via Hootsuite
Affourtit: Reviewing AmpliSeq Human Exome RDY; 58MB footprint, 50ng input; dry primers for better uniformity / ease of use #IWT14
6:18am September 15th 2014 via Hootsuite
Jason Affourtit (Thermo Fisher Scientific): "Ion AmpliSeq™ Gene Panels—DNA and RNA, latest and how to use in your research" #IWT14
6:14am September 15th 2014 via Hootsuite
Dowds: In Ion Reporter, showing multi-sample visualization: under new 'variant impact' tab; mouseover shows rich data #IWT14
6:09am September 15th 2014 via Hootsuite
Dowds: Aneuploidy in Ion Reporter: now doing mtDNA copy number ratio, based on recent research of how impt it is to monitor #IWT14
6:05am September 15th 2014 via Hootsuite
Dowds: AmpliSeq RNA fusion analysis in Ion Reporter allows visual inspection #IWT14
6:04am September 15th 2014 via Hootsuite
Dowds: Reviewing Ion Reporter to filter out 50K variants from an exome to 12, and then down to details on each one #IWT14
6:01am September 15th 2014 via Hootsuite
Dowds: Also in Torrent Suite 4.2.1: multi-run summary view; can run as virtual machine to try new versions, try plug-ins #IWT14
5:55am September 15th 2014 via Hootsuite
Dowds: Now Torrent Suite run-plans with template ability; runs and data tab shows list of reports, now ability to filter here #IWT14
5:53am September 15th 2014 via Hootsuite
Dowds: Showed demo movie of an http://t.co/6puEapf9xO design, v. straightforward process. (Much more interesting than static figs) #IWT14
5:48am September 15th 2014 via Hootsuite
Dowds: Overview: design via http://t.co/6puEapf9xO, Torrent Suite software, and then Ion Reporter for filtering, reporting #IWT14
5:44am September 15th 2014 via Hootsuite
Next: Carl Dowds (Thermo Fisher Scientific) "Ion bioinformatics latest tools and updates" #IWT14
5:40am September 15th 2014 via Hootsuite
Affourtit: Q: for lincRNA? A: For >125bp, fine. Can be done at http://t.co/YMIeplhn73 can just put in gene name to see. #IWT14
5:39am September 15th 2014 via Hootsuite
Affourtit:Q:AmpliSeq Transcriptome for alt splicing? A:Yes - can do isoform-spec panel for AS RNA, quantitatively. #IWT14
5:38am September 15th 2014 via Hootsuite
Affourtit: PGM Dx will have important templating (OneTouch2) in-process control #IWT14
5:37am September 15th 2014 via Hootsuite
Affourtit: Mentioned availability of new long mate-pair kit called TrueMate (Behind the Bench blog here http://t.co/P4NiRINw2S ) #IWT14
5:36am September 15th 2014 via Hootsuite
Affourtit: (More about AmpliSeq Transcriptome on the Behind the Bench blog: http://t.co/eU1HZ3liSb ) #IWT14
5:34am September 15th 2014 via Hootsuite
Affourtit: AmpliSeq Transcriptome has correlation R^2 0.96 with TaqMan; 0.94 with RNA-Seq; Microarray = 0.87 #IWT14
5:30am September 15th 2014 via Hootsuite
Affourtit: 10ng input FFPE-compat. RNA input; 'people use quite a bit less than that'; multiple isoforms from a single primer pair #IWT14
5:29am September 15th 2014 via Hootsuite
Affourtit: New product AmpliSeq Transcriptome: scaling AmpliSeq RNA to >20K genes. Diff gene exp to RefSeq in one tube #IWT14
5:28am September 15th 2014 via Hootsuite
Affourtit: PII expected to go into early access before end of the year. ISPs and well geometry locked; RNA-Seq on PII has R=0.98 #IWT14
5:25am September 15th 2014 via Hootsuite
Affourtit: Proton PI v3 is current kit. 2 runs per init now supported on TS 4.2.1; user bulletin on Ion Comm. http://t.co/5XUCH70Fxz #IWT14
5:21am September 15th 2014 via Hootsuite
Affourtit: Hi-Q PGM data on Ion Chef: 200 and 400bp PGM sequencing both loading and yield improve #IWT14
5:19am September 15th 2014 via Hootsuite
Affourtit: Hi-Q on Proton is Q1 2015; on Ion AmpliSeq Exome indel FP rate 50% reduced (to 2 per megabase) #IWT14
5:17am September 15th 2014 via Hootsuite
Affourtit: Q4 2014 will have new Hi-Q template kit. Can move seq kit to HiQ now, template kit change before end of year #IWT14
Affourtit: Showed 2300 amplicon panel, 43% reduction in indel rate; HP in size from 1 to 14bp. Another panel no change of indel error #IWT14
5:15am September 15th 2014 via Hootsuite
