AP: 10ng input is about 400 cells, '10 transcripts per 400 cells' "I could hardly believe it but that's what the data said" #gensoltour
10:38am October 16th 2014 via Twitter Web Client
AP: Calculated coeff. of variation as a function of reads; reproducible detection of 10 transcript reads per 400 cells #gensoltour
AP: Another w/FFPE samples, targets detected ranged from 12% to 65%; but the low performers gave nothing via other approaches #gensoltour
AP: She thought it didn't work well due to missing transcripts, but it turned out to be the neural developmental state #gensoltour
AP: "Can you do it again?" "A week ago, 'I can't believe these results, these are beautiful' when I didn't think it worked" #gensoltour
AP: Data in 1w? Tried brain organoids for collaborator; '85% of what should be there is; I'm putting it in my grant' #gensoltour
AP: "My technician looks forward to doing this" (AmpliSeq Transcriptome). Low input, fast protocol, easy to analyze #gensoltour
AP: Ion "AmpliSeq Whole Transcriptome surprised me on how much we like this" Behind the Bench: http://t.co/5y4SCMzL7c #gensoltour
AP: Get >70M reads from Ion PI; >90bp mean read length; >90% mapped; 17k genes at >10x, 'we see high accuracy' #gensoltour
10:37am October 16th 2014 via Twitter Web Client
AP: Ion Total RNA-Seq Kit v2, ribominus, RNase III shearing, stranded; also NuGEN Ovation v2, low input, rRNA red + ampl #gensoltour
AP: Doing some service work on Ion Chef + Ion Proton; 'it makes it much better' for their RNA work. Median RL 160bp #gensoltour
AP: miRs also: distinct between polysomes vs. cytosol. 3 types of RNAs interacting (lincRNA, miRNAs, coding RNA) #gensoltour
10:36am October 16th 2014 via Twitter Web Client
AP: Also pseudogenes and lincRNA make it to polysomes, different allelic ratios between compartments as well #gensoltour
AP: Polysome transcripts and allelic distribution: striking differences between isoforms in cytosol vs. polysomes #gensoltour
AP: Allelic variation - affecting RNA stability, RNA structure, genetic var's acting on multiple levels; ribosome processing #gensoltour
AP: Their theory: DNA variation causes RNA variation in common disease; Sadee et al 2014 reference http://t.co/vu8lJEMFPj #gensoltour
Next: Audrey Papp (The Ohio State Univ) "Transcriptome Sequencing: what's your question?" #gensoltour
CL:Q:which V regions most useful? A:It is a consensus, can be examined on a per-variable region basis or together #gensoltour
CL:Q:How many samples/chip? A:Per 316, a few samples; need a few hundred thousand reads/sample. He did 1 per 314 chip #gensoltour
CL: Also used the RAST server website here: http://t.co/KRuGv40pE4 also found it difficult to use #gensoltour
10:35am October 16th 2014 via Twitter Web Client
CL: He went to training at DOE/JGI, and discussed results using img/mer tool: http://t.co/UUxV1H18V5 'tedious to get answers' #gensoltour
CL: Taxonomic distribution showed: from Phyla to Species. 30-40% unmapped from Atlantic City beach sites. Cp to Ocean City site #gensoltour
CL: Using MicroSEQ ID and Greengenes, species cutoff >99%, genus cutoff >97%; showed Krona visualization. 'It's very good' #ge
CL: Showed results of 107K and 221K reads/run per 314 run; summary of Ion Reporter results 'in only 3h' #gensoltour
10:34am October 16th 2014 via Twitter Web Client
CL: Uses the new metagenomics analysis kit, with V2-4-8, V3-6-7-9 regions, 400bp seq kit. Torrent Browser 'gives very good ctrl' #gensoltour
CL: After PGM on 314, either Ion Reporter plugin, or upload FASTQ to JGI-DOE resources, also MG-RAST #gensoltour
CL: Bioremediation paper 2013 He et al http://t.co/HEhjojd3hO Fecal source paper 2013 Milani et al http://t.co/JyWUazLpAA #gensoltour
CL: Areas of application for 16S rRNA: bioremediation, bioreactors, fecal source tracing #gensoltour
First up: Dr. Charlie Li (EMSL Analytical) "16S Metagenomic Analysis from Microbial Communities in Marine Water" #gensoltour
Next set of #gensoltour tweets is to get them from the Ion Torrent handle to my own - apologies in advance! http://t.co/mwUQWPOhAT
10:33am October 16th 2014 via Twitter Web Client
New post: Targeted sequencing of cell-free DNA by Ion Ampliseq | Behind the Bench http://t.co/w8lqu2CWlC
8:20am October 16th 2014 via Hootsuite
RT @zachklein: Genius: http://t.co/M2SvC99p35… via @drk
10:00pm October 15th 2014 via Hootsuite
"An accessible visualization of geographic distribution": The Racial Dot Map | Weldon Cooper Center http://t.co/SMwXZcD09v
9:05pm October 15th 2014 via Hootsuite
RT @BW: Survey finds that women who played sports in college get further in the corporate world: http://t.co/xhPQOM8Wre
8:00pm October 15th 2014 via Hootsuite in reply to
RT @ThePoke: Childhood. (via @GeniusFootball) http://t.co/xrifoH1G2p
7:00pm October 15th 2014 via Hootsuite in reply to
RT @gizmag: NASA readies its fleet of scientific assets for a once-in-a-life-time photoshoot - http://t.co/CNeJHNVVBO
6:05pm October 15th 2014 via Hootsuite in reply to
RT @m_m_campbell: Ebola’s evolution. Its distant past & possible future. Good explainer: http://t.co/dd6yhW0366 #Ebola by @carlzimmer
5:05pm October 15th 2014 via Hootsuite in reply to
RT @iontorrent: Dale Yuzuki gives a preview of #ASHG14 San Diego CA 10/18-22 Behind the Bench: http://t.co/MPB9fVQmys http://t.co/c1ychroJfy
4:05pm October 15th 2014 via Hootsuite
hESC Stem cell tharpy appears safe for dry AMD | Science News http://t.co/lfeI1MLBsP
3:02pm October 15th 2014 via Hootsuite
Genetic testing for Altzheimer’s without revealing results | WSJ http://t.co/bK3h8gARPq
2:05pm October 15th 2014 via Hootsuite
Humans may only survive 68 days on Mars - Yahoo News http://t.co/XQ8hn8aCOx
12:00pm October 15th 2014 via Hootsuite
RT @claritas4kids: Patrice Milos and D Miller noon (ET) "Exomes and the Clinical Research Conundrum." http://t.co/pNWpnDToj4 #sciencewebinar
11:36am October 15th 2014 via Hootsuite
Payscale List: http://t.co/2TtX8B9Bcl MT @Forbes: Which college majors all but guarantee a healthy starting salary? http://t.co/vOI5rsAciO
11:05am October 15th 2014 via Hootsuite
Warming up for the @iontorrent webinar: Exome sequencing the clinical research conundrum. http://t.co/dhfSv8EMvo http://t.co/GSmYE4Jfk1
10:44am October 15th 2014 via Hootsuite in reply to
RT @markdlim: #NIH invests almost $32 million to make #bigdata less of a buzzword and more of a source of knowledge http://t.co/iB26Vtxhcz
10:05am October 15th 2014 via Hootsuite
If your household assets hit $798K, you are a 1%-er | Telegraph http://t.co/PUO6GC64xD
9:03am October 15th 2014 via Hootsuite
Previewing the American Society of Human Genetics Annual Meeting | Behind the Bench Blog http://t.co/EHGOJQVeqk #ASHG14
8:01am October 15th 2014 via Hootsuite
RT @iontorrent: Last chance: Register for the webinar tomorrow: Exome sequencing the clinical research conundrum. http://t.co/dhfSv8EMvo
7:53am October 15th 2014 via Hootsuite in reply to
RT @aliciacollin: Why Americans Are Drowning in Medical Debt - The Atlantic http://t.co/g0Fh2rKVHq by @olgakhazan via @medskep
7:05am October 15th 2014 via Hootsuite in reply to
RT @cureffi: <1 week until our crowdsourced genetics session at #ASHG14 with @erlichya, @Foldit, @atulbutte & @itsikp http://t.co/gSe
6:10am October 15th 2014 via Hootsuite
