Haynes: Modeling as nascent isoform cp to not-modeled: can change results. Data suggests unprocessed RNA picked up #RNASeq2014
9:42am June 19th 2014 via Hootsuite
Haynes: (QFI is a TM of Asuragen). Elevated intronic coverage from FFPE; most pipelines ignore it; ILM pulls out exonic #RNASeq2014
9:40am June 19th 2014 via Hootsuite
Haynes: "FFPE of low quality can be rescued" - by adding more. High quality: more not helpful (100ng to 600ng) #RNASeq2014
9:39am June 19th 2014 via Hootsuite
Haynes: QFI is qPCR-based, best predictor of FFPE whole transcriptome data quality. 100ng to 600ng chart shown... #RNASeq2014
Haynes: FFPE challenges on QC: %DV200 on BioAnalyzer by 'unique exonic r2': 0.17, 0.31, 0.34, 0.66 (BA, nanodrop, Qubit, QFI) #RNASeq2014
9:38am June 19th 2014 via Hootsuite
Haynes: FFPE can look 'good' but function poorly; also can look poor but function well. #RNASeq2014
9:36am June 19th 2014 via Hootsuite
Haynes: FFPE quality varies on 2 axes: irrev. chemical modifications & extent of degradation #RNASeq2014
Brian Haynes (Asuragen): "RNA-Seq of FFPE specimens for biomarker discovery & development" #RNASeq2014
9:33am June 19th 2014 via Hootsuite
Li:Q&A: The RNA amplification method was NuGEN's Ovation. #RNASeq2014
9:31am June 19th 2014 via Hootsuite
Li: Points out need to narrow down the inherent sample hetergeneity; mentions existing compute infrastructure & cloud movement #RNASeq20
Li: Doesn't recommend RNA ampl (? what method?); strandedness consistency important metric; some SW not sens. to strand #RNASeq2014
9:28am June 19th 2014 via Hootsuite
Li: lincRNA example cp protocols: varying results dep on library prep; miRNA picked up in all methods #RNASeq2014
9:25am June 19th 2014 via Hootsuite
Li: mRNA reads limited to 'small region': picked up via RT-PCR but not RNA-Seq; mRNA could be tied up in lipid. #RNASeq2014
9:23am June 19th 2014 via Hootsuite
Li: Case 3: Looking at RNA in exosome compartment; cp. protocols, +/- ampl.; different frag; 3 seq platforms (SOLiD, Ion + ILM) #RNASeq2014
9:22am June 19th 2014 via Hootsuite
Li: DESeq dispersion looked poor; switched to Partek's tool, a mIR212/132 modulation of xcr demonstrated #RNASeq2014
9:21am June 19th 2014 via Hootsuite
Li: Analysis parameters do matter. 2nd case: map reads ~40%; using RPKM # detected genes differ substantially (3K vs 12K) #RNASeq2014
9:19am June 19th 2014 via Hootsuite
Li: Their discrepant DE results: dispersion est. driven by 1 out of 3 repl. samples; rec'd move to pooled estimate on DESeq #RNASeq2014
9:16am June 19th 2014 via Hootsuite
Li: Calc DESeq and EdgeR params for dispersion and quantile normalization: p<0.05, v. different numbers of genes #RNASeq2014
9:13am June 19th 2014 via Hootsuite
Li: Using ERCC, saw more scatter at lower conc; amplified material looked poor #RNASeq2014
9:11am June 19th 2014 via Hootsuite
Li: Used RiboMinus for rRNA removal (40% contam); 2nd round didn't help much. 100M-700M reads/sample. 10-30% map to exons #RNASeq2014
9:08am June 19th 2014 via Hootsuite
Li: Used SOLiD / 5500xl 50x35PE reads; after alignment they used Partek for gene- and isoform-level analysis #RNASeq2014
9:06am June 19th 2014 via Hootsuite
Li: Looking at WT / KO mice and diff exp genes; 5 total neural tissues along with microglial samples (need to amplify RNA) #RNASeq2014
9:04am June 19th 2014 via Hootsuite
Qingqin Li (J & J Biomarkers): "Comparison of RNA-Seq data analysis parameters using multiple datasets" #RNASeq2014
9:02am June 19th 2014 via Hootsuite
RT @kbradnam: My latest '101 questions with a bioinformatician' interview is Mr. Bioinformatics himself: @ewanbirney http://t.co/jGzuuBj1OL
8:20am June 19th 2014 via Hootsuite
RT @scicurious: Today at Eureka! Lab, I'm reviewing a science site for students, written by students themselves. http://t.co/Gz4h2dgtxU…
8:05am June 19th 2014 via Hootsuite
RT @engadget: 4SRS: the FBI built a list of Twitter slang to keep up with the kids http://t.co/GbjmysUyzB
7:10am June 19th 2014 via Hootsuite
NEJM reference RT @DrDanielSwan: Paper: Screening an Asymptomatic Person for Genetic Risk http://t.co/ht6zJV62au
6:10am June 19th 2014 via Hootsuite
RT @BioMickWatson: Gundlach nanopore technology, which @illumina licensed, sequences phi X http://t.co/rBqpgD7gtm
5:20am June 19th 2014 via Hootsuite
RT @TEDTalks: How great teachers create magic and inspire you to learn: http://t.co/qX83BfIJIH
4:20am June 19th 2014 via Hootsuite
MT @KevinADavies: First healthy baby (@razibkhan's son) born with entire genome decoded in advance | Tech Review http://t.co/RSgn7CdnXG
3:05am June 19th 2014 via Hootsuite
RT @GENbio: Clinically Actionable Genomics: From Sequencing to Personalized Medicine. View free webcast http://t.co/awyQJsNm0p
2:50am June 19th 2014 via Hootsuite
RT @DailyNewsGW: NIH, NSF Team to Help Biomedical Startups Translate Technologies to Market http://t.co/Lr22pc20DP
1:35am June 19th 2014 via Hootsuite
RT @ScienceNewsOrg: If the world is a computer, life is an algorithm http://t.co/vLPtdPLauR
12:25am June 19th 2014 via Hootsuite
RT @theNCI: The strongest risk factor for breast cancer is age. What are some other risk factors? http://t.co/dDAYTVOme0
11:25pm June 18th 2014 via Hootsuite
RT @TheAtlantic: How millennials are changing international travel http://t.co/EI94mDEath
10:50pm June 18th 2014 via Hootsuite
RT @Rndubois: Most states are cutting support for higher education pretty significantly: http://t.co/tlwwNfQbfv
10:20pm June 18th 2014 via Hootsuite
How to Anonymize Everything You Do Online | WIRED http://t.co/yf3zcCyXv4
9:10pm June 18th 2014 via Hootsuite
RT @findlungcancer: FDA Finally Proposes Social Media Guidelines http://t.co/F0voh5K1Wu via @WSJ #doctors20 #hcldr #hcsm #lcsm
8:25pm June 18th 2014 via Hootsuite
RT @mims: So here's what I consider the definitive take on disruption, by @monkbent http://t.co/RWhz1O7QPE
7:25pm June 18th 2014 via Hootsuite
RT @washingtonpost: Someone built a 114-foot tower entirely out of Legos http://t.co/uW06NkaWI7 http://t.co/H0Kja1Vpok
6:40pm June 18th 2014 via Hootsuite
RT @AMAnet: The slow demise of the frequent-flier program. (via @washingtonpost) #Biz #Travel #Management | http://t.co/9xpJHfSl6E
6:35pm June 18th 2014 via Hootsuite
RT @THebertMcGill: Social media and its effects... even the big companies are listening. http://t.co/yFiBOuhTXD
5:15pm June 18th 2014 via Hootsuite
Jackson: Listed validated methods / demonstrated methods / illumina-qualified as a partnership with them / NEB list also #RNASeq2014
4:30pm June 18th 2014 via Hootsuite
Jackson: What do customers want? Library quality, implementation, higher throughput, minimal hands-on time, flexibility #RNASeq2014
4:22pm June 18th 2014 via Hootsuite
Alisa Jackson (Beckman): "Automated solutions for highly reproducible RNA-Seq libraries for improved transcriptome analysis" #RNASeq2014
4:20pm June 18th 2014 via Hootsuite
Crosby:Q&A: Could RiboZero be obtaining pre-mRNAs? Perhaps. #RNASeq2014
4:17pm June 18th 2014 via Hootsuite
Crosby: Conclude: Arrays may be more sensitive than RNA-Seq (surprising); NGS lib prep can impact ability to detect fold change. #RNASeq2014
4:13pm June 18th 2014 via Hootsuite
Crosby: Conclude: different microarrays, different transcripts "only 1/2 RefSeq genes shared xcr pattersn" #RNASeq2014
4:12pm June 18th 2014 via Hootsuite
Crosby: Showed good RNA-Seq performance to the '7034'; 2x NGS lib preps (SMARTer, Epicentre) very similar #RNASeq2014
4:06pm June 18th 2014 via Hootsuite
Crosby: Microarray p-values <0.05; used an in-house developed direct labeling for microarrays; 30M reads/sample for RNA-Seq. #RNASeq2014
4:04pm June 18th 2014 via Hootsuite
