AGBT tweets 2012 (2)

Chris Gunter @girlscientist

Day 2 of #AGBT starts with Rick Myers of @HudsonAlpha. That's my boss up there, so I expect only good tweets from y'all.

Sumit Middha @bioinfosm

#agbt tweeps, wassup with the tweetup; when and where? #anotherParty

Chris Gunter @girlscientist

.@bioinfosm #AGBT tweetup is in hotel lobby bar at 9:30ish after sessions end tonight.

@bffo@mastodon.social BF Francis Ouellette @bffo

C U all there! RT @girlscientist: .@bioinfosm #AGBT tweetup is in hotel lobby bar at 9:30ish after sessions end tonight.

Chris Gunter @girlscientist

R Myers echoes theme of meeting: you learn a lot more when you integrate a number of different data types, as in ENCODE. #AGBT

Olivier Elemento @ElementoLab

#AGBT Rick Myers: we will learn a lot by integrating interactome, transcriptome, methylome and allelic variation

@bffo@mastodon.social BF Francis Ouellette @bffo

RM:Encode neophytes should look at the guide paper, from PLoS Biology paper http://t.co/gvTjRKCf #AGBT

Illumina @illumina

Rick Myers, HudsonAlpha Inst, Encode: Integrate data from interactome, transcriptome, methylome with allelic variation #AGBT

Olivier Elemento @ElementoLab

#AGBT Rick Myers: has performed ChIP-seq for ~80 transcription factors in many cell lines for ENCODE

Deanna Church (she/her) @deannachurch

RM: analyzed over 80 transcription factors as part of ENCODE #AGBT

Dean Gaalaas @dgaalaas

Good morning. Rick Myers from Hudson Alpha talking ENCODE and ChIP-Seq at #AGBT

Illumina @illumina

Myers: NSRF is almost exclusively a repressor, binds ~2000 sites. Could not find NRSF binding site upstr of neuro D, until ChIP-Seq #AGBT

Deanna Church (she/her) @deannachurch

RM: by integrating binding data with variation data they can find both allele biased ans allele specific binding. #AGBT

Olivier Elemento @ElementoLab

#AGBT Rick Myers: found a lot of allele-specific binding

Todd Smith @finchtalk

#AGBT Rick Meyers on the gene regulation and the ENCODE project. Allele specific expression is wide spread.

Illumina @illumina

Myers: ChIP-seq on over 80 TFs many cell lines. Allele specific occupancy of protein on DNA & only G allele bound by GABP #AGBT

Olivier Elemento @ElementoLab

#AGBT Rick Myers: have developed transposon mediated method to make RNA-seq libraries, Gertz et al, 2012, Genome Research

Olivier Elemento @ElementoLab

#AGBT Rick Myers: can work with very small quantities of RNA, down to 1ng

Chris Gunter @girlscientist

Myers: recent paper on transposase-mediated construction of RNA-seq libraries, in @genomeresearch: http://t.co/1lpB7JY0 #AGBT

Todd Smith @finchtalk

#AGBT RM on RNA-seq, alignment and gene models are an unsolved problem. Transposon based "shearing" improves lib prep.

Illumina @illumina

Myers: w/RNA-seq 40M reads gives 40 reads for 1 kb. really really sensitive #AGBT

prithwishpal @omespeak

Rick Myers mentions difficulty of sequencing methylation using bisulfite (too expensive now). Perhaps nanopores will change that? #AGBT

Illumina @illumina

Myers RNA seq library contruction by transposon hopping, much more easier and quite sensitive only 10 pg mRNA #AGBT

Olivier Elemento @ElementoLab

#AGBT Rick Myers: did RRBS on 82 cell lines and tissues for ENCODE, clearly cell lines massively hypermethylated compared to tissues

Genome Biology @GenomeBiology

DNA methylation profiling of 82 cell lines and tissues on encode project. RM #agbt