Beechem: Looking at simultaneous protein, mRNA readout, same tissue slice, and cluster diagram. Shows correlation, R2 0.88 #AGBT18
12:12pm February 13th 2018 via Hootsuite
Beechem: throughput - 20 slides/day; can plex from 10 to 1M (or higher w/sequencing). Shows MiSeq readout. Just two tags #AGBT18
12:11pm February 13th 2018 via Hootsuite
Beechem: And then can use optical image to generate a mask. Can differentiate between tumor and the microenvironment #AGBT18
12:10pm February 13th 2018 via Hootsuite
Beechem: A read-write microscope. (NB - writing is via UV light.) Digital multimirror device. Can see PanCK/DNA stain image #AGBT18
12:09pm February 13th 2018 via Hootsuite
Beechem: The barcodes are simply pulled off the tissue, 10's to 100's of Abs, or 1000's of mRNAs. 30s is all it takes to pull off#AGBT18
12:07pm February 13th 2018 via Hootsuite
Beechem: IHC is 1-4 answers; now reverse it. Instead of sticking assays to tissue, make photocleavable tags, using the microscope #AGBT18
12:06pm February 13th 2018 via Hootsuite
Beechem: 3D biology, Digital Spatial Profiling (DSP), and Hyb&Seq (H&S). Inbetween DSP and H&S: relating the two=spatial genomic
12:05pm February 13th 2018 via Hootsuite
NanoString workshop at #AGBT18 "Spatial genomics and the next frontier of NGS" Joe Beechem, R&D
12:04pm February 13th 2018 via Hootsuite
RT @pathogenomenick: Now @thekrachael presenting on our consortium direct RNA sequencing project. Full length direct RNA and cDNA sequencin…
11:48am February 13th 2018 via Hootsuite
RT @DrKenMcGrath: Rachael Workman measuring poly-a lengths in direct RNA sequencing on @nanopore #AGBT18 https://t.co/HVikK4lfpJ
11:47am February 13th 2018 via Hootsuite
RT @shgoodwin1: RW: Nice! 87% read ID for direct RNA seq on nanopore #agbt18
Q: Bias in sampling w/abundant alt splices? Workman: Dropouts on the <100nt transcripts #AGBT18
Workman: Concl: isoform and features of interest; unique info can be used to improve reference; mods '16 https://t.co/CUml4kAsUL #AGBT18
11:46am February 13th 2018 via Hootsuite
Workman: Detecting RNA mods. '17 review https://t.co/goylyMfgkM Used NEB HiScribe T7 synthesis for spike-ins of m6A mod #AGBT18
11:45am February 13th 2018 via Hootsuite
Workman: Ionic current dwell-time can be used to est PolyA lengths. Tool under dev on Github https://t.co/tk9OxjYkgr #AGBT18
11:42am February 13th 2018 via Hootsuite
Workman: Unique benefits - several isoforms of VEGFA gene UCSC track here: https://t.co/3R4TrBxc9I #AGBT18
11:41am February 13th 2018 via Hootsuite
Workman: Normalized transcript counts, Nanopore cDNA vs Nanopore direct, r=0.87; ILMN cDNA vs Nanopore direct, r=0.7 #AGBT18
11:39am February 13th 2018 via Hootsuite
Workman: Direct RNA 'show good alignment to GENCODE'. 10.8M aligned reads, 83% aligned, 87% read identity. Shows read length dist. #AGBT18
11:38am February 13th 2018 via Hootsuite
Workman: Capture PolyA, splint polyT adapter ligation, RT (opt), sequencing adapter ligation. #AGBT18
11:36am February 13th 2018 via Hootsuite
Workman: Nanopore RNA consortium, six Univs, GM12878 polyA RNA, now on Github https://t.co/7yIWvKVENi #AGBT18
Rachel Workman (Hopkins MD): Direct RNA and cDNA sequencing of human transcripts using the Oxford Nanopore sequencing platform #AGBT18
11:35am February 13th 2018 via Hootsuite
Q: Permeabilization? Cp to 10X? Shendure: They fix cells limits egress of RNA; 10X data comparable. UMI's/cell, not # genes/cell #AGBT18
11:34am February 13th 2018 via Hootsuite
Q: Are cell types representative? In Drop-Seq sees over-rep Shendure: Need more ground-truth on an organism-level #AGBT18
11:32am February 13th 2018 via Hootsuite
Q: Plots are calculating what? Shendure: A binary matrix, whether reads were observed or not. #AGBT18
11:30am February 13th 2018 via Hootsuite
Shendure: sci-type protocols can scale - through add'l rounds of indexing.#AGBT18
11:29am February 13th 2018 via Hootsuite
Shendure: #AGBT18 CRISPR work published here: '16 Science https://t.co/mGuxaQT3UG
Shendure: Zebrafish, inject guide RNAs as a zygote, and look at lineage. Barcodes and lineages built based on shared edits. (Clever) #AGBT18
11:28am February 13th 2018 via Hootsuite
Shendure: In-vivo CRISPR, Genome Editing of Synthetic Target Arrays for Lineage Tracing (GESTALT) method #AGBT18
11:27am February 13th 2018 via Hootsuite
Shendure: Looking at cell types underlying GWAS signals in Alzheimers. UK Biobank - >2K traits to measure, investigate w/this method #AGB
11:26am February 13th 2018 via Hootsuite
@h2so4hurts Yes spoke w/BCCA #AGBT18 speaker on pediatric work - WGS and whole transcriptome est cost "$20K-$30K" p… https://t.co/k1T3lnhF4V
11:25am February 13th 2018 via Hootsuite in reply to h2so4hurts
Shendure: Shows spatial heterogeneity across prefrontal cortex (upper vs lower layers and PCA), and Kidney #AGBT18
11:23am February 13th 2018 via Hootsuite
Shendure: Now chromatin assembly from 100K mouse cells and 13 tissues. ~85 distinct architectures (unpublished) #AGBT18
11:22am February 13th 2018 via Hootsuite
Shendure: single-cell data is sparse; much value is re-aggregating simlar cells. Shows comparison bet gene exp via FACS and sci-ATAC #AGBT18
11:19am February 13th 2018 via Hootsuite
Shendure: Germ layers readiliy ID'd at 6-8h/10-12h. Shows clustering data, 20,029 cells along top, by accessability, nice division #AGBT18
11:17am February 13th 2018 via Hootsuite
Shendure: Drosophila through germ layers. Multipotent: 6,372 cells; meso/ecto-diff. 7,092 cells; terminal diff: 6,465 cells #AGBT18
11:16am February 13th 2018 via Hootsuite
Shendure: #AGBT18 ATAC-seq via sci: Indexed Tn5 transposition, split. '15 https://t.co/64lsSxxD5g Now looking at fly embryogenesis w/EMBL
11:15am February 13th 2018 via Hootsuite
Shendure: Can do on human fixed or fresh cells, shows good correlation of expression. #AGBT18
11:13am February 13th 2018 via Hootsuite
Shendure: Thus it was '50x coverage' of entire organism. c elegans - have a known # of celltypes. Has expected vs obs: w/in 2-fold #AGBT18
11:11am February 13th 2018 via Hootsuite
Shendure: #AGBT18 40K transcriptomes of c elegans '17 Science https://t.co/q9rIGBQkuR 576 x 960 sci-RNA-seq only 762 cells in L2 worm
11:10am February 13th 2018 via Hootsuite
Shendure: Shoutout to Frank Steemers of Illumina who developed method. ATAC-Seq https://t.co/tfFUjHp3aA #AGBT18
11:09am February 13th 2018 via Hootsuite
Shendure: sci-: single-cell combinatorial index. Unique label nucleic acid via split-pool tagging in situ. Labelled in splitting 2x #AGBT18
11:08am February 13th 2018 via Hootsuite
Shendure: whole organism single-cell RNAseq in c elegans; ATAC-seq in drosophila, lineage tracing. Single-cell methods - many #AGBT18
11:06am February 13th 2018 via Hootsuite
Shendure: John Sulston, 2y of pen-and-paper work, won him a Nobel. Problem: opaque clls, spatial coordinates, scale #AGBT18
11:05am February 13th 2018 via Hootsuite
Shendure: 'Cell lineage trees are central to developmental biology'. Only place where the tree of cell div's sorted: c elegans #AGBT18
11:04am February 13th 2018 via Hootsuite
Jay Shendure (Univ Wash HHMI): Global views of development #AGBT18
11:02am February 13th 2018 via Hootsuite
Shen: Now establishing PROFYLE (PRecision Oncology For Younge peopLE) - dividing Canada into three regions, for pts 0-29 yo #AGBT18
10:18am February 13th 2018 via Hootsuite
RT @bffo: Great documentatry on the POG project on @youtube https://t.co/7PFVbhI6q4 #AGBT18 CC/ @BCCancer
10:16am February 13th 2018 via Hootsuite
Shen: Pt improved, relapsed, back on Rx with improvement. Reviews cases;'expression data plays essential role in decision' #AGBT18
Shen: 2nd case, indirect driver gene detection - EWSR1 fusion, targeted via downstream gene RNAseq analyses. Rx JAK inh #AGBT18
10:12am February 13th 2018 via Hootsuite
Shen: Shows clinical example of NTRK1/2, where there is an ongoing pediatric clinical trial, with excellent improvement #AGBT18
10:09am February 13th 2018 via Hootsuite
