Beechem #AGBT19 Dev bio have been doing spatial biology forever; I-O another driver. Chen: discovery will be a driv… https://t.co/4JK5g38Sqx
3:42pm February 27th 2019 via Hootsuite Inc.
Q: a few years ago lots of hesitation around sc genomics; same today wrt spatial? #AGBT19 Rimkunas A different mind… https://t.co/Fm3Clj0TVo
3:40pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 There needs to be new methods of statistical analysis. High-dimensional data; before computation vi… https://t.co/f5IsjHXw6B
3:36pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 It takes time to show something is possible (taking a couple of technologies and combining them) befor… https://t.co/x3xbmp70rh
3:33pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Sample preparation and storage and affects on the assay are very important. Thanks to high multiple… https://t.co/R5BCFlORho
3:28pm February 27th 2019 via Hootsuite Inc.
Chen: #AGBT19 You need simple-to-run, low-cost, scalable metrics at the beginning. And then add'l controls, like ERCC.
3:26pm February 27th 2019 via Hootsuite Inc.
Beechem: #AGBT19 IHC 1-plex: can put into a panel 'and it won't fail', only 2 out of a thousand that have failed. A… https://t.co/ASk0WwSTpI
3:25pm February 27th 2019 via Hootsuite Inc.
Q: Varying degrees of sample quality? #AGBT19 Rimkunas For protein, you need a valid IHC study, cold ischemic time.… https://t.co/HvdWHiXFT6
3:23pm February 27th 2019 via Hootsuite Inc.
Q: What do you think of all this spatial technologies? #AGBT19 Rimkunas: H3 all about I-O and microenvironment; IHC… https://t.co/zCmRaGgGjZ
3:14pm February 27th 2019 via Hootsuite Inc.
Q: Any plans to dive into up-regulated luminal markers? Rimkunas #AGBT19 Yes, PPARg is expressed but unk effect on immune system.
2:59pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Volcano plot shows luminal markers in tumor enriched side. DSP 'has been a game-changer' - from 15… https://t.co/1M2bs2rImT
2:57pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 PPARg low have high TIS (shows data), high degree of TIL using CD3. Shows PPARg hi - low TIS, lower degree of TIL.
2:56pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Used illustration from '13 ref https://t.co/pzIWmMkAaw Hypothesis: immune markers in space, what's… https://t.co/VVsGQfSj8p
2:53pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 PPARg - mutated, ampl, amplified in muscle-invasive bladder ca. PPARg knockdown does not impact ce… https://t.co/klJQdKrGjj
2:51pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 DSP in patient paired biopsies - standard gene exp profiling confirmed.
2:49pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Measurement of tumor content: vary widely. Added spec probes (5 custom genes to @nanostringtech I-… https://t.co/JahThcp4CX
2:47pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Goal for DSP: look at pharmacodynamic markers, look at ER expression. 'Majority of clinical trial… https://t.co/Cj5aFEUtaW
2:45pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 In Ph 1, H3B-6545 suppresses both ERaMUT and ERaWT activity. Called a Selective Estrogen Receptor… https://t.co/96dKQwY32U
2:44pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Using DSP for target engagement and tumor immunity. ER+ br cancer: aromatase inh relapse may be due to ESR1 gene mutations.
2:43pm February 27th 2019 via Hootsuite Inc.
RT @TPU_ICR: The next talk. H3 company. #agbt #agbt19 https://t.co/Eqk7HlqQ1C
2:41pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Has 3 small molecules in PhI clinical trials. Uses data from FMI and others; H3 mission to generat… https://t.co/YNO2Yanbb7
Vicki Rimkunas (Eisai / H3) #AGBT19 Utilizing digital spatial profiling to guide drug development
2:40pm February 27th 2019 via Hootsuite Inc.
Okay #AGBT19 tweeps - send Stephane some love via retweeting this handy map! https://t.co/jCEi9vZggB
2:36pm February 27th 2019 via Twitter Web Client
Vickovic #AGBT19 Plans: combine with Mass Cytometry (sc); deconvolve ST with scRNAseq in tumors via machine learnin… https://t.co/RrwctLcJ3V
2:34pm February 27th 2019 via Hootsuite Inc.
Vickovic #AGBT19 Cross validation - combining spatial transcriptomics (ST) and scRNAseq data. In ALS - look at vent… https://t.co/oPxDb04PWq
2:32pm February 27th 2019 via Hootsuite Inc.
Vickovic AGBT19 20K - 30K UMI's spot, 5-6K genes. Morphology / exp profile. BioRxiv preprint https://t.co/YtgcAoMmDc
2:28pm February 27th 2019 via Hootsuite Inc.
Vickovic AGBT19 Position fresh-frozen tissue; cells are permeabilized; cDNA synthesis is done in-situ. Digest tissu… https://t.co/6jZLvX30gH
2:24pm February 27th 2019 via Hootsuite Inc.
Vickovic AGBT19 A 100um spot - millions of copies of barcodes, UMI, polydT. In 100um spot: between 3 and 30 cells,… https://t.co/nnDr5eLAfq
2:22pm February 27th 2019 via Hootsuite Inc.
Vickovic AGBT19 Shows TMA (tissue microarray) from 50 pts. The Q: how can they go HTP? Imaging + RNAseq keeping inf… https://t.co/sz7KJBJoMR
2:21pm February 27th 2019 via Hootsuite Inc.
Sonja Vickovic (Broad Inst) #AGBT19 Spatial transcriptomics for monitoring ALS disease dynamics
2:19pm February 27th 2019 via Hootsuite Inc.
RT @maqcsociety: #DataIntegration: What is challenging but doable, and what is science fiction? Come ask @mason_lab… https://t.co/AyTzsdrxw8
2:05pm February 27th 2019 via Hootsuite Inc.
Q: in a single cell, how many RNAs can you count? Moffitt #AGBT19 Limited by diffraction; can do 200-400 RNAs in ne… https://t.co/7B0oeKWg92
1:55pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Generalizable across tissues and organisms. Can define parts and how they fit. Lab website: https://t.co/SYHYRck6AQ
1:53pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Concl: Each round of Merfish going through multiple rounds of hybridization, imaging, stripping.
1:52pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Merfish has sensitivity (down to a few copies / cell) showing signal difference in different behavi… https://t.co/HYw9SiGNww
1:51pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Clustering shows 80% corresponding with scRNA-seq. Moves quickly through different types of neurons… https://t.co/tLUYkOXQJj
1:50pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Shows cross-validation w/scRNAseq cell classes, very good agreement. Merfish ID'd 70 neuronal types… https://t.co/QmK9ASxLgx
1:47pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Shows 200um x 200um slides of preoptic region: overlays MERFISH, transcriptional hetergeneity. Zoom… https://t.co/Gbq9XInDhy
1:44pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Preoptic region of hypothalamus: collected data from 31K cells via DropSeq, '15 Science… https://t.co/iNu52JJubv
1:41pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Can find single-cell perturbation, to map out gene regulatory networks, work out organization of tr… https://t.co/SMX857vGYC
1:40pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Shows Merfish images - each spot is a single RNA molecule. Shows cycle 1 to 16, RNAs lighting up or… https://t.co/NfGjpKNPxJ
1:38pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Misreading of 0 or 1; 16 rounds of imaging is the whole transcriptome, but need to correct for erro… https://t.co/uPTGzdgTrX
1:36pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Single-molecule FISH: DNA oligos to target RNA. '08 Nature Methods https://t.co/pPvHkDrlY3 Explains… https://t.co/zRgvYrJcQ6
1:35pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Single-cell approaches suffer from dis-association. Cells organize their transcriptomes internally.… https://t.co/c6W0Aw3uO0
1:33pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Why: the best way to study a complex system (i.e. a car) is to study it's parts. But you have to re… https://t.co/pZAgkkWEZx
1:32pm February 27th 2019 via Hootsuite Inc.
Jeffery Moffitt (Harvard) #AGBT19 Mapping the brain with multiplexed error robust fluorescence in-situ hybridization (Merfish)
1:31pm February 27th 2019 via Hootsuite Inc.
Q: How many transcripts per bead? Chen #AGBT19 About 500 UMIs per cell. Lot of room to grow there. Will be optmizing, want 10x that.
1:27pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 Case 3 Spatially-differentiated gene exp. Striations of patterns of zebrin in Purkinje cells.
1:18pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 Case 2: local gene expression changes. Illustrates with neural damage.
1:16pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 Can overlay scRNA-Seq. Shows cool 3D reconstruction of tissue transcriptomics.
1:13pm February 27th 2019 via Hootsuite Inc.
