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.
Chen #AGBT19 Onto case studies of how this type of data could be used: construct tissue architecture. ID regional s… https://t.co/Lc0jjjGHr9
1:12pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 (NB - said bioRxiv paper would go up today with this technique, not there yet.) Shows validation, diff… https://t.co/J6Z4VodZsP
1:10pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 All up-front: put slice of tissue, map gene expression in space.
1:09pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 Describes DropSeq: take beads (10um), bead w/PCR handle, spatial barcode, UMI. Put beads on surface; u… https://t.co/YYYr8EJgxb
1:07pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 Describing the problem over coffee w/inventor of Drop-seq. Methods are in-situ (Starmap, Merfish, ExFi… https://t.co/QJHwozpyoQ
1:05pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 Shows a diagram from this '15 Cell (Drop-Seq) https://t.co/QHv1Bv7RC7 Slide-seq - genome-wide expression at 10um
1:03pm February 27th 2019 via Hootsuite Inc.
Fei Chen (Broad Institute) #AGBT19 Tools for in-situ molecular interrogation spanning the resolution and throughput spectrum
1:01pm February 27th 2019 via Hootsuite Inc.
Q: H&E stained? Beechem #AGBT19 Can use it as an overlay to help visualize area to focus in on.
12:57pm February 27th 2019 via Hootsuite Inc.
Q: How large an area? Beechem #AGBT19 1-2 cm on a side. Typically 10-20 ROI's, 10 mm2 each. Slides can be reprobed on different days.
Beechem #AGBT19 Summarizing, 20K barcodes, 'add another zero for next year'; up to 20 sections / day throughput.
12:55pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Thursday @nanostringtech workshop Thursday afternoon (John McPherson), poster 514 Friday, plenary b… https://t.co/VlzELYIUsL
12:54pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 a plot of 5K mRNA vs 418 probes - scaling. https://t.co/58HfGFcgGi
12:50pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Shows exon-level PTEN data with exon-4 dropping out.
12:48pm February 27th 2019 via Hootsuite Inc.
RT @nanostringtech: Our #SpatialGenomics Summit panel: Joe Beechem, PhD, NanoString, Fei Chen, PhD, The Broad, Jeffrey Moffitt, PhD, Boston…
Beechem #AGBT19 They had multiple different barcodes for the same mRNA probe - and thus every mRNA species have 10… https://t.co/lnCHwrhIe1
12:47pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Illustrates chemokine data at the RNA - a whole cascade by location and interaction.
12:46pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Points out poster #614 Friday at 440pm for their pathway analysis in space. Tumor center, invasive… https://t.co/kKpV7Kikp0
12:44pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Figure of probing the reactome. https://t.co/lVy1SLbrYn
12:43pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 High-profile Nature Med Nov 2018 https://t.co/hdS1boNxBN Three centers of excellence - Holland, OHS… https://t.co/kJOlr51rLr
12:42pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 (Correction - with PD-L1 on back of CD68.) Unusual microscope - integrates with clinical informatio… https://t.co/inyKHzQz4A
12:40pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Work with David Rimm (Yale) looking at tumor microenv in melanoma, 44 proteins across 59 patients.… https://t.co/Qo8IxVIRpH
12:38pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Now you get 100% cellularity of the tumor. The mask is inverted - just like Photoshop 'at single-cell resolution'.
12:36pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Shows a CRC sample, with PanCK in yellow (tumor) and CD45+ (immune cells in microenvironment). Show… https://t.co/UwyCJynnVa
Beechem #AGBT19 Needed dual digital micromirror chips, each with 1M mirror features. Can configure to any tissue geometry.
12:34pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 35-50bp of RNA, UMI's, spatial indexes, RNA ID index. Readout on any ILMN instrument.
Beechem #AGBT19 explaining how GeoMx DSP works. https://t.co/W0KiZacxem
12:33pm February 27th 2019 via Hootsuite Inc.
Here at #AGBT19 @nanostringtech putting on a great Spatial Genomics workshop just getting started (Palms Ballroom) https://t.co/TBgxttySnS
12:32pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Affinity reagent mix; read-out by moving scope (guided by colors) then cleave spec area. Sip it up… https://t.co/C5mca6t2zi
12:31pm February 27th 2019 via Hootsuite Inc.
