Macosko #AGBT19 Transfer to tube and do standard sequence, then deconvolute x-y position via bead barcode. Mapping… https://t.co/JSLXiZSSto
3:39pm March 2nd 2019 via Twitter Web Client
Macosko #AGBT19 Slide-seq decouples barcoding from downstream assay. Deposit beads - 90k beads in 3mm circle. Seque… https://t.co/wpMa7DE0VQ
3:38pm March 2nd 2019 via Twitter Web Client
Macosko #AGBT19 Spatial methods: in-situ (Starmap, Merfish, ExFish). Sequencing: Spatial Transcriptomics. Issue: li… https://t.co/euiy5BWINJ
3:37pm March 2nd 2019 via Twitter Web Client
Macosko #AGBT19 Need 2: relate gene expression to tissue pathology. Showing architecture of Prostate Ca and predicting disease course
3:35pm March 2nd 2019 via Twitter Web Client
Macosko #AGBT19 Having started with DropSeq, collab with Fei Chen extending the method. Critical method: hi-res map… https://t.co/xtMmmqUY83
Evan Macosko (Broad) #AGBT19 Slide-Seq: A scalable technology for measuring genome-wide expression at high spatial resolution
3:33pm March 2nd 2019 via Twitter Web Client
Lappalainen #AGBT19 ANEVA their tool est regulatory variation. Shows constraints - mutational target, UTR, promoter… https://t.co/mgHt337sJB
2:48pm March 2nd 2019 via Twitter Web Client
Lappalainen #AGBT19 The ideal vs 'the complicated reality': four different genes, each dots is an individual, four very different plots.
2:44pm March 2nd 2019 via Twitter Web Client
Lappalainen #AGBT19 ASE to capture genetic regulatory variants in cis. 85% heritability '15 ref… https://t.co/8Q0vbR5qT7
2:43pm March 2nd 2019 via Twitter Web Client
Lappalainen #AGBT19 eQTLs and ASE. '17 Cell https://t.co/653C9zxJ3i GTeX v8 release: 17,382 post-mortem tissue samp… https://t.co/dI8WOquWqU
2:38pm March 2nd 2019 via Twitter Web Client
Lappalainen #AGBT19 Fn interpretation of genetic var. How can interpretation of GWAS loci, regulatory code, personal genome be scaled?
2:35pm March 2nd 2019 via Twitter Web Client
Tuuli Lappalainen (New York Genome Center) #AGBT19 Functional variation in the human genome: Lessons from the transcriptome
Wu #AGBT19 Can see 2.9kb or smaller. Found a 290kb loop. Have walked along three chromosomes, want to do many more.… https://t.co/8EYrvwzL6A
2:27pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Shows a 5kb resolution map (with help from the Aiden lab).
2:24pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Each of their homologues they are looking at are different. Looking at commonality in entanglement dista… https://t.co/V4CIVkhlr7
2:22pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Shows pair of homologous and direct chromosome imaging https://t.co/EVDC7LhtJs
2:21pm March 2nd 2019 via Twitter for iPhone
Wu #AGBT19 Shows many people, including Peng Yin and others at Harvard working on chromosome imaging. Bruker help i… https://t.co/0KorueITj6
2:19pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Shows image and scale - the smallest dot is 42-bp resolution imaging. '16 ref https://t.co/WYsGIOsdSb
2:16pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Also used for MERFISH, seqFISH. They are doing super-res imaging. OligoDNA-Paint ref… https://t.co/2SFHWdGAC7
2:14pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Onto imaging: oligo paints simple tool - both ends have non-human sequence, with labeled oligos for mult… https://t.co/NjlcrnhqJ6
2:13pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Along some thom maps (Maternal/Paternal) the pairing is destroyed.
2:11pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Maternal/Paternal - the same. Thus: in Drosophila it is 'railroad track' geometry. Impact: pairing is st… https://t.co/7oCWIRrnwj
2:09pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Mentions many papers, including Shendure's. Are homologues close-enough to be captured? Maternal/Materna… https://t.co/8cjP7fOPtk
2:08pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Nettie Stevens in 1908 - not only ID'd the Y-chr directly, also observed pairing homologues. They use haplotype-resolved Hi-C
2:06pm March 2nd 2019 via Twitter Web Client
Wu #AGBT19 Better understanding of chr organization can lead to better diagnostics, and Rx. Different family member… https://t.co/EhMaD1vgu9
2:04pm March 2nd 2019 via Twitter Web Client
Chao-Ting Wu (Harvard) #AGBT19 Looking at chromosomes
2:03pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Across time - shows HDACi response. Gives a shout-out to Frank Steemers at Illumina, and Jay Shendure / Vijay Ramani
1:59pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Showing effect of driving response away. Example: Trametinib cells. Cells cluster of 2/3. MEK and… https://t.co/cp8oFi6gEI
1:52pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 4,512 conditions, 500K cells, 3 lines, 199 compounds, 4 doses, 2 replicates.
1:51pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Able to 'stain' nuclei with plain oligos. Shows mouse/human hash separation. sci-Chem: single-cell… https://t.co/Pn1LiOsTaw
1:50pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Look at many cells, many perturbation.s. Single-cell 'hashing' - labeling cells that show up in RN… https://t.co/mIULADIEiS
1:48pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 MOI not clearly known, HDAC inhibitors derepress tumor suppressors. Histone deacetylases have othe… https://t.co/sPFlMfy8DG
1:47pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 What else can we do with ultra-scalable scRNA-seq? Now massively multiplexed scRNA-seq for drug re… https://t.co/iM7WpFVLsy
1:46pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Photo of part of his video of cellular lineage. https://t.co/Tnq2WqdQHZ
1:46pm March 2nd 2019 via Twitter for iPhone
Trapnell #AGBT19 This work published '19 Nature https://t.co/9nHdbfQk7K
1:45pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Has a site to access https://t.co/ZMcIioXnS8
1:44pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Monocle 2 works with thousands of cells, not for millions. tSNE to umap coordinates, shows 2D to 3… https://t.co/xgveTA6TbL
1:42pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 61 embryos over 5d. Note even 1x cell coverage: from 2M cells: shows colors in 3D changing over ti… https://t.co/jaLqW8MU7k
1:40pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 (Split pooling idea described last night, similar). Can take all RNA-seq reads, and determine what… https://t.co/Uto0CitewX
1:38pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 And then learning the trajectory. Combinatorial indexing - take cells, solubilize, distribute, per… https://t.co/pqb6pLH1TW
1:36pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Shows a video illustrating Waddington's landscape - illustrating developmental landscapes using sc… https://t.co/wpDOw3usbL
1:35pm March 2nd 2019 via Twitter Web Client
Cole Trapnell (Univ Washington) #AGBT19 Single-cell transcriptome analysis at whole-embryo scale
1:33pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Rapid Run mode gap now closed with S-prime (SP) cell. Same readlengths, 150bp vs 250bp inserts hard to keep head-to-head.
12:41pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Support of Orien - research network for data sharing. RNA-Seq now 50M-100M. Exomes now 100x-400x. WGS… https://t.co/5Rv9ysDtG9
12:38pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Shows charts on pricing and outputs. https://t.co/FfHoJgva2n
12:37pm March 2nd 2019 via Twitter for iPhone
Levy #AGBT19 Plots out the growth of Illumina platforms. NovaSeq called 'the Keureg of sequencers'. Reagent managem… https://t.co/MistDkkTfs
12:35pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Shows one of his boys on Microarray, then 454, SOLiD, PGM, HiSeq, then iSeq/NovaSeq.
12:33pm March 2nd 2019 via Twitter Web Client
Shawn Levy (Hudson Alpha) #AGBT19 Will be talking about transition to NovaSeq 6000; longer reads, 'holism of sequen… https://t.co/nerccmWYoC
12:31pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 the value of the NovaSeq 6000, 325-400GB, 38h, $13.75/Gb vs the HiSeq 2500 RR at $41.73.
12:29pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Shows 2x251bp on the iSeq 100. NextSeq 550 update: the v2.5 kits ambient ship, new control SW to sc… https://t.co/WKqGoPVFP1
12:25pm March 2nd 2019 via Twitter Web Client
