Jay Shendure
@JShendure · Seattle, WA · joined 11 May 2011
Genomics technology developer. Developmental biology adult learner. Professor at @uwgenome @HHMINEWS @BrotmanBaty SeaHub @AllenInstitute /him.
14 295Followers
332Following
558Posts total
448.6KViews on collected posts
โพสต์ล่าสุด
กำลังค้นหาโพสต์ใหม่…
@CXchengxiangQIU @LukeKoblan @WilliamNColgan @JswLab @HaedongK @sophieseid @MollyGasp @jb_lalanne @ksimeono @coletrapnell @_Choi_Junhong @AllenInstitute @biohub @BrotmanBaty @uwgenome @hhmi_science Again all data avail w/ preprint - annotated tree browsable @ https://t.co/6j6L9m2
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@CXchengxiangQIU @LukeKoblan @WilliamNColgan @JswLab @HaedongK @sophieseid @MollyGasp @jb_lalanne @ksimeono @coletrapnell @_Choi_Junhong ..and thanks to amazing community of scientists & funders made this possible, inc. Seattle Hub for Synthetic Biology @AllenInstitute @biohub @
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@CXchengxiangQIU @LukeKoblan @WilliamNColgan @JswLab Huge kudos to all the co-authors: Qi Yu, @HaedongK, @sophieseid, J. Acosta-Clark, B. Martin, K. OConnor, R. Daza, @MollyGasp, J. Nathans, M. Lam, E. Gamo, S.VijayKumar, L. Kuo, @jb_lalanne, @ksimeono, M. P. @coletrapnell, J. G
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@CXchengxiangQIU H/T to an exciting and complementary PEtracer preprint from @LukeKoblan, @WilliamNColgan & @JswLab , reconstructing lineage w/ >1.5M cells across 16 embryos from E7.5-E10. Hoping these together are inflection point for developmental recording field.
https://t.co/
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@CXchengxiangQIU You can walk tree in either direction. Descending: blastomere A → one pre-gastrulation founder → a E7.43 progenitor whose 624 sampled descendants exhibit clonally demarcated contributions to three endodermal organs. Zoom in further to homogenous liver subclade. 1
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@CXchengxiangQIU Fun result - although tree built from TAPE edits
alone , clade co-occurrence recovers germ layer organization & sweeping developmental time turns that into a *dated* hierarchy of couplings 14/n https://t.co/uaPC68AmYX
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@CXchengxiangQIU At tips, 51% of tree siblings share cell type, 9× chance, & extremes track anatomy, e.g. lung & airway 139×, DRG neurons 69× (cell types that commit from spatially restricted pool & expand locally). Recent terminal differentiations are legible among heterotypic t
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@CXchengxiangQIU The tree resolves 182 ancestral lineages at E6.0; follow them to E13.5 & just 24 account for half the embryo, where a neutral birth-death process predicts 35. Clonal dominance is set early, then simply inherited. (see paper re: 2nd phase of clonal dominance) 12/n
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@CXchengxiangQIU Then, near silence for 4 days! Followed by fast re-start of keystrokes at ~E6 at ~9 edits/cell/day, fading slowly as TAPEs fill. Avg. 55 / 66 sites written by E13.5. Analogous to 13.5 page book w/ pp2-5 torn out (pre-gastrulation arguably dull anyways :). Not ide
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@CXchengxiangQIU Plot twist: At 2-cell stage there is burst of edits (major ZGA!). Daughter A got 23, B got 19, none shared. Thankfully as we only had one mouse, this hands us an internal replicate. Trees made & measured twice in two half-embryos that shared a zygote. All finding
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Annotation didn't start from scratch. Our E8–P0 mouse atlas (by @CXchengxiangQIU, B. Martin, Ian Welsh from JAX) covered essentially every cell type at E13.5, so we could immediately label all 1,340,794 tips — 25 major trajectories, 135 cell types. 9/n
https://t.co/rF2A8JVCFa ht
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Phylogenetic tree building methods don't scale well, so @sophieseid did it in 2 steps. 1) Build a 640,012 cell backbone by NJ on an ordered edit distance (SciPhy) & strict molecular clock dating, then 2) distance-based placement of more cells to get to 1,340,794 tips. 8/n https:
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Building on GESTALT (2016, w/ @aaron_mckenna @TheGenomeLab @jamiegagnon @schierlab ) we previously developed DNA Typewriter (2022, w/ @_Choi_Junhong @wchenomics ), a sequential recorder that leverages prime editing (h/t @davidrliu) to write insertional symbols to DNA TAPE. 5/n ht
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How to read TAPE? Not easy on mRNA-poor nuclei we use for whole-animal scRNA-seq. Fix from @HaedongK: circular TAPE which, together with sci-RNA-seq3 by Qi Yu and Beth Martin, yielded (11 × 6 TAPE) × 1,753,895 cell-by-gene matrix w/ ~50% of TAPE entries genotyped. 7/n
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To get DNA Typewriter in vivo, Qi Yu & @AllenInstitute SeaHub in vivo platform injected PEMax, epegRNAs, blank TAPE into B6 zygotes w/ piggyBac, then let development proceed to E13.5. 100 injected → 78 transferred → 10 embryos → 1 w/ great recording, on 11 x 6-unit TAPEs. 6/n htt
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Preprint: https://t.co/g9TB5G8SPl
This is the product of many years of effort, and particularly amazing summer teamwork by Qi Yu, @HaedongK @sophieseid @CXchengxiangQIU and many others from Shendure Lab & SeaHub (a @AllenInstitute @biohub @UWMedicine collab) 2/n
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We've also built NextCell (h/t @claude_code), an interactive browser for the entire annotated phylogeny — https://t.co/6j6L9m2yKj
Open science, so the trees and data are released there too (or will be very soon, lmk if anything missing). 3/n https://t.co/n6y85uqomS
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For background: in 1983 Sulston & colleagues completed the cell lineage of C. elegans by watching every division under a microscope, & forty years later
it is still the only complete animal cell lineage we have. You obviously cannot build a mouse cell lineage this way. 4/n https
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Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote
1/n http
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New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee &
@CGBiar! Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n https://t.co/kbx1kA4d97 https://t.co/1gu5MC
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Our latest w/ @sudpinglay Lab -- Shred-seq for gigabase-scale deletion scanning of the human genome! Amazing work by @JonasKoeppel
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Really thrilled by the framing and scale of this new @biohub initiative, including the combination of internal & external investment in tech-dev, open data, modeling and collaborative science, all good things!
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Super excited re: first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to brilliant Chase Suiter & @Green_Ahn @UWproteindesign on the work! Preprint:
https://t.co/7gh8ZtcKUO htt
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Excited to share our lab's latest preprint, led by @CXchengxiangQIU, @bethkarenmartin & Ian Welsh of @jacksonlab.
We set out to build a single cell roadmap for all of mouse prenatal development, from single cell zygote to free-living pup.
Preprint: https://t.co/GDS65Qf58X 1/n
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เทียบกับบัญชีขนาดเดียวกัน
21 โพสต์จาก 90 วันที่ผ่านมา เทียบกับช่วง 10K–100K ผู้ติดตาม แสดงในวงกว้าง แต่มีผู้ชมตอบสนองน้อย.
ยอดดูมัธยฐาน1 507บัญชีนี้924ค่ามัธยฐานของ 10K–100K
การเข้าถึง, %10.54%บัญชีนี้3.62%ค่ามัธยฐานของ 10K–100K
การมีส่วนร่วม, %0.86%บัญชีนี้1.52%ค่ามัธยฐานของ 10K–100K
| ตัวชี้วัด | บัญชีนี้ | ค่ามัธยฐานของ 10K–100K | อัตราส่วน |
|---|---|---|---|
| ยอดดูมัธยฐานต่อโพสต์ | 1 507 | 924 | 1.63× |
| การเข้าถึง (ยอดดู ÷ ผู้ติดตาม) | 10.54% | 3.62% | 2.91× |
| อัตราการมีส่วนร่วม | 0.86% | 1.52% | 0.57× |
บัญชีอื่นในช่วงนี้ → เปรียบเทียบกับบัญชีอื่น → ค่าอ้างอิงเหล่านี้คำนวณอย่างไร →
Growth & engagement
How the posts we collected actually performed: views and reaction rate post by post, what the audience did with them, and where the follower count goes.
Views per post
2.2K31 Jul
1.8K
2.6K
1.5K
1.4K
1.4K
1.3K
1.2K
1.2K
1.1K
1.1K
1.4K
1.5K
2351 Aug
Last 14 collected posts, oldest on the left. The scale is logarithmic: one post can outrun the rest a hundred times over.
Engagement rate per post
0.78%31 Jul
0.84%
0.51%
1.06%
0.86%
0.87%
0.86%
1.01%
0.95%
1.69%
1.00%
0.79%
1.21%
0.85%1 Aug
Reactions — likes, reposts, replies and quotes — divided by views. Median for 10K–100K accounts is 1.52%.
What the audience does
Likes64.5%2 056 in total
Reposts17.1%546 in total
Replies1.8%56 in total
Quotes2.1%66 in total
Bookmarks14.6%465 in total
Share of every reaction we collected for this account. Replies mean argument, reposts mean endorsement, bookmarks mean the post was worth keeping.
The follower curve appears once this account has two daily snapshots — we take one a day, and this one is on its first.
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