G
Geoff Stanley
Researcher at Stanford University
Publications - 10
Citations - 589
Geoff Stanley is an academic researcher from Stanford University. The author has contributed to research in topics: Biology & Transcriptome. The author has an hindex of 5, co-authored 6 publications receiving 371 citations.
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Posted ContentDOI
Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq 4000 DNA sequencing
Rahul Sinha,Geoff Stanley,Gunsagar S. Gulati,Ezran C,Travaglini Kj,Eric X Wei,Charles Chan,Ahmad N. Nabhan,Su T,Rachel M. Morganti,Stephanie D. Conley,Hassan Chaib,Kristy Red-Horse,Michael T. Longaker,Snyder M,Mark A. Krasnow,I.L. Weissman +16 more
TL;DR: It is shown that low levels of free index primers persist after the most common library purification procedure recommended by Illumina, and that the amount of signal spreading among samples is proportional to the level of freeindex primer present in the library pool.
Journal ArticleDOI
Single-cell analysis of early progenitor cells that build coronary arteries
Tianying Su,Geoff Stanley,Rahul Sinha,Gaetano D'Amato,Soumya Das,Siyeon Rhee,Andrew H. Chang,Aruna Poduri,Brian C. Raftrey,Thanh Theresa Dinh,Walter A. Roper,Walter A. Roper,Guang Li,Kelsey E. Quinn,Kathleen M. Caron,Sean M. Wu,Lucile Miquerol,Eugene C. Butcher,Eugene C. Butcher,Irving L. Weissman,Stephen R. Quake,Kristy Red-Horse +21 more
TL;DR: It is shown that vein cells of the developing heart undergo an early cell fate switch to create a pre-artery population that subsequently builds coronary arteries, which are built by vein-derived coronary arteries that can differentiate independently of blood flow upon the release of inhibition mediated by COUP-TF2 and cell cycle factors.
Journal ArticleDOI
Computational correction of index switching in multiplexed sequencing libraries.
TL;DR: Allele-specific quantification by ATAC-PCR correlated strongly with the allelic accessibility determined byATAC-seq (R = 0.962) (Supplementary Fig. 4), thus demonstrating accurate quantification of targeted and allelespecific accessibility by ATac- PCR enabled by APT.
Journal ArticleDOI
High-content CRISPR screening
Christopher J Bock,Paul Datlinger,Florence M. Chardon,Matthew A. Coelho,Matthew B. Dong,Keith A. Lawson,Tian Lu,Laetitia Maroc,Thomas M. Norman,Bicna Song,Geoff Stanley,Sidi Chen,Mathew J. Garnett,Wei Li,Jason Moffat,Lei S. Qi,Rebecca S. Shapiro,Jay Shendure,Jonathan S. Weissman,Xiao-Xi Zhuang +19 more
Posted ContentDOI
Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris
Nicholas Schaum,Jim Karkanias,Norma F. Neff,Andrew May,Tony Wyss-Coray,Spyros Darmanis,Joshua Batson,Botvinnik O,Michelle B. Chen,Chen S,Foad Green,Robert C. Jones,Ashley Maynard,Lolita Penland,Sit Rv,Geoff Stanley,James T. Webber,Fabio Zanini,Baghel As,Bakerman I,Bansal I,Daniela Berdnik,Biter Bilen,Douglas Brownfield,Cain C,Cho M,Cirolia G,Stephanie D. Conley,Demers A,Kubilay Demir,Kubilay Demir,Morree Ad,Divita T,Bois Hd,Dulgeroff Lbt,Ebadi H,F. H. Espinoza,Matt Fish,Matt Fish,Gan Q,Benson M. George,Astrid Gillich,Genetiano G,Xueying Gu,Gunsagar S. Gulati,Yan Hang,Shayan Hosseinzadeh,Huang A,Tal Iram,Taichi Isobe,Ives F,Kevin S. Kao,Karnam G,Aaron M. Kershner,Kiss B,Kong W,Maya E. Kumar,Jonathan Y. Lam,Davis P. Lee,Song Eun Lee,Gordon Li,Qi Li,Lin Liu,Lo A,Wan Jin Lu,Anoop Manjunath,May Kl,May Ol,McKay M,Ross J. Metzger,Marco Mignardi,Min D,Ahmad N. Nabhan,Katharine M. Ng,Joseph J. Noh,Patkar R,Weng Chuan Peng,Robert Puccinelli,Eric Rulifson,Shaheen S. Sikandar,Rahul Sinha,Krzysztof Szade,Krzysztof Szade,Tan W,Cristina M. Tato,Krissie Tellez,Kyle J. Travaglini,Carolina Tropini,Lucas M. Waldburger,Weele LJv,Wosczyna Mn,Joy S. Xiang,Shifeng Xue,Youngyunpipatkul J,Macy E. Zardeneta,Feijie Zhang,Lu Zhou,Castro P,Derek Croote,Joseph L. DeRisi,Angela Oliveira Pisco,Bernhard Kiss,Christin S. Kuo,Christin S. Kuo,Benoit Lehallier,Nguyen Pk,Serena Y. Tan,Bingying Wang,Hanadie Yousef,Philip A. Beachy,Chan Ckf,Kerwyn Casey Huang,Kenneth I. Weinberg,Sen Wu,Ben Anthony Barres,Michael F. Clarke,Seokho Kim,Mark A. Krasnow,Mark A. Krasnow,Norma F. Neff,Roel Nusse,Roel Nusse,Thomas A. Rando,Justin L. Sonnenburg,Wa Bm +124 more
TL;DR: A compendium of single cell transcriptome data from the model organism Mus musculus comprising more than 100,000 cells from 20 organs and tissues, which represent a new resource for cell biology, revealing gene expression in poorly characterized cell populations and allowing for direct and controlled comparison in cell types shared between tissues.