Evidence map›Paper›PMID 38915722›Full record

ArticlebioRxiv : the preprint server for biology2024

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types.

Yoav Ben-Simon, Marcus Hooper, Sujatha Narayan, Tanya Daigle, Deepanjali Dwivedi, Sharon W Way, Aaron Oster, David A Stafford, John K Mich, Michael J Taormina and 104 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. VIP-to-SST Cell Circuit Motif Shows Differential Short-Term Plasticity across Sensory Areas of Mouse Cortex.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

114 authors.

Yoav Ben-SimonAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-7075-097X
Marcus HooperAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-1228-5958
Sujatha NarayanAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3741-1319
Tanya DaigleAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9700-8452
Deepanjali DwivediAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9992-9167
Sharon W WayAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-9598-2240
Aaron OsterAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-7074-6444
David A StaffordUniversity of California, Berkeley, Berkeley, CA 94720.
John K MichAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-1626-1139
Michael J TaorminaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-4634-4039
Refugio A MartinezAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0007-3737-3862
Ximena Opitz-ArayaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-4960-3622
Jada R RothAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-7946-2176
Shona AllenUniversity of California, Berkeley, Berkeley, CA 94720.ORCID 0000-0003-0186-0574
Angela AyalaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0002-8512-6851
Trygve E BakkenAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-3373-7386
Tyler BarcelliAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0000-0231-1441
Stuard BartaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-7180-3466
Jacqueline BendrickAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-2694-9914
Darren BertagnolliAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-6626-1567
Jessica BowlusAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0009-7335-3855
Gabriella BoyerAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0007-2146-2078
Krissy BrounerAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-5790-7154
Brittny CasianAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0009-9965-0364
Tamara CasperAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-1638-3651
Anish B ChakkaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-1095-1817
Rushil ChakrabartyAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-1722-8557
Rebecca K ChanceUniversity of California, Berkeley, Berkeley, CA 94720.ORCID 0000-0001-7059-6119
Sakshi ChavanAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-8964-8852
Maxwell DeparteeAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0002-3723-6474
Nicholas DonadioAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-6250-1148
Nadezhda DotsonAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-3414-3176
Tom EgdorfAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9059-8904
Mariano GabittoAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-6911-344X
Jazmin GarciaAllen Institute for Brain Science, Seattle, WA 98109.
Amanda GaryAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-6397-1520
Molly GasperiniAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-4559-8432
Jeff GoldyAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-5140-6922
Bryan B GoreAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-1721-4235
Lucas GraybuckAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-8814-6818
Noah GreismanAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0006-2436-8151
Francoise HaeseleerAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-1887-1798
Carliana HaltermanAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0006-2297-2590
Olivia HelbackAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0001-7892-6319
Dirk HockemeyerUniversity of California, Berkeley, Berkeley, CA 94720.ORCID 0000-0002-5598-5092
Cindy HuangAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0002-5386-6345
Sydney HuffAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-2304-6023
Avery HunkerAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-0508-3637
Nelson JohansenAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-4436-969X
Zoe JuneauAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-8860-5260
Brian KalmbachAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-3136-8097
Shannon KhemAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0002-6949-1381
Emily KussickAllen Institute for Brain Science, Seattle, WA 98109.
Rana KutsalAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0008-7190-6498
Rachael LarsenAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-0178-003X
Changkyu LeeAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-6146-0404
Angus Y LeeUniversity of California, Berkeley, Berkeley, CA 94720.
Madison LeiblyAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0000-1277-9400
Garreck H LenzAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3233-0763
Elizabeth LiangAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0000-1781-6784
Nicholas LuskAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-6346-2083
Jocelin MaloneAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-0794-4250
Tyler MollenkopfAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-2899-2879
Elyse MorinAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-7310-1561
Dakota NewmanAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3835-0853
Lydia NgAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-7499-3514
Kiet NgoAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0002-5548-1983
Victoria OmsteadAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3796-970X
Alana OyamaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-4492-0533
Trangthanh PhamAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-4738-5062
Christina A PomAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9057-040X
Lydia PotekhinaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-8879-7920
Shea RansfordAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-6093-0806
Dean RetteAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0002-5202-6627
Christine RimorinAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-1491-8552
Dana RochaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0001-2121-8899
Augustin RuizAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-8361-5152
Raymond E A SanchezAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9141-090X
Adriana Sedeno-CortesAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-7959-8970
Joshua P SevignyAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-9297-4800
Nadiya ShapovalovaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-8618-8272
Lyudmila ShulgaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0002-9785-328X
Ana R SiglerAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-5094-8073
La' Akea SivertsAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-1385-086X
Saroja SomasundaramAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3729-9849
Kaiya StewartAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-7837-2715
Eric SzelenyiAllen Institute for Brain Science, Seattle, WA 98109.
Michael TieuAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9286-5623
Cameron TraderAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-8214-1541
Cindy T J van VelthovenAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-5120-4546
Miranda WalkerAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3767-1591
Natalie WeedAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-0891-0327
Morgan WirthlinAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-7967-7070
Toren WoodAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0009-7437-4260
Brooke WynaldaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0004-7755-4295
Zizhen YaoAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-9361-5607
Thomas ZhouAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0008-1589-8059
Jeanelle ArizaAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-0829-7887
Nick DeeAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-2831-9254
Melissa RedingAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9845-1827
Kara RonellenfitchAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0009-0007-6221-8485
Shoaib MuftiAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-8173-3884
Susan M SunkinAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9893-3834
Kimberly A SmithAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3142-1970
Luke EspositoAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-3565-9126
Jack WatersAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-2312-4183
Bargavi ThyagarajanAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-3871-6410
Shenqin YaoAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0003-2992-4752
Ed S LeinAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-9012-6552
Hongkui ZengAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-0326-5878
Boaz P LeviAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-8346-872X
John NgaiUniversity of California, Berkeley, Berkeley, CA 94720.ORCID 0000-0002-1191-8971
Jonathan TingAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0001-8266-0392
Bosiljka TasicAllen Institute for Brain Science, Seattle, WA 98109.ORCID 0000-0002-6861-4506

Funding

Generation of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI NGAI, JOHN J. · 2017 to 2021
$64.7M
Development of tools for cell-type specific labeling of human and mouse neocortical neuronsRF1MH114126 · NIMH · ALLEN INSTITUTE · PI LEIN, ED, LEVI, BOAZ PIRIE · 2017 to 2017
$4.5M
Cell type selective viral tools to interrogate and correct non-human primate and human brain circuitryUG3MH120095 · NIMH · ALLEN INSTITUTE · PI KALUME, FRANCK K, LEIN, ED · 2020 to 2022
$3.8M
Cell class- or type-specific viruses for brain-wide labeling and neural circuit examinationRF1MH121274 · NIMH · ALLEN INSTITUTE · PI TASIC, BOSILJKA · 2019 to 2019
$2.6M
NIMH NIH HHS RF1 MH114126NIMH NIH HHS RF1 MH121274NIMH NIH HHS U19 MH114830NIMH NIH HHS UG3 MH120095
6 · The paper itself

Abstract

The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and disease. We used transcriptomic and epigenomic cortical cell type taxonomies from mouse and human to define marker genes and putative enhancers and created a large toolkit of transgenic lines and enhancer AAVs for selective targeting of cortical cell populations. We report evaluation of fifteen new transgenic driver lines, two new reporter lines, and >800 different enhancer AAVs covering most subclasses of cortical cells. The tools reported here as well as the scaled process of tool creation and modification enable diverse experimental strategies towards understanding mammalian cortex and brain function.

Indexed as

AAVCell typeEnhancerEpigeneticsHumanMouseNeocortexRecombinaseTranscriptomicsTransgenic

Identifiers

PMID38915722
PMCPMC11195086

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.