Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Schaum N; Karkanias J; Neff NF; May AP; Quake SR; Wyss-Coray T; Darmanis S; Batson J; Botvinnik O; Chen MB; Chen S; Green F; Jones RC; Maynard A; Penland L; Pisco AO; Sit RV; Stanley GM; Webber JT; Zanini F; Baghel AS; Bakerman I; Bansal I; Berdnik D; Bilen B; Brownfield D; Cain C; Cho M; Cirolia G; Conley SD; Demers A; Demir K; Morree A; Divita T; Bois H; Dulgeroff LBT; Ebadi H; Espinoza FH; Fish M; Gan Q; George BM; Gillich A; Genetiano G; Gu X; Gulati GS; Hang Y; Hosseinzadeh S; Huang A; Iram T; Isobe T; Ives F; Kao KS; Karnam G; Kershner AM; Kiss BM; Kong W; Kumar ME; Lam JY; Lee DP; Lee SE; Li G; Li Q; Liu L; Lo A; Lu WJ; Manjunath A; May KL; May OL; Mckay M; Metzger RJ; Mignardi M; Min D; Nabhan AN; Ng KM; Noh J; Patkar R; Peng WC; Puccinelli R; Sikandar SS; Sinha R; Szade K; Tan W; Tato C; Tellez K; Travaglini KJ; Tropini C; Waldburger L; Weele LJ; Wosczyna MN; Xiang J; Xue S; Youngyunpipatkul J; Zardeneta ME; Zhang F; Zhou L; Castro P; Croote D; DeRisi JL; Kuo CS; Lehallier B; Nguyen PK; Tan SY; Wang BM; Yousef H; Wyss-Coray T; Beachy PA; Chan CKF; Wang BM; Weinberg K; Wu SM; Yousef H; Barres BA; Chan CKF; Clarke MF; Huang KC; Kim SK; Krasnow MA; Nusse R; Rando TA; Sonnenburg J; Weissman IL; Wu SM

Nature, Vol.562, No.7727, 367-+, 2018

DOI10.1038/s41586-018-0590-4 Export Citation

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Schaum N, Karkanias J, Neff NF, May AP, Quake SR, Wyss-Coray T, Darmanis S, Batson J, Botvinnik O, Chen MB, Chen S, Green F, Jones RC, Maynard A, Penland L, Pisco AO, Sit RV, Stanley GM, Webber JT, Zanini F, Baghel AS, Bakerman I, Bansal I, Berdnik D, Bilen B, Brownfield D, Cain C, Cho M, Cirolia G, Conley SD, Demers A, Demir K, Morree A, Divita T, Bois H, Dulgeroff LBT, Ebadi H, Espinoza FH, Fish M, Gan Q, George BM, Gillich A, Genetiano G, Gu X, Gulati GS, Hang Y, Hosseinzadeh S, Huang A, Iram T, Isobe T, Ives F, Kao KS, Karnam G, Kershner AM, Kiss BM, Kong W, Kumar ME, Lam JY, Lee DP, Lee SE, Li G, Li Q, Liu L, Lo A, Lu WJ, Manjunath A, May KL, May OL, Mckay M, Metzger RJ, Mignardi M, Min D, Nabhan AN, Ng KM, Noh J, Patkar R, Peng WC, Puccinelli R, Sikandar SS, Sinha R, Szade K, Tan W, Tato C, Tellez K, Travaglini KJ, Tropini C, Waldburger L, Weele LJ, Wosczyna MN, Xiang J, Xue S, Youngyunpipatkul J, Zardeneta ME, Zhang F, Zhou L, Castro P, Croote D, DeRisi JL, Kuo CS, Lehallier B, Nguyen PK, Tan SY, Wang BM, Yousef H, Wyss-Coray T, Beachy PA, Chan CKF, Wang BM, Weinberg K, Wu SM, Yousef H, Barres BA, Chan CKF, Clarke MF, Huang KC, Kim SK, Krasnow MA, Nusse R, Rando TA, Sonnenburg J, Weissman IL, Wu SM

Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.