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How many tissues to use for each sample?

NP Norbert Perrimon
BD Bart Deplancke
SQ Stephen R. Quake
LL Liqun Luo
SA Stein Aerts
HL Hongjie Li

Last updated date: May 8, 2022 Views: 604 Forks: 0

original An abbreviated version of this protocol was published in Science
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
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How many tissues to use for each sample? 

During sample preparation, we estimated the required tissue number based on three factors: total cell/nucleus number in the tissue, targeted cell number for 10x Genomics and Smart-seq2, and the FACS recovery rate. Our FACS recovery rate is about 5%. For example, if a tissue contains 10,000 nuclei, we were able to collect 500 nuclei after FACS. So if we want to collect 10,000 nuclei after FACS, we will dissect 20 tissues. Please note that since we don’t have the exact number of cells for many tissues, our dissection labs have prepared more samples than estimated. Here we list the numbers of tissues we prepared. If not specified, the number is used for each sex to target one 10x run, which is about 10,000 cells: 
Head, 100 heads for a total 6 10x runs; body, 50 bodies for a total 6 10x runs; antenna, 300; haltere, 500; proboscis with maxillary palp, 100; wing, 200; leg, 120; gut, 200; body wall, 40; heart, 250; male reproductive gland, 200; testis, 600; ovary, 30; malpighian tubule, 300; fat body, 250; oenocyte, 250; trachea, 100; insulin-producing cell (IPC), 250 for one 384-well plate; corpora cardiaca cell (CC), 250 for one 384-well plate.

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Perrimon, N, Deplancke, B, Quake, S, Luo, L, Aerts, S and Li, H(2022). How many tissues to use for each sample?. Bio-protocol Preprint. bio-protocol.org/prep1661.
  2. Li, H., Janssens, J., De Waegeneer, M., Kolluru, S. S., Davie, K., Gardeux, V., Saelens, W., David, F. P. A., Brbić, M., Spanier, K., Leskovec, J., McLaughlin, C. N., Xie, Q., Jones, R. C., Brueckner, K., Shim, J., Tattikota, S. G., Schnorrer, F., Rust, K., Nystul, T. G., Carvalho-Santos, Z., Ribeiro, C., Pal, S., Mahadevaraju, S., Przytycka, T. M., Allen, A. M., Goodwin, S. F., Berry, C. W., Fuller, M. T., White-Cooper, H., Matunis, E. L., DiNardo, S., Galenza, A., O’Brien, L. E., Dow, J. A. T., Jasper, H., Oliver, B., Perrimon, N., Deplancke, B., Quake, S. R., Luo, L. and Aerts, S.(2022). Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science 375(6584). DOI: 10.1126/science.abk2432

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