Dataset related to the article: Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins Landrein B, Formosa-Jordan P, Malivert A, Schuster C, Melnyk CW, Yang W, Turnbull C, Meyerowitz EM, Locke JCW, Jönsson H. Proc Natl Acad Sci U S A. 2018 Jan 23. pii: 201718670. doi: 10.1073/pnas.1718670115. Data is made of z-stacks (Format: Zeiss .lsm files that can be opened with Fiji (ImageJ)) obtained by confocal microcopy. Each file is a stack of a single meristem. Images were taken with a Zeiss LSM780 or with a Zeiss LSM700 confocal microscope and with a 20X water objective (Plan-Apochromat 20x/1.0 DIC CG=0.17 M27 75mm). Unless stated otherwise, the same settings were applied for all meristems within an experimental repeat. Each folder contains the data related to a figure (or multiple figures if the same set of data was used to generate multiple figures) from the article. Then subfolders separate genotypes or/and markers (if available) and experimental replicates. Fig.1-Fig.S1 Z-stacks of Col-0 meristems labelled with FM4-64, thickness: 2 µm. The weights of the corresponding shoots are available in a text file within the folder. Two experimental repeats. Plants were grown in constant light on different types of soils: 1/3 Soil + 2/3 Sand, ˝ Soil + ˝ Sand, 2/3 Soil + 1/3 Sand, 1/1 Soil (aka LowN), 1/1 Soil + Fertilizer (aka HighN). Fig.2-Fig.S3-S4-S5 Z-stacks of Col-0 meristems not labelled with FM4-64 and expressing pTCSn::GFP, pWUS::GFP, WUS-GFP and pCLV3::dsRED (together with pTCS::GFP which is not analysed in the paper), thickness: 2 µm. Channel 2 for pTCSn::GFP, pWUS::GFP and WUS-GFP and channel 3 for pTCS::GFP x pCLV3::dsRED correspond to the autofluorescence of the plastids. Two experimental repeats for pTCSn::GFP, pWUS::GFP and WUS-GFP, 3 experimental repeats for the pCLV3::dsRED. Plants were grown in constant light on different types of soils: 1/3 Soil + 2/3 Sand, ˝ Soil + ˝ Sand, 2/3 Soil + 1/3 Sand, 1/1 Soil (aka LowN), 1/1 Soil + Fertilizer (aka HighN). Fig.3-Fig.S6 Z-stacks of Col-0 and cytokinin-associated mutant meristems labelled with FM4-64, thickness: 2 µm. The weights of the corresponding shoots are available in a text file within the folder. Two experimental repeats. Plants were grown in constant light on different types of soils: 1/1 Soil (aka LowN), 1/1 Soil + Fertilizer (aka HighN). Fig.4-Fig.S9-S10 Z-stacks of grafted Col-0 and cytokinin-associated mutant meristems labeled with FM4-64, thickness: 2 µm. Note that some of the grafted plants having Col-0 shoots also express pTCS::GFP x pCLV3::dsRED but that these markers were not analyzed. The presence of these markers is indicated in the name of the file. R: Root genotype, S: Shoot genotype. Folders: Grafting-Col-0, Grafting-ckx3.5, Grafting-log4.7, Grafting-log1.3.4.7, Grafting-ipt3.5.7, Grafting-cyp735a1.2, two experimental repeats except for Grafting-Col-0 (6 repeats). One growth condition: constant light, 1/1 Soil + Fertilizer (aka HighN). Folder: Grafting-ipt357-Impact-Nutrition, two experimental repeats. Two growth conditions: constant light, 1/1 Soil (aka LowN) or constant light, 1/1 Soil + Fertilizer (aka HighN). Fig.5 Time-lapses of cut meristems expressing pTCSn::GFP or pWUS::GFP and growing in vitro in Apex Culture Medium with 1% Sucrose with no cytokinins (Control), 50 µM tZR or 50 µM tZ in a phytotron (constant light). Three time points: t0h (just after dissection), t24h, t48h. Two experimental repeats. Plants were grown in constant light on 1/1 Soil + Fertilizer (aka HighN). Fig.6-Fig.S12-S13-S15 Folders: pTCSn::GFP, pCLV3::dsRED, pWUS::GFP Z-stacks of Col-0 meristems not labeled with FM4-64 and expressing pTCSn::GFP, pWUS::GFP and pCLV3::dsRED (together with pTCS::GFP which is not analyzed), thickness: 2 µm. Channel 2 for pTCSn::GFP and pWUS::GFP and channel 3 for pTCS::GFP x pCLV3::dsRED correspond to the autofluorescence of the plastids. Two experimental repeats. Plants were grown in constant light in pots of sand with terragreen and watered once a week with a nutritive solution containing 1.8 mM of NO3. Before experiments (at the beginning of the bolting stage), 8-12 plants were taken for imaging day-0 and the remaining plants were separated in three different populations that were watered with a nutritive solution containing either 0 mM of NO3 (aka NoNO3), 1.8 mM of NO3 (aka LowNO3) or 9 mM of NO3 (aka HighNO3). Different meristems from different plants were imaged each day. For pTCSn::GFP, replicate 1: meristems at day-0 were imaged using a Zeiss LSM700 but meristems from day-1 to day-3 were imaged using a Zeiss LSM780. To compare the different days, one meristem (pTCSn-GFP-1-1-sand-9-mM-NO3-Day-1-1) at day 1 was imaged successively on the LSM700 using the same settings as day-0 and on the LSM780 using new settings and analyzed so that it could be used to normalize the signal at day-0 obtained on the LSM700 with the signal of the other days obtained on the LSM780. Similarly, all the images acquired with the LSM780 were done with a gain for the GFP of 800, but the meristems from the plants watered with 9mM of NO3 at day 3 were having too much signal and saturating the images taken with such gain. These meristems were therefore imaged with a gain for the GFP of 700 but one meristem (pTCSn-GFP-1-1-sand-9-mM-NO3-Day-3-1) was imaged with both 700 and 800 gains and used to normalize the image obtained with the gain of 700 with the images obtained with the gain of 800. For pTCSn::GFP, replicate 2: Plants at day-0 were imaged on the LSM780 with a laser on “Standby” instead of “On”, a mistake that was noticed just at the end of the imaging. One meristem (“pTCSn-GFP-Day-0-Control-1”) was therefore imaged with both settings (“Standby” and “On”) and used to normalize the signal at day-0 obtained with the laser on “Standby” to the signal on the other days obtained with the laser on “On”. Also, the signal of meristems from day-1 to day-3 was saturating with the gain of 800 of the day-0 so the gain was reduced to 750 for these days. At day-1, two meristems (pTCSn-GFP-Day-1-9mM-NO3-1 and 2) were imaged with both settings and used for normalizing the data from day-0. For pCLV3::dsRED, replicate 2, which also express pTCS::GFP: the pTCS::GFP signal was not analyzed in the paper. But it is worth noting that the digital gain (DG) of the GFP was either set to 2 or 4, depending on the meristem. The digital gain parameter linearly modulates the signal outcome of the image, which was confirmed in our quantification. Hence, the signal of meristems imaged with a DG of two were was multiplied by 2 in order to normalize it to the meristems imaged with a DG of 4. Folder: CK-associated-mutants Z-stacks of Col-0 and cytokinin-associated mutant meristems labeled with FM4-64, thickness: 2 µm. Two experimental repeats. Plants were grown in constant light in pots of sand with terragreen and watered once a week with a nutritive solution containing 1.8 mM of NO3. At the beginning of the bolting stage, plants were separated in two different populations and watered with a nutritive solution containing either 0 mM of NO3 (aka NoNO3) or 9 mM of NO3 (aka HighNO3). Meristems were imaged three days after the watering. Fig. S11 Time-lapses of dissected and cut meristems expressing p35S::XVE-IPT3-TFP and pTCS::GFP x pCLV3::dsRED or pWUS::GFP growing on Apex Culture Medium with 1% Sucrose with no cytokinins and without (control) or with 5 µM of ß-estradiol in a phytotron (constant light). Three time points: t0h (just after dissection, before induction), t24h, t48h. Two experimental repeats. Plants were grown in constant light on 1/1 Soil + Fertilizer (aka HighN).