Nature - USA (2020-10-15)

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nature research | reporting summary

April 2020

Corresponding author(s): Anne Schaefer

Last updated by author(s):August 19, 2020

Reporting Summary

Nature Research wishes to improve the reproducibility of the work that we publish. This form provides structure for consistency and transparency

in reporting. For further information on Nature Research policies, see our Editorial Policies and the Editorial Policy Checklist.

Statistics

For all statistical analyses, confirm that the following items are present in the figure legend, table legend, main text, or Methods section.

n/a Confirmed

The exact sample size (n) for each experimental group/condition, given as a discrete number and unit of measurement

A statement on whether measurements were taken from distinct samples or whether the same sample was measured repeatedly

The statistical test(s) used AND whether they are one- or two-sided

Only common tests should be described solely by name; describe more complex techniques in the Methods section.

A description of all covariates tested

A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons

A full description of the statistical parameters including central tendency (e.g. means) or other basic estimates (e.g. regression coefficient)

AND variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals)

For null hypothesis testing, the test statistic (e.g. F, t, r) with confidence intervals, effect sizes, degrees of freedom and P value noted

Give P values as exact values whenever suitable.

For Bayesian analysis, information on the choice of priors and Markov chain Monte Carlo settings

For hierarchical and complex designs, identification of the appropriate level for tests and full reporting of outcomes

Estimates of effect sizes (e.g. Cohen's d, Pearson's r), indicating how they were calculated

Our web collection on statistics for biologists contains articles on many of the points above.

Software and code

Policy information about availability of computer code

Data collection RNA/DNA quality check: 2100 Expert Software (v8.02.07.SI532)

RNA/DNA sequencing: NextSeq System Suite, Illumina bcl2fastq2 Conversion Software v2.17

qPCR: StepOne Software (v2.3)

Imaging : Zen 2012 software (v8.1)

Microglia imaging: NIS-Elements AR (Ver4.40.00)

Mouse behavior: EthoVision (v9), Fusion (v5.0)

FACS Analysis: AttuneNXT software v4.2

Software and script usage is described in the method section.

Data analysis Bulk RNA seq bioinformatics: TopHat2 (v2.1.0), HTSeq-count (v0.6.0), SPEctRA (v1.0), DESeq2 package (v1.20.0), R (v3.1.1), Enrichr

10X single nuclei sequencing: 10X Cell Ranger (v2.1.0), Loupe Browser (v2.0.0), ggplot2 (v3.2.1)

Data representation: Multiple Experiment Viewer 4.8 (v.10.2), GraphPad Prism (v7.0a)

Imaging analysis: ImageJ (v1.48 and v1.52), Zen2011 (v8.1), Neurolucida (v11)

Calcium imaging analysis: NoRMCorre (CalmAn v1.6.3), Suite2P (v0.6.16), MatLab (R2018a and R2019b)

Microglia imaging analysis: HyperStackReg (v5.6), Coloc2 (v3.0.0), Manual Tracking (v2.1.1)

sEPSCs analysis: Clampfit10.3

FACS analysis: FCS Express 7 Plus Software

The code used for analysis of calcium transience in neurons to analyze event rates, magnitude, spatial correlation and synchrony can be found

at https://github.com/GradinaruLab/striatum2P

Software and script usage is described in the method section.

For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and

reviewers. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research guidelines for submitting code & software for further information.