| Antibodies |
| Goat anti c-Fos |
Santa Cruz Biotechnology |
Cat# sc-52-G; RRID: AB_2629503 |
| Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 546 |
Thermo Fisher Scientific |
Cat# A-11056; RRID: AB_2534103 |
| Rabbit polyclonal anti-H3K4me3 |
Diagenode |
Cat# pAb-003-050; RRID: AB_2616052 |
| Rabbit polyclonal anti-H3K27ac |
Diagenode |
Cat# C15410196; RRID: AB_2637079 |
| Chemicals, Peptides, and Recombinant Proteins |
| TO-PRO-3 Iodide (642/661) |
Thermofisher |
Cat# T3605 |
| cOmplete mini protease Inhibitor cocktail |
Roche (Sigma) |
Cat# 11836153001 |
| PhosSTOP |
Roche (Sigma) |
Cat# 4906845001 |
| Tetrodotoxin 1 mg |
Tocris (FISHER) |
Cat# 1078 |
| DL-AP5 Sodium salt 50 mg |
Tocris (FISHER) |
Cat# 36-935-0R |
| Triptolide |
Sigma |
Cat# 645900-1 MG |
| Actinomycin D |
Sigma |
Cat# A1410-2MG |
| Critical Commercial Assays |
| RNAscope® Fluorescent Multiplex Kit v2 |
ACD bio / Bio-Techne |
Cat# 323100 |
| RNAscope® Target Retrieval Reagents |
ACD bio / Bio-Techne |
Cat# 322000 |
| TSA Plus Fluorescein Evaluation Kit |
Perkin Elmer |
NEL741E001KT |
| TrueMicroChIP |
Diagenode |
Cat. No. C01010130 (AB-002-0016) |
| DynabeadTM mRNA DIRECTTM Micro kit |
Ambion |
Cat# 61021 |
| Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 |
10x Genomics |
Cat# PN-120237 |
|
|
|
| Deposited Data |
| Chip-seq, RNA-seq, Single nuclei-seq |
This paper |
GEO: GSE148252
|
| MM10/GRCm38p6 for Mouse |
UCSC genome browser |
http://genome.ucsc.edu
|
| NPAS4 ChIP-seq |
(Kim et al., 2010) |
GEO: GSE21161
|
| NPAS4 ChIP-seq |
(Brigidi et al., 2019) |
GEO: GSE127793
|
| Experimental Models: Organisms/Strains |
| Mouse: Npas4−/−
|
M.E. Greenberg, Harvard Medical School, Boston MA |
Lin et al., 2008
|
| Mouse: Npas4fx/fx
|
M.E. Greenberg, Harvard Medical School, Boston MA |
Lin et al., 2008
|
| Mouse: Camk2a::iCreBAC |
(Casanova et al., 2001) |
MGI: 2181426 |
| Oligonucleotides |
| Primer: Npas4−/−, WT forward: TGCTGAGAGGGTCTTTCTATGCG; WT reverse: TCCAGGTAGTGCTGCCACAATG; Null forward: AAAGACCCCAACGAGAAGCG; Null reverse: GCAAGTAAAACCTCTACAAATGTGG |
(Lin et al., 2008) |
N/A |
| Primer: Npas4fx/fx, forward: CCCTGCCCTTCTAATCAGAC; reverse: GGCATTGTTCTTTCTGTCTCC |
(Lin et al., 2008) |
N/A |
| Primer: Camk2a::iCreBAC, forward: TCTGATGAAGTCAGGAAGAACC; reverse: GAGATGTCCTTCACTCTGATTC |
(Casanova et al., 2001) |
N/A |
| Software and Algorithms |
| Code for data pre-processing, clustering, differential gene expression analysis, and peak calling |
(Berto et al., 2021) and this paper |
https://doi.org/zenodo.5111722
|
| Code for the Wavelet Analysis |
This paper |
https://doi.org/10.5281/zenodo.5106445
|
| BWA (v0.7.16a) |
(Li and Durbin, 2009) |
https://github.com/lh3/bwa/releases
|
| SAMtools (v1.3.1) |
(Li et al., 2009) |
http://samtools.sourceforge.net/
|
| SPP |
(Kharchenko et al., 2008) |
https://github.com/hms-dbmi/spp
|
| Picard |
|
http://broadinstitute.github.io/picard/
|
| MACS2 (v2.1.1) |
(Zhang et al., 2008) |
https://github.com/macs3-project/MACS/tree/master/MACS2
|
| STAR (v2.7.1a) |
(Dobin et al., 2013) |
https://github.com/easybuilders/easybuild-easyconfigs/pull/8388
|
| RseqQC |
(Wang et al., 2012) |
https://github.com/MonashBioinformaticsPlatform/RSeQC
|
| Htseq (v0.9.1) |
(Anders et al., 2015) |
https://github.com/simon-anders/htseq
|
| ToppGene |
(Chen et al., 2009) |
https://toppgene.cchmc.org/
|
| bedtools (v2.25.0) |
Quinlan and Hall, 2010
|
https://bedtools.readthedocs.io/en/latest/
|
| Chipseeker |
(Yu et al., 2015) |
https://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html
|
| HOMER (v4.9.1) |
(Heinz et al., 2010) |
http://homer.ucsd.edu/homer/
|
| CellRanger v3.0.1 |
10x Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
|
| FASTQC v0.11.5 |
Babraham Bioinformatics |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc
|
| UMI-tools v0.5.4 |
(Kulkarni et al., 2019);(Smith et al., 2017) |
https://github.com/CGATOxford/UMI-tools/releases
|
| Subread package (v1.6.2) |
(Liao et al., 2014) |
http://subread.sourceforge.net/
|
| Seurat v3 R analysis pipeline |
(Butler et al., 2018) |
https://satijalab.org/seurat/
|
| Uniform Manifold Approximation and Projection (UMAP) |
(Becht et al., 2018); (Kulkarni et al., 2019) |
https://umap-learn.readthedocs.io/en/latest/
|
| ClockLab |
Actimetrics |
https://www.actimetrics.com/products/clocklab/
|
| ARTool |
(Wobbrock et al., 2011) |
http://depts.washington.edu/acelab/proj/art/index.html
|
| Prism |
GraphPad Inc. |
https://www.graphpad.com/scientific-software/prism/
|
| Other |
|
|
| smFISH probe: Mm-Per1-C2 |
ACD bio / Bio-Techne |
Cat#438751-C2 |
| smFISH probe: Mm-Fos-C2 |
ACD bio / Bio-Techne |
Cat#316921-C2 |
| smFISH probe: Egr1-C2 |
ACD bio / Bio-Techne |
Cat#423371-C2 |
| smFISH probe: Mm-Avp |
ACD bio / Bio-Techne |
Cat#401391 |
| smFISH probe: Mm-Vip-C3 |
ACD bio / Bio-Techne |
Cat#415961-C3 |
| smFISH probe: Mm-Gfap-C3 |
ACD bio / Bio-Techne |
Cat#313211-C3 |
| smFISH probe: Mm-Map2-C3 |
ACD bio / Bio-Techne |
Cat#431151-C3 |
| smFISH probe: Mm-Cck-C3 |
ACD bio / Bio-Techne |
Cat#402271-C3 |
| smFISH probe: Mm-Prok2 |
ACD bio / Bio-Techne |
Cat#447941 |
