| Antibodies |
| anti-H3K27ac |
Abcam |
Cat# Ab4729, RRID: AB_2118291 |
| anti-ARNT2 |
This paper |
N/A |
| anti-NPAS4 |
Lin et al., 2008 |
N/A |
| anti-NPAS3 |
Gift of Steven McKnight Lab |
|
| anti-NCoR2 |
Thermo Fisher |
Cat# PA1–843, RRID:AB_2149135 |
| anti-NCoR2 |
Millipore |
Cat# 06–891, RRID: AB_310286 |
| anti-TBL1 |
Abcam |
Cat# Ab24528 |
| anti-TBL1 |
Santa Cruz |
Cat# sc-137006, RRID:AB_2199796 |
| anti-HDAC3 |
Santa Cruz |
Cat# sc11416X |
| anti-β-TUBULIN3 |
Covance |
Cat# MMS-435P |
| anti-GAPDH |
Sigma |
Cat# G9545, RRID:AB_796208 |
| anti-MYC |
Millipore |
Cat# 05–724, RRID:AB_309938 |
| anti-MYC, clone 9E10 |
Developmental Studies Hybridoma Bank http://dshb.biology.uiowa.edu/
|
NA |
| anti-FOS |
Santa Cruz |
Cat# sc-7202 X; RRID:AB_2106765 |
| anti-GFP |
Invitrogen |
G10362 |
| anti-Histone H3 |
Abcam |
Cat# 1791; RRID:AB_302613 |
| Rabbit IgG |
Santa Cruz |
Cat# sc-66931; RRID:AB_1125055 |
| anti-M2-FLAG |
Sigma Aldrich |
Cat# A2220 |
| Bacterial and Virus Strains |
| AAV2/1-CAG-Cre-GFP |
Boston Children’s Hospital Viral Core |
|
| AAV2/1-CAG-ΔCre-mCherry |
Boston Children’s Hospital Viral Core |
|
| AAV2/1-U6-shRNA-CAG-mCherry |
Boston Children’s Hospital Viral Core |
|
| AAV2/1-U6-non-targeting shRNA-CAG-GFP |
Boston Children’s Hospital Viral Core |
|
| FUW Lentivirus (pMDL/RSV/VSVG packaging) |
This paper |
|
| Chemicals, Peptides, and Recombinant Proteins |
| TTX |
Abcam |
Cat# ab120055 CAS: 18660–81-6 |
| Kainic acid monohydrate |
Sigma Aldrich |
Cat# K0250 CAS: 58002–62-3 |
| DL-AP5 |
Thermo Fisher |
Cat# 01–061-0 CAS: 76326–31-3 |
| CPP |
Tocris |
Cat# 0173 CAS: 126453–07-4 |
| NBQX |
Tocris |
Cat#0190 CAS:118876–58-7 |
| Gabazine |
Tocris |
Cat# SR 95531 CAS: 104104–50-9 |
| EGS (ethylene glycol bis(succinimidyl succinate) |
Fisher |
Cat# 21565 CAS: 70539–42-3 |
| Critical Commercial Assays |
| Dual-Luciferase Reporter Assay System |
Promega |
E1910 |
| Nextera DNA Library Prep Kit |
Illumina |
FC-121–1030 |
| Ovation Ultralow System V2 |
Nugen |
0344–32 |
| NEBNext® rRNA Depletion Kit |
New England Biolabs |
E6310X |
| NEBNext Ultra Directional RNA Library Prep Kit |
New England Biolabs |
E7420L |
| Deposited Data |
| Raw and analyzed data |
This paper |
GEO: GSE121660
|
| Raw and analyzed visual cortex scRNA-seq data |
Hrvatin et al. 2018 |
GEO: GSE102827
|
| Experimental Models: Organisms/Strains |
| Npas4fl/fl
|
Lin et al., 2008 |
Greenberg Lab |
| NCoR2f/lfl
|
Shimizu et al., 2015 |
Hollenberg Lab |
| C57BL6/J |
The Jackson Laboratory |
JAX 000664 |
| B6.Cg-Tg(Camk2a-cre)T29–1Stl/J |
The Jackson Laboratory |
JAX 005359 |
| B6;129-Gt(ROSA)26Sor<tm5(CAG-Sun1/sfGFP)Nat>/J https://www.jax.org/strain/021039
|
The Jackson Laboratory |
JAX 021039 |
| Oligonucleotides |
| Primers for Luciferase Assays (Table S1) |
|
|
| non-targeting GCGCGATAGCGCTAATAATTT |
|
|
|
Arnt2 shRNA#1 TGTCGGACAAGGCAGTAAAT |
|
|
|
Arnt2 shRNA#2 CGCTATTATCATGCCATAGAT |
|
|
|
Ncor2 shRNA#1 CCTGTCTAAAGCCTTAACTAA |
|
|
|
Ncor2 shRNA#2 CCAGTGTAAGAACTTCTACTT |
|
|
|
NCoR2 shRNA#3 GAAAGGCACTCATGGGTAAAT |
|
|
|
Npas4 shRNA#1 GGTTGACCCTGATAATTTA |
|
|
|
Npas4 shRNA#2 ACACAGAGAAAGAGCAAAA |
|
|
| Recombinant DNA |
| FUW-U6-Npas4-shRNA#1 |
This Paper |
|
| FUW-U6-Npas4-shRNA#2 |
This Paper |
|
| FUW-U6-Arnt2-shRNA#1 |
This Paper |
|
| FUW-U6-Arnt2-shRNA#2 |
This Paper |
|
| FUW-U6-Ncor2-shRNA#1 |
This Paper |
|
| FUW-U6-Ncor2-shRNA#2 |
This Paper |
|
| FUG-U6-Ncor2-shRNA#3 |
This Paper |
|
| pGL4.11 Genomic Binding Sites; See Table S1
|
This Paper |
Addgene #59744 |
| FUW-Npas4-full-length |
This Paper |
|
| FUW-Npas4ΔPas |
This Paper |
|
| FUGW |
Lois et al., 2002 |
Addgene #14883 |
| pEF1a-Arnt-Myc |
This Paper |
|
| pEF1a-Arnt2-Myc |
This Paper |
|
| pEF1a-Ephexin5-Myc |
This Paper |
|
| pGEX-Arnt2–312:712 |
This paper |
|
| AAV-CAG-Cre-GFP |
Gift from Matt During (Ohio State University) |
|
| AAV-CAG-ΔCre-mCherry |
This paper; modified from Matt During |
|
| AAV-U6-shRNA-CAG-mCherry (see sequences above) |
This paper; modified from Matt During |
|
| AAV-U6-non-targeting shRNA-CAG-GFP |
This paper; modified from Matt During |
|
| Software and Algorithms |
| Subread v1.5.1 |
Liao et al., 2013 |
http://subread.sourceforge.net/ |
| Trimmomatic (v0.36) |
Bolger et al., 2014 |
http://www.usadellab.org/cms/?page=trimmomatic |
| bedGraphToBigWig (UCSC-tools v363) |
UCSC-tools |
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ |
| featureCounts (Subread package, v1.5.1) |
Liao et al., 2013 |
http://subread.sourceforge.net/ |
| MACS2 (v 2.1.0) |
Zhang et al., 2008 |
https://github.com/taoliu/MACS |
| IDR |
Li, 2011 |
https://drive.google.com/file/d/0B_ssVVyXv8ZSX3luT0xhV3ZQNWc/view?usp=sharing |
| EdgeR(v3.16.5) |
Robinson et al., 2010 |
https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Limma(v3.30.13) |
Ritchie et al., 2015 |
https://bioconductor.org/packages/release/bioc/html/limma.html |
| Bh-tsne (commit 36b169c) |
van der Maaten, 2014 |
https://github.com/lvdmaaten/bhtsne |
| GEM software (v3.4) |
Guo et al., 2018 |
http://groups.csail.mit.edu/cgs/gem/kmac/ |
| Other |
