| Antibodies |
|
|
|
| Alexa 488 conjugated anti-NeuN |
Millipore |
Cat# MAB377X; RRID: AB_2149209 |
| anti-H3K27ac |
Active Motif |
Cat# 39135; RRID: AB_2614979 |
|
| Bacterial and virus strains |
|
|
|
| AAV8.CamKIIα.eYFP |
UNC Vector Core |
Custom order |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| (±) DOI (1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane hydrochloride) |
Sigma Aldrich |
Cat# D101 |
| Isoflurane |
Henry Schein |
Cat# 1182097 |
| Protease Inhibitor Cocktail |
Sigma Aldrich |
Cat# P8340–5ML |
| Recombinant Ribonuclease Inhibitor |
Takara Bio |
Cat# 2313B |
| OptiPrep Density Gradient Medium |
Sigma Aldrich |
Cat# D1556–250ML |
| Normal Goat Serum (10%) |
Life Technologies |
Cat# 50062Z |
| Micrococcal Nuclease |
Thermo Scientific |
Cat# PI88216 |
| SPRIselect beads |
Beckman Coulter |
Cat# B23317
|
| Superscript II reverse transcriptase |
Life Technologies |
Cat# 18064014 |
| KAPA HiFi HotStart ReadyMix |
KAPA Biosystems |
Cat# KK2601 |
| dNTP mix |
Life Technologies |
Cat# 18427088 |
|
| Critical commercial assays |
|
|
|
| Locomotor activity monitoring |
Omnitech Inc |
Fusion V5.3 |
| Pre-pulse inhibition of the startle |
San Diego Instruments |
SR-LAB Startle Response System |
| Fear acquisition and extinction |
Med Associates |
MED-VFCNIR-M |
| Confocal microscopy |
Carl Zeiss |
CLM710 |
| Voltage-clamp recording |
Molecular Devices |
Multiclamp 700B amplifier, Digitizer 1140A, Cornerstone S-900 stimulator |
| Cell Sorter |
BD Biosciences |
BD FACSAria III |
| RNAeasy mini kit |
QIAGEN |
Cat #74104 |
| RNase-Free DNase Set |
QIAGEN |
Cat #79254 |
| Nextera XT DNA Library Prep kit |
Illumina |
Cat# FC-131–1024 |
| ACCEL-NGS 2S Plus DNA library kit |
Swift Biosciences |
Cat# 21024 |
| 2S Indexing Kit |
Swift Biosciences |
Cat# 26396 |
| Sequencing platform |
Illumina |
Illumina Hi-seq 4000 |
| High Sensitivity DNA analysis kit |
Agilent |
Cat# 5067–4626 |
| TapeStation |
Agilent |
Ca# 2200 |
| KAPA library quantification |
Kapa Bio |
Cat# KK4809 |
|
| Deposited data |
|
|
|
| ChIP-seq and RNA-seq raw and processed data |
Gene Expression Omnibus |
GEO: GSE161626
|
|
| Experimental models: Organisms/strains |
|
|
|
| Mouse 129S6/SvEv |
Taconic Farms |
Cat #129SVE-M |
| Mouse C57BL/6NTac |
Taconic Farms |
Cat # B6-M |
| Mouse 5-HT2AR−/−
|
González-Maeso et al., 2007
|
N/A |
| Mouse C57BL/6J |
JAXS |
Cat #00064 |
|
| Oligonucleotides |
|
|
|
| TSO: AAGCAGTGGTATCAACGCAGAG TACATrGrG+G (rG: riboguanosines; +G: LNA-modified guanosine) |
Integrated DNA Technologies |
N/A |
| Oligo-dT30VN: AAGCAGTGGTATCAACG CAGAGTACT30VN (N: any base; V: T, C or G) |
Integrated DNA Technologies |
N/A |
| ISPCR oligo: AAGCAGTGGTATCAACGCAGAGT |
Integrated DNA Technologies |
N/A |
|
| Software and algorithms |
|
|
|
| NeuronStudio |
Mount Sinai Imaging Center |
v0.9.92 https://biii.eu/neuronstudio
|
| Prism |
GraphPad |
v9 https://www.graphpad.com/scientific-software/prism/
|
| Voltage-clamp recording |
Molecular Devices |
clampex 10.2 https://support.moleculardevices.com/
|
| Voltage-clamp offline analysis |
Molecular Devices |
Campfit 10.2 https://support.moleculardevices.com/s/
|
| Trim Galore! |
N/A |
https://github.com/FelixKrueger/TrimGalore
|
| Bowtie2 |
(Langmead and Salzberg, 2012) |
https://github.com/BenLangmead/bowtie2
|
| MACS2 |
Zhang et al., 2008
|
https://github.com/macs3-project/MACS
|
| SAMTools |
Li et al., 2009
|
https://github.com/samtools/samtools
|
| BEDTools |
(Quinlan and Hall, 2010) |
https://github.com/arq5x/bedtools
|
| SeqMonk |
N/A |
https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ RRID: SCR_001913 |
| HISAT2 |
Kim et al., 2015
|
http://daehwankimlab.github.io/hisat2/
|
| FeatureCounts |
(Liao et al., 2014) |
http://subread.sourceforge.net/
|
| DESeq2 |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| WGCNA |
(Langfelder and Horvath, 2008) |
https://cran.r-project.org/web/packages/WGCNA/index.html
|
|
| Other |
|
|
|
| KIMBLE Dounce tissue grinder set |
Sigma aldrich |
Cat# D9063 |
