KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-H3K27ac antibody | Abcam | Cat# ab4729, RRID: AB_2118291 |
| Anti-H3K4me3 antibody | ThermoFisher | Cat# 49-1005, RRID: AB_2533856 |
| Anti-H3K27me3 antibody | Cell Signaling | Cat# 9733, RRID: AB_2616029 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | ThermoFisher | Cat# A-21206, RRID: AB_2535792 |
| SON DNA Binding Protein (SON) (N-Term) antibody | Antibodies-online | Cat# 7ABIN768615, RRID: AB_11207358 |
| Donkey anti-goat secondary antibody | Jackson Immuno | Cat# 705-005-003, RRID: AB_2340384 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Formamide | Ambion | Cat# AM9342 |
| 20xSSC | Ambion | Cat# AM9763 |
| Triton-X | Sigma | Cat# T8787 |
| Glucose oxidase | Sigma | Cat# G2133 |
| Phusion® Hot Start Flex 2X Master Mix | New England Biolabs | Cat# M0536 |
| HiScribe™ T7 Quick High Yield RNA Synthesis Kit | New England Biolabs | Cat# E2050 |
| Maxima H Minus Reverse Transcriptase | ThermoFisher | Cat# EP0752 |
| dNTP mix | ThermoFisher | Cat# R1121 |
| Eagle’s Minimum Essential Media (EMEM) | ATCC | Cat# 30-2003 |
| Fetal Bovine Serum Plasma | Sigma | Cat# F1141 |
| 32% Paraformaldehyde | Fisher Scientific | Cat# 50-980-494 |
| MEGAscript Transcription Kit | ThermoFisher | AMB13345 |
| aminoallyl-UTP | ThermoFisher | R1091 |
| Yeast tRNA | ThermoFisher | 15401029 |
| Stellaris RNA FISH hybridization buffer | Biosearch | SMF-HB1-10 |
| PA-Tn5 | Diagenode | C01070002 |
| 1M HEPES | ThermoFisher | 15630080 |
| Spermidine | Sigma | S2626-5G |
| T4 DNA ligase | New England Biolabs | M0202L |
| T4 DNA polymerase | New England Biolabs | M0203L |
| DAPI | ThermoFisher | Cat# D1306 |
| RNase inhibitor, Murine | New England Biolabs | Cat# M0314 |
| RNasin™ Plus RNase Inhibitor | Promega | Cat# PRN2615 |
| 1M Tris, pH 8 | ThermoFisher | Cat# 15568025 |
| Catalase | Sigma | Cat# C3155 |
| 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox) | Sigma | Cat# 238813 |
| tris(2-carboxyethyl)phosphi ne (TCEP) | Sigma | Cat# C4706 |
| UltraPure™ BSA (50 mg/mL) | ThermoFisher | Cat# AM2618 |
| Experimental Models: Cell lines and animals | ||
| hTERT-RPE1 | ATCC | Cat# CRL-4000 |
| P56, C57BL6 male mice | Charles River | Cat# 027 |
| Time-pregnant mice E13.5 | Charles River | Cat# 027 |
| Oligonucleotides | ||
| Primers, readout probes | Integrated DNA Technologies | See Table S1 |
| Encoding oligonucleotide probe libraries | Twist Bioscience | See Tables S1 |
| Software and Algorithms | ||
| Software for analyzing epigenomic MERFISH data | This paper | Github: https://github.com/TianLuHarvard/Code |
| Bowtie 2.1.041 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools v1.16.1 | (Li, 2011) | https://www.htslib.org/ |
| MACS 2.1.142 | (Zhang et al., 2008) | https://pypi.org/project/MACS2/ |
| IDR 2.0.243 | (Li et al., 2011) | Github: https://github.com/nboley/idr |
| Bedtools v2.30.0 | (Quinlan and Hall, 2010) | https://bedtools.readthedocs.io/en/latest/index.html |
| diffBind v1.16.3 | (Ross-Innes et al., 2012) | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| featureCounts 2.0.1 | (Liao et al., 2014) | http://subread.sourceforge.net/ |
| DESeq2 1.36.0 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| deepTools v1.5.12 | (Ramírez et al., 2016) | https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html |
| Deposited Data | ||
| Epigenomic MERFISH data | This paper | Zenodo: https://doi.org/10.5281/zenodo.7075964 |
| CUT&Tag data and sequencing data of in situ transcribed RNAs from tagged DNA fragments | This paper | GEO: GSE191069 |
| Hi-C data | (Deng et al., 2015) | GEO: GSE59779 |
| ATAC-seq data | (Gray et al., 2017) | GEO: GSE87548 |
| ChIP-seq data | (Gorkin et al., 2020) | ENCODE: Forebrain (ENCSR311YPF), Midbrain (ENCSR671NSS), Hindbrain (ENCSR344HHI) |