KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, Peptides, and Recombinant Proteins | ||
| Dextran Sulfate | Fisher Scientific | bp1585100 |
| PureLink™ RNase A (20 mg/mL) | Thermo Fisher Scientific (Invitrogen) | 12091021 |
| OmniPur® Formamide, Deionized | Merck Millipore | 4650–500ML |
| Ethylene carbonate 98% | Sigma Aldrich | E26258 |
| Critical Commercial Assays | ||
| Phusion Hot Start Master Mix | Life Technologies | Thermo Scientific F565S |
| NEB HiScribe T7 Quick High Yield RNA Synthesis Kit | BioConcept | E2050S |
| Zymo-Spin V Columns | LucernaChem | C1012–25 |
| DNA Clean & Concentrator-5 w/ Zymo-Spin IC Columns (Capped) | LucernaChem | D4013 |
| Zymo Oligo Binding Buffer | LucernaChem | D4060–1-10 |
| Maxima H Minus Reverse Transcriptase (200 U/µL) | Fisher Scientific | EP0751 |
| Deposited Data | ||
| Raw imaging data from Figure 1 and Figure S3 | Mendeley Data | doi:10.17632/5tzxfssddm.1 |
| C. elegans reference genome (UCSC version ce10/ WormBase Release WS220) | WormBase | ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/ |
| Hi-C dataset, wild-type late/mixed stage embryos | (Crane et al., 2015) | NCBI GSE63717 |
| LEM-2 ChIP datasets, wild-type and cec-4 embryos | (Gonzalez-Sandoval et al., 2015) | NCBI GSE74133 |
| Experimental Models: Organisms/Strains | ||
| C. elegans Bristol strain N2 (wild-type) | Caenorhabditis Genetics Center | WB strain: N2 |
| C. elegans cec-4 strain RB2301 (F32E10.2(ok3124)) | Caenorhabditis Genetics Center | WB strain: RB2301; WBVar00094202 |
| Oligonucleotides | ||
| Sequences for probe amplification, see Data S1 | This paper | S1 |
| Readout (secondary probe) sequences, see Data S1 | This paper | S1 |
| Primary probe sequences for chrV, see Data S2 | This paper | S2 |
| Primary probe sequences for chrV left arm, see Data S4 | This paper | S4 |
| Primary probe sequences for chrV center, see Data S5 | This paper | S5 |
| Primary probe sequences for chrV right arm, see Data S6 | This paper | S6 |
| Primary probe sequences for chrI, see Data S3 | This paper | S3 |
| Software and Algorithms | ||
| MATLAB R2016b, R2019b | MathWorks | https://mathworks.com |
| OligoArray 2.1 | (Rouillard et al., 2003) | http://berry.engin.umich.edu/oligoarray2_1/OligoArrayInst.exe |
| NCBI-BLAST 2.2.26 | NCBI | https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/ |
| NCBI BLAST+ 2.7.1 | NCBI | https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ |
| OligoArrayAux | The UNAFold Web Server | http://unafold.rna.albany.edu/?q=DINAMelt/OligoArrayAux |
| Seurat 2.3 | (Butler et al., 2018) | https://satijalab.org/seurat/ |
| Raincloud-shiny | (Allen et al., 2019) |
https://gabrifc.shinyapps.io/raincloudplots/ https://micahallen.org/2018/03/15/introducing-raincloud-plots/ |