KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-CTCF (IP, ChIP) | Abcam Cat# ab70303 | RRID:AB_1209546 |
| Anti-CTCF (WB) | Millipore # 07-729 | RRID:AB_441965 |
| Anti-Lamin B | Abcam Cat# ab16048 | RRID:AB_10107828 |
| Anti-Gapdh | Abcam Cat# ab8245 | RRID:AB_2107448 |
| Anti-YY1 | Santa Cruz # sc-7341 X | RRID:AB_2257497 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Triptolide | Sigma-Aldrich Cat# T3652 | N/A |
| DRB | Sigma-Aldrich Cat# D1916 | N/A |
| Indole-3-acetic acid sodium salt (auxin analog) | Sigma-Aldrich Cat# I5148-2G | N/A |
| CHIR99021 | Stemgent | N/A |
| PD0325901 | Stemgent | N/A |
| Critical Commercial Assays | ||
| TruSeq Stranded mRNA Kit | illumina | N/A |
| Kapa Library Prep Kit | Roche | N/A |
| Arima Hi-C Kit | Arima | N/A |
| Deposited Data | ||
| Hi-C, 5C, RNA-Seq, scRNA-Seq and ChIP-Seq data | This paper | GSE125595 |
| Unprocessed gel images for Figures 2, S1 and S2 | This paper | https://doi.org/10.17632/xbrf8x7k22.1 |
| Experimental Models: Cell Lines | ||
| mESC e14 CTCF-GFP-Tir1-TIGER | Nora et al., 2017 | N/A |
| mESC e14 CTCF-GFP-Tir1-TIGER-WT-Rescue | This paper | N/A |
| mESC e14 CTCF-GFP-Tir1-TIGER-ZF1Δ-Rescue | This paper | N/A |
| mESC e14 CTCF-GFP-Tir1-TIGER-ZF10Δ-Rescue | This paper | N/A |
| mESC e14 CTCF-GFP-Tir1-TIGER-ZF1-H284N-Rescue | This paper | N/A |
| mESC e14 CTCF-GFP-Tir1-TIGER-ZF10-H528S-Rescue | This paper | N/A |
| Recombinant DNA | ||
| pLVX-EF1a-IRES-mCherry Vector (pLVX) | Clontech | Cat# 631987 |
| Oligonucleotides | ||
| See Table S2 | This paper | N/A |
| Software and Algorithms | ||
| RStudio | RStudio | RRID:SCR_000432 |
| Samtools | Li et al., 2009 | RRID:SCR_002105 |
| Integrative Genomics Viewer | Robinson et al., 2011; Thorvaldsdóttir et al., 2013 | RRID:SCR_011793 |
| Bowtie2 | Langmead and Salzberg, 2012 | RRID:SCR_005476 |
| deepTools | Ramírez et al., 2016 | RRID:SCR_016366 |
| MACS | Zhang et al., 2008; https://github.com/taoliu/MACS/ | RRID:SCR_013291 |
| HiC-Pro | Servant et al., 2015 | https://github.com/nservant/HiC-Pro |
| DESeq2 | https://www.bioconductor.org | RRID:SCR_015687 |
| HiC-Bench | Lazaris et al., 2017 | https://github.com/NYU-BFX/hic-bench |
| Juicer 1.5 | Durand et al., 2016; https://github.com/aidenlab/juicer/wiki | RRID:SCR_017226 |
| tophat 2.1.1 | Trapnell et al., 2012; https://github.com/cole-trapnell-lab/cufflinks | RRID:SCR_013035 |
| Homer 4.10 | Heinz et al., 2010; http://homer.ucsd.edu/homer/ | RRID:SCR_010881 |
| DiffBind | Stark and Brown, 2011; http://bioconductor.org/packages/DiffBind/ | RRID:SCR_012918 |
| ChIPseeker | Yu et al., 2015 | http://bioconductor.org/packages/ChIPseeker/ |
| DeepBind | Alipanahi et al., 2015 | http://tools.genes.toronto.edu/deepbind/ |