KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Histone H3 (acetyl K27) antibody - ChIP Grade | Abcam plc. | Cat#ab4729 |
| Anti-Histone H3K4me1 antibody - ChIP Grade | Abcam plc. | Cat#ab8895 |
| Anti-Histone H3K4me3 antibody - ChIP Grade | Abcam plc. | Cat#ab8580 |
| CTCF Antibody - N-terminal region | Aviva Systems Biology Corp. | Cat#ARP38820_P050 |
| Normal Rabbit IgG | Cell Signaling Technology, Inc. | Cat#2729 |
| Anti-IgG antibody | Santa Cruz Biotechnology | Cat#sc2712 |
| GKLF/EKLF/LKLF Antibody (F-8): | Santa Cruz Biotechnology | Cat#sc-166238X |
| Rabbit anti-SATB1/2 antibody | Proteintech Group, Inc. | Cat#15400-1-AP |
| Bacterial and Virus Strains | ||
| RCAS-Zic1 Wild-type | This paper | N/A |
| RCAS-Zic1 Dominant-negative | This paper | N/A |
| RCAS-SATB2 Wild-type | This paper | N/A |
| RCAS-Zic1 -deltaC | Wu et al., 2018b | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| TRIzol RNA Isolation Reagents | Invitrogen (Thermo Fisher Scientific Inc.) | Cat#15596026 |
| AMPure XP beads | Beckman Coulter, Inc. | Cat#A63880 |
| Collagenase Type 1 | Worthington Biochemical Corp. | Cat#LS004196 |
| Dynabeads Protein A | Invitrogen (Thermo Fisher Scientific Inc.) | Cat#100-02D |
| Protein G | Invitrogen (Thermo Fisher Scientific Inc.) | Cat#100-04D |
| DpnII destruction enzyme | New England Biolabs | Cat#R0543 |
| Streptavidin magnetic beads | Invitrogen (Thermo Fisher Scientific Inc.) | Cat#65001 |
| TDE1 Tagment DNA Enzyme | Illumina, Inc. | Cat#15027865 |
| TD Tagment DNA Buffer | Illumina, Inc. | Cat#15027866 |
| NEBNext High-Fidelity 2X PCR Mater Mix | New England Biolabs | Cat# M0541S |
| Critical Commercial Assays | ||
| TruSeq RNA Prep Kit v2 | Illumina, Inc. | Cat#RS-122-2001 Cat#RS-122-2002 |
| NEBNext Ultra End Repair/dA-Tailing Module | New England Biolabs | Cat#E7442S |
| NEBNext Ultra Ligation Module | New England Biolabs | Cat#E7445S |
| KAPA HiFi HotStart ReadyMix | Kapa Biosystems, Inc. | Cat#KK2601 |
| SimpleChIP Enzymatic Chromatin IP Kit Agarose Beads | Cell Signaling Technology, Inc. | Cat#9002 |
| SimpleChIP Universal qPCR Master Mix | Cell Signaling Technology, Inc. | Cat#88989 |
| NEBNext DNA Library Prep Master Mix Set for Illumina | New England Biolabs | Cat#E6040 |
| NEBNext Multiplex Oligos for Illumina | New England Biolabs | Cat#E7500 |
| SeqCap EZ Hybridization and Wash Kit | F. Hoffmann-La Roche Ltd | Cat#05634261001 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO: GSE136224 |
| Chicken UCSC Genome Browser assembly ID: galGal4 (GG4) | Genomic Institute, University of California Santa Cruz | http://hgdownload.soe.ucsc.edu/goldenPath/galGal4/bigZips/galGal4.fa.gz |
| Experimental Models: Organisms/Strains | ||
| Gallus gallus (chicken): white leghorn strain | Charles River Laboratories | SPAFAS |
| Oligonucleotides | ||
| Cot-1 DNA equivalent chicken Hybloc DNA | Applied Genetics Lab | Cat. #CHB |
| 1xGen Universal Blocking Oligo—TS-p5 | IDT | N/A (contact IDT) |
| 1xGen Universal Blocking Oligo—TS-p7(6nt) | IDT | N/A (contact IDT) |
| ISH Probe: Chr25-FK3 FW 5’-aggaagcccaaagtctgaca-3’ |
This paper | N/A |
| ISH Probe: Chr25-FK3 RV 5’-tctggtacaggttgcaatgg-3’ |
This paper | N/A |
| ISH Probe: Chr25-FK12 FW 5’-tgaggtggacatcctgtgaa-3’ |
This paper | N/A |
| ISH Probe: Chr25-FK12 RV 5’-acaatgggatgcctgacttc-3’ |
This paper | N/A |
| ISH Probe: Chr27-FK1 FW 5’-cccggagaaattcatccata-3’ |
This paper | N/A |
| ISH Probe: Chr27-FK1 RV 5’-ccaagtctgagctcatgcaa-3’ |
This paper | N/A |
| ISH Probe: Chr27-FK12 FW 5’-ggtgctggatgaagaaggaa-3’ |
This paper | N/A |
| ISH Probe: Chr27-FK12 RV 5’-aggctccacagtgcaagatt-3’ |
This paper | N/A |
| ISH Probe: Chr27-FK39 FW 5’-ctggacggcagaacagactc-3’ |
This paper | N/A |
| ISH Probe: Chr27-FK39 RV 5’-agagagcagcaggagcagag-3’ |
This paper | N/A |
| ISH Probe: Chr25-FK45 FW 5’-attgacagacctgcagtgga-3’ |
This paper | N/A |
| ISH Probe: Chr25-FK45 RV 5’-cagctgtccatctgcctttt-3’ |
This paper | N/A |
| Primer: P5 5’-aatgatacggcgaccaccga-3’ |
This paper | N/A |
| Primer: P7 5’-caagcagaagacggcatacgagat-3’ |
This paper | N/A |
| Primer: RCAS-Zic1 wild-type form FW 5’-ggggacaagtttgtacaaaaaagcaggcttcaccatgcttctggatgctggaccgca-3’ |
This paper | N/A |
| Primer: RCAS-Zic1 wild-type form RV 5’-ggggaccactttgtacaagaaagctgggtcttacacgtaccattcgttaaaat-3’ |
This paper | N/A |
| Primer: RCAS-Zic1 dominant-negative form FW5’-ggggacaagtttgtacaaaaaagcaggcttcaccatggcgggggccttcttccg-3’ |
This paper | N/A |
| Primer: RCAS-Zic1 dominant-negative form RV 5’-ggggaccactttgtacaagaaagctgggtcttacacgtaccattcgttaaaat-3’ |
This paper | N/A |
| Primer: RCAS-SATB2 FW 5’-ggggacaagtttgtacaaaaaagcaggcttcaccatggagcggaggagcgaga-3’ |
This paper | N/A |
| Primer: RCAS-SATB2 RV 5’-ggggaccactttgtacaagaaagctgggtcctatctctggtcgatgtctgc-3’ |
This paper | N/A |
| Probes for NG Capture-C | This paper | Table S3 |
| Primers for 3C-PCR | This paper | Table S3 |
| Primers for ChIP-qPCR | This paper | Table S3 |
| Recombinant DNA | ||
| Chicken BAC clone: galgal4 chr27:421,977-608,328 | BACPAC Resources Center, BACPAC Genomics, Inc. | CH261-64J24 |
| Chicken BAC clone: galgal4 chr27:567,425-727,740 | BACPAC Resources Center, BACPAC Genomics, Inc. | CH261-154N1 |
| Chicken BAC clone: galgal4 chr27:695,282-892,074 | BACPAC Resources Center, BACPAC Genomics, Inc. | CH261-61E3 |
| Chicken BAC clone: galgal4 chr27:864,805-1,067,678 | BACPAC Resources Center, BACPAC Genomics, Inc. | CH261-160M5 |
| Chicken BAC clone: galgal4 chr25:942,403-1,159,746 | BACPAC Resources Center, BACPAC Genomics, Inc. | CH261-170A15 |
| Chicken BAC clone: galgal4 chr25:835,251-960,765 | BACPAC Resources Center, BACPAC Genomics, Inc. | CH261-27I14 |
| Chicken BAC clone: galgal4 chr25:780,190-942,274 | BACPAC Resources Center, BACPAC Genomics, Inc. | CH261-178I11 |
| Software and Algorithms | ||
| TopHat2 | Kim et al., 2013 | http://ccb.jhu.edu/software/tophat/downloads/ |
| Cufflinks package | Trapnell et al., 2010 | http://cole-trapnell-lab.github.io/cufflinks/install/ |
| Deeptools | Ramírez et al., 2014 | https://deeptools.readthedocs.io/en/develop/content/installation.html |
| Ingenuity Pathway Analysis (IPA) | QIAGEN Inc. | https://analysis.ingenuity.com/pa/installer/select |
| Partek Genomics Suite (PGS) | Partek Inc. | https://documentation.partek.com/display/PGS/Node+Locked+Installation |
| Bowtie 1.2 | Langmead et al., 2009 | https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.0/ |
| Bowtie 2 | Langmead and Salzberg, 2012 | https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.5.1/ |
| Samtools | Li et al., 2009 | http://www.htslib.org/download/ |
| MACS2 | Feng et al., 2012; Zhang et al., 2008 | https://github.com/taoliu/MACS/wiki/Install-macs2 |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/download.html |
| CaptureC analyser package: CCanalyser3.pl dpngenome3_1.pl dpnII2E.pl |
Davies et al., 2016 |
https://github.com/Hughes-Genome-Group/captureC/releases |
| Trim Galore! | Dr. Felix Krueger at the Babraham Institute | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| FLASH (Fast Length Adjustment of SHort reads) | Magoc and Salzberg, 2011 | http://ccb.jhu.edu/software/FLASH/ |
| MATCH: a weight matrix-based program for predicting transcription factor binding sites | Kel et al., 2003 | http://gene-regulation.com/pub/programs.html |
| pyGenomeTracks | Ramírez et al., 2018 | https://github.com/deeptools/pyGenomeTracks |
| Integrative Genomics Viewer (IGV) | Robinson et al., 2011 | https://software.broadinstitute.org/software/igv/download |
| GraphPad Prism | GraphPad Software Inc. | https://www.graphpad.com/scientific-software/prism/ |
| OmniGraffle | The Omni Group | https://www.omnigroup.com/omnigraffle |
| RNA-seq analysis pipeline | This paper | Table S7 |
| ChIP-seq analysis pipeline | This paper | Table S7 |
| Software for manuscript preparation | This paper | Table S7 |
| Other | ||
| Tissue grind pestle | Kimble Chase Life Science and Research Products, LLC. | Cat#885302-0002 |