KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-CTCF | Millipore Sigma | Cat# 07-729 |
| IgG from rabbit serum | Sigma | Cat# I8140 |
| Biological Samples | ||
| Human brain tissue from adults diagnosed with FXS | University of California at Davis Medical Investigation of Neurodevelopmental Disorders Institute Brain Repository | http://www.ucdmc.ucdavis.edu/mindinstitute/ |
| Healthy human brain tissue | Miami Brain Tissue Bank | http://miamibrainbank.org/ |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Protein A agarose beads | Thermo Fisher | Cat#15918014 |
| Protein G agarose beads | Thermo Fisher | Cat#15920010 |
| Power SYBR Green PCR Master Mix | Thermo Fisher | Cat#4367660 |
| AMPureXP beads | Beckman Coulter | Cat#A63881 |
| Critical Commercial Assays | ||
| NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® | New England BioLabs | Cat#E7645S |
| NEBNext® Ultra™ DNA Library Prep Kit for Illumina® | New England BioLabs | Cat#E7370S |
| NEBNext Multiplex Oligos for Illumina Set1 | New England BioLabs | Cat#E7335S |
| KAPA Illumina Library Quantification Kit | KAPA Biosystem | Cat#KK4835 |
| mirVana miRNA isolation kit | Lifetech | Cat#AM1560 |
| SuperScript First-Strand Synthesis System | Lifetech | Cat#11904-018 |
| Qubit™ dsDNA HS Assay Kit | Thermo Fisher | Cat#Q32851 |
| Qubit™ RNA HS Assay Kit | Thermo Fisher | Cat#Q32852 |
| Qiagen DNeasy Blood and Tissue Kit | Qiagen | Cat#69504 |
| Qiagen Gel Extraction Kit | Qiagen | Cat#28706 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO: GSE111170 |
| Human H1 ESC Hi-C | Dixon, J. R. et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331-336 (2015). | GEO: GSE52457 |
| Human cortical plate Hi-C | Won, H. et al. Chromosome conformation elucidates regulatory relationships in developing human brain. Nature 538, 523-527 (2016). | GEO: GSE77565 |
| Human H1, MES, MSC, NPC, TRO TAD boundaries | Schmitt, A. D. et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep 17, 2042-2059 (2016). | GEO: GSE87112 |
| Mouse Early Development Hi-C | Du, Z. et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature 547, 232-235 (2017). | GEO: GSE82185 |
| Human H1-hESC CTCF ChIP-seq | Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63. | UCSC – wgEncodeEH000085 |
| hg19 CpG island annotation | Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. | USCS Table Browser (group: Regulation, track: CpG Islands, table: cpgIslandExt) |
| hg19 RefSeq genes (exons, introns, 5’UTR, 3’UTR) | Pruitt, K. D. et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 42, D756–63 (2014). Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. |
USCS Table Browser (assembly: Feb. 2009 hg19, group: Genes and Gene Predictions, track: RefSeq Genes, table: refGene) |
| Human H1 ESC H3K9me3 | Hawkins RD, Hon GC, Lee LK, Ngo Q et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 2010 May 7;6(5):479-91. | GEO: GSM605325 |
| GM12878 H3K27acetyl | Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63. | UCSC - wgEncodeEH000030 |
| Experimental Models: Cell Lines | ||
| Human: EBV transformed B-lymphocyte | Coriell | Cat # GM09236 |
| Human: EBV transformed B-lymphocyte | Coriell | Cat # GM09237 |
| Human: Fibroblast | Coriell | Cat # AG06103 |
| Human: EBV transformed B-lymphocyte | Coriell | Cat # GM04024 |
| Human: Fibroblast | Coriell | Cat # GM04025 |
| Oligonucleotides | ||
| See Supp Table 7 for list of 5C primers | This paper | N/A |
| GAPDH primer F: 5'-CACTAGGCGCTCACTGTTCT-3' R: 5'-GACCAAATCCGTTGACTCCG-3' |
This paper | N/A |
| FMR1 primer F: TACGGCAAATGTGTGCCAAAG R: GTGCTCGCTTTGAGGTGACT |
This paper | N/A |
| Primers for CTCF peak 1 F: TGTTGGCTCTTGAGGGAAACAA R: GTTGCTACAGTCGATGGATGG |
This paper | N/A |
| Primers for CTCF peak 2 F: TCTTGTCTGGCCTGTATGGTT R: CCATATTGCACAATGCAGCTCT |
This paper | N/A |
| Software and Algorithms | ||
| Bowtie/Bowtie2 | Langmead et al., 2009, Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/ |
| Python | ||
| MACS | Zhang et al., 2008 | https://github.com/taoliu/MACS |
| BEDTools | Quinlan 2014 | http://code.google.com/p/bedtools/ |
| ICED matrix balancing | Imakaev et al., 2012 | https://github.com/hiclib/iced |
| MEME Suite | Bailey et al, 2009 | http://meme-suite.org |
| Quantile normalization | Bolstad et al., 2003 | https://www.ncbi.nlm.nih.gov/pubmed/12538238 |
| deepTools | Ramirez et al., 2016 | https://github.com/deeptools/deepTools |