| Antibodies |
|
|
|
| Sall4 |
Santa Cruz |
Cat# EE-30; RRID: AB_1129262 |
| SALL4 |
Abcam |
Cat# Ab29112; RRID: AB_777810 |
| SALL4 |
Cell signaling |
Cat# 8459 |
| Normal mouse IgG |
Santa Cruz |
Cat# SC-2025; RRID: AB_737182 |
| Normal Rabbit IgG |
Abcam |
Cat# Ab171870; RRID: AB_2687657 |
| Actin |
Sigma |
Cat# A2066; RRID: AB_476693 |
| H3K9Me3 (D4W1U) |
Cell Signaling |
Cat# 13969: RRID: AB_2798355 |
| Histone 3 |
Abcam |
Cat# Ab1791: RRID: AB_302613 |
| FLAG (M2) |
Sigma |
Cat# F3165: RRID: AB_259529 |
| HDAC1 |
Cell Signaling |
Cat# 2062 |
| HP1 |
Abcam |
Cat# Ab77256: RRID: AB_1523784 |
| KDM3A |
Abcam |
Cat# Ab80598 |
|
| Bacterial and Virus Strains |
|
|
|
| BL21 (DE3) |
Novagen |
Cat# 69450 |
|
| Chemicals |
|
|
|
| EMSA Buffer B1 |
Active Motif |
Cat# 37480 |
| EMSA Buffer B2 |
Active Motif |
Cat# 37481 |
| EMSA Buffer C1 |
Active Motif |
Cat# 37484 |
| EMSA Buffer D |
Active Motif |
Cat# 37488 |
| FBS |
Sigma |
Cat# F2442 |
| RPMI |
Thermo Fisher |
Cat# 11875119 |
| DMEM |
Thermo Fisher |
Cat# 11965118 |
| OptiMEM |
Thermo Fisher |
Cat# 31985070 |
| Trypsin-EDTA (0.25%) |
Thermo Fisher |
Cat# 25200114 |
| iScript |
BIO-RAD |
Cat# 1708891 |
| IQ SYBR Green supermix |
BIO-RAD |
Cat# 1708882 |
| FLAG-M2 beads |
Sigma |
Cat# A2220 |
| Glutathione Sepharose |
GE Healthcare |
Cat# GE17-0756-01 |
| Concanavalin A beads |
Bangs Laboratories |
Cat# BP531 |
| proteinA-micrococcal nuclease |
This paper |
|
| DAPI |
Sigma |
Cat# 5087410001 |
| Vectashield antifade mounting medium |
Vector Laboratories |
Cat# H-1000-10 |
| TransIT-LT1 |
Mirus |
Cat# MIR2300 |
| Digitonin |
Sigma |
Cat# D141 |
|
| Critical Commercial Assays |
|
|
|
| TruSeq stranded mRNA Kit |
Illumina |
Cat# RS-122-21001 |
| NEBNext Ultra II DNA Library prep kit |
NEB |
Cat# M0541 |
| NEBNext Multiplex Oligos for Illumina (index primers set 1 |
NEB |
Cat# E7335 |
| LightShift Chemiluminescent EMSA kit |
Thermo Fisher |
Cat# 20148 |
|
| Deposited Data |
|
|
|
| CUT&RUN and RNA-seq data |
Gene Expression Omnibus |
GSE136332 |
|
| Experimental Models: Organisms/Strains |
|
|
|
| SNU-398 |
ATCC |
Cat# CRL-2233 |
| SNU-387 |
ATCC |
Cat# CRL-2237 |
| HEK293T |
ATCC |
Cat# CRL-1573 |
| HeLa |
ATCC |
Cat# CCL-2 |
|
| Oligonucleotides |
|
|
|
| PBM EMSA WT oligo 1: GTGAAAAAAAATATTAACGTACAGCGGGGAGGCGGC |
This paper |
N/A |
| PBM EMSA Mutant oligo 1: AAAAGCGCAGGCATTAAAGGTATACGTGTGAAAAGA |
This paper |
N/A |
| PBM EMSA WT oligo 2: TTAAGCAGAAATATTACGGTCTCCGGATTTGGCGCT |
This paper |
N/A |
| PBM EMSA Mutant oligo 2: ATTTACAACAGGCCAGAAGTTCTTTGGCTTATCCAT |
This paper |
N/A |
| ITC WT oligo 1: GAGTTATTAATG |
This paper |
N/A |
| ITC Mutant oligo 1: GAGTCGCTAATG |
This paper |
N/A |
| ITC WT oligo 2: GATAAATATTTG |
This paper |
N/A |
| ITC Mutant oligo 2: GATAAACGCTTG |
This paper |
N/A |
|
KDM3A EMSA WT oligo: TCTTCATTTATCCTTCAAAA |
This paper |
N/A |
|
KDM3A EMSA Mutant oligo: TCTTCTTTTAACCTTCAAAA |
This paper |
N/A |
| RT-qPCR, ChIP-qPCR primers, shRNA/CRISPR target regions |
This paper |
Table S5 |
|
| Software and Algorithms |
|
|
|
| GenePix Pro v7.2 |
Molecular Devices |
https://mdc.custhelp.com/app/answers/detail/a_id/18792/~/genepix%E2%AE-pro-7-microarray-acquisition-%26-analysis-software-download-page |
| Masliner |
Dudley et al., 2002
Berger et al., 2006
|
http://arep.med.harvard.edu/masliner/supplement.htm |
| Universal PBM Analysis Suite |
Berger and Bulyk, 2009 |
http://thebrain.bwh.harvard.edu/PBMAnalysisSuite/indexSep2017.html |
| Enologos |
Dobin et al., 2013 |
http://www.benoslab.pitt.edu/cgi-bin/enologos/enologos.cgi |
| Trimmomatic |
Bolger et al., 2014 |
http://www.usadellab.org/cms/?page=trimmomatic |
| BWA |
Li et al., 2009 |
http://bio-bwa.sourceforge.net/ |
| Samtools |
Li et al., 2009 |
http://samtools.sourceforge.net/ |
| Stampy |
Lunter and Goodson, 2011 |
https://www.rdm.ox.ac.uk/research/lunter-group/lunter-group/stampy |
| deepTools |
Ramírez et al., 2014 |
https://deeptools.readthedocs.io/en/develop/ |
| Bedtools |
Quinlan and Hall, 2010; Kent et al., 2010
|
https://bedtools.readthedocs.io/en/latest/ |
| SEACR |
Meers et al., 2019 |
https://github.com/FredHutch/SEACR |
| ChIPSeeker |
Yu et al., 2015 |
https://guangchuangyu.github.io/software/ChIPseeker/ |
| HOMER |
Heinz et al., 2010 |
http://homer.ucsd.edu/homer/ |
| BBMap |
|
https://sourceforge.net/projects/bbmap/ |
| BamCoverage |
Ramírez et al., 2014 |
https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html |
| STAR |
Dobin et al., 2013 |
https://github.com/alexdobin/STAR |
| RseQC |
Wang et al., 2012 |
http://rseqc.sourceforge.net/ |
| htseq-count |
Anders et al., 2015 |
https://htseq.readthedocs.io/en/release_0.11.1/ |
| EnhancedVolcano |
|
https://github.com/kevinblighe/EnhancedVolcano |
| ImageJ |
|
https://imagej.nih.gov/ij/ |
| MEME-ChIP |
Bailey et al., 2009 |
http://meme-suite.org/tools/meme-chip |
