REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
SALL4	Abcam	ab29112; RRID: AB_777810
SALL4	Santa Cruz Biotechnology	sc-101147; RRID: AB_1129262
CHD4	Abcam	ab70469; RRID: AB_2229454
MTA1	Santa Cruz Biotechnology	sc-9446; RRID:AB_649545
MTA1	Santa Cruz Biotechnology	sc-373765; RRID: AB_10917039
SALL1	Abcam	ab41974; RRID: AB_777807
GATAD2A	Abcam	ab87663; RRID: AB_1952305
MBD3	Bethyl	A302-528A; RRID: AB_1998980
HDAC1	Santa Cruz Biotechnology	sc-6298; RRID: AB_2279712
HDAC1	Santa Cruz Biotechnology	sc-81598; RRID: AB_2118083
OCT4	Abcam	ab19857; RRID: AB_445175
TUJ1	BioLegend	801201; RRID: AB_2313773
Chemicals, peptides, and recombinant proteins
Recombinant ZFC4 (SALL4 residues 859-1028)	This paper	N/A
Recombinant ZFC1 (SALL4 residues 320-486)	This paper	N/A
Recombinant ZFC2 (SALL4 residues 551-662)	This paper	N/A
Critical commercial assays
KAPA RNA Hyperprep Kit with RiboErase (RNA-seq library preparation)	Roche	08098131702
KAPA Hyperprep Kit (ChIP-seq library preparation)	Roche	07962347001
Deposited data
Raw and processed data used to generate the Figures	This paper	Mendeley Data: https://doi.org/10.17632/rwzttj9pn2.1
RNA-seq of WT, S4KO, ZFC4mut and ZFC4Δ ESCs	This paper	Array Express: E-MTAB-7343
RNA-seq of WT, S4KO, ZFC4mut and ZFC1-2Δ ESCs	This paper	Array Express: E-MTAB-7655
ChIP-seq of anti-SALL4 in WT, S4KO, ZFC4mut and ZFC1-2Δ ESCs	This paper	Array Express: E-MTAB-9197
Time-course (day 0, 2 and 5) RNA-seq of WT, S4KO, ZFC4mut and ZFC1-2Δ ESCs	This paper	Array Express: E-MTAB-9198
RNA-seq of S4KO cells integrated with Sall4 cDNA or EGFP cDNA with a doxycycline inducible promoter	This paper	Array Express: E-MTAB-9202
HT-SELEX of recombinant C2H2 zinc finger domains of SALL4	This paper	Array Express: E-MTAB-9236
ATAC-seq in WT ESCs	This paper	Array Express: E-MTAB-9245
ChIP-seq of H3K4me1 and H3K27ac in WT ESCs	Chronis et al., 2017	Gene Expression Omnibus: GSE90893
Experimental models: cell lines
Mouse: Wild-type embryonic stem cell line; E14Ju09	Hooper et al., 1987	N/A
Mouse: Sall4 knockout embryonic stem cell line	Provided by Brian Hendrich laboratory (Miller et al., 2016)	N/A
Mouse: Sall4 ZFC4mut embryonic stem cell line	This paper	N/A
Mouse: Sall4 ZFC4Δ embryonic stem cell line	This paper	N/A
Mouse: Sall4 ZFC1-2Δ embryonic stem cell line	This paper	N/A
Mouse: Sall4 knockout embryonic stem cell line with doxycycline-inducible Sall4 construct	This paper	N/A
Mouse: Sall4 knockout embryonic stem cell line with doxycycline-inducible EGFP construct	This paper	N/A
Experimental models: organisms/strains
Mouse: Sall4 ZFC4mut	This paper	N/A
Oligonucleotides
DNA pulldown oligonucleotides	This paper; see Table S1	N/A
CRISPR/Cas9 oligonucleotides and genotyping primers	This paper; see Table S1	N/A
RT-qPCR primers	This paper; see Table S1	N/A
HT-SELEX oligonucleotides	This paper; see Table S1	N/A
Recombinant DNA
Cas9/gRNA expression plasmid	Ran et al., 2013	Addgene PX330
PiggyBac vector with doxycycline-inducible construct and Hygromycin resistance cassette	This paper	N/A
PiggyBac vector with constitutively expressed Tet-On 3G and Zeocin resistance cassette	This paper	N/A
Hyperactive PiggyBac transposase expression plasmid	Yusa et al., 2011	N/A
Software and Algorithms
Logolas	Dey et al., 2018	N/A
sailfish v0.9.2	Patro et al., 2014	N/A
DESeq2 v1.28.0	Love et al., 2014	N/A
bedtools nuc	Quinlan and Hall, 2010	N/A
deepTools	Ramírez et al., 2014	N/A
clusterProfiler	Yu et al., 2012	N/A
Trimmomatic v0.33	Bolger et al., 2014	N/A
bwa-mem v0.7.17	Li, 2013)	N/A
Picard toolkit	http://broadinstitute.github.io/picard/	N/A
computeGCBias	Benjamini and Speed, 2012	N/A
MACS v2.1.2	Zhang et al., 2008	N/A
MEME-ChIP v5.1.0	Machanick and Bailey, 2011	N/A
Bioinformatics analysis – command line arguments	This paper (Methods S1)	N/A