REAGENT or RESOURCE	SOURCE	IDENTIFIER
Genetically Modified Organisms
Bcl6tm2Rdf/Bcl6tm2Rdf mouse	Ye et al., 1997	MGI Cat# 3582783, RRID: MGI:3582783
Antibodies
Chicken anti-GFP	Abcam	Cat# ab13970, RRID: AB_300798
Rabbit anti-Pax6	Covance	Cat# PRB-278P, RRID: AB_291612
Mouse anti-β3-tubulin (Tuj1)	Covance	Cat# MMS-435P, RRID: AB_2313773
Goat Sox2	Santa Cruz Biotechnology	Cat# sc-17320, RRID: AB_2286684
Mouse PCNA	Millipore	Cat# MAB424, RRID: AB_95106
Rat Phospho-Histone H3	Abcam	Cat# ab10543, RRID: AB_2295065
Rabbit Tbr2	Abcam	Cat# ab183991, RRID: AB_2721040
Rabbit Neurod2	Abcam	Cat# ab104430, RRID: AB_10975628
Alexa Fluor 488 anti-chicken	Thermo Fisher Scientific	Cat# A-11039 RRID: AB_2534096
Cyanine3 donkey anti-mouse	Jackson ImmunoResearch	Cat# 715-165-150, RRID: AB_2340813
Cyanine3 donkey anti-rabbit	Jackson ImmunoResearch	Cat# 711-165-152, RRID: AB_2307443
Rabbit IgG isotype control	Abcam	Cat# ab171870, RRID: AB_2687657
Rabbit anti-Bcl6	Santa Cruz Biotechnology	Cat# sc-858, RRID: AB_2063450
Rabbit anti-H1.4K26ac	Sigma-Aldrich	Cat# H7789, RRID: AB_1079058
Rabbit anti-H4K16ac	Millipore	Cat# 07-329, RRID: AB_310525
Rabbit anti-Sirt1	Millipore	Cat# 07-131, RRID: AB_10067921
Rabbit anti-Tcf7l1	Prof. Brad Merrill	N/A
Chemicals, Peptides, and Recombinant Proteins
CHIR 99021	Tocris	Cat# 4423
Cyclopamine	Calbiochem	Cat# 239803
Doxycycline hydrochloride	Sigma-Aldrich	Cat# D3447
ESGRO Recombinant LIF	Merck	Cat# ESG1107
N-2 Supplement	Thermo Fisher Scientific	Cat# 17502048
Critical Commercial Assays
HiSeq PE Cluster Kit v4	Illumina	Cat# PE-401-4001
RNeasy mini kit	QIAGEN	Cat# 74104
TruSeq SBS Kit v3-HS	Illumina	Cat# FC-401-3002
TruSeq stranded mRNA library prep	Illumina	Cat# RS-122-2101
DIG RNA labeling kit	Roche	Cat# 11175025910
qPCR Primers
Oligonucleotides	Eurogentec	See Table S4
Experimental Models: Cell Lines
A2 lox.Cre Bcl6 ES cells	Tiberi et al., 2012a	N/A
Experimental Models: Organisms/Strains
Mouse: ICR (CD1)	Janvier labs	Strain code 022
Deposited Data
ChIP-seq	This paper	GEO: GSE132964
RNA-seq	This paper	GEO: GSE133031
Software and Algorithms
Bowtie	Langmead et al., 2009	https://github.com/BenLangmead/bowtie
EdgeR 3.20.1	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
Fiji/ImageJ 1.49b	Schindelin et al., 2012	https://fiji.sc/
Genomic HyperBrowser	Sandve et al., 2010	https://hyperbrowser.uio.no/hb/
GOrilla		http://cbl-gorilla.cs.technion.ac.il
GREAT 3.0	McLean et al., 2010	http://great.stanford.edu/public/html/
HTSeq 0.9.1	Anders et al., 2015	https://github.com/simon-anders/htseq
i-cisTarget	Imrichová et al., 2015	https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/
MACS	Zhang et al., 2008	https://github.com/taoliu/MACS/
STAR 2.5.3a	Dobin et al., 2013	https://github.com/alexdobin/STAR
UCSC Genome Browser	Kent et al., 2002	https://genome.ucsc.edu
ZEN Black microscope software	Zeiss	N/A
Other
Axioplan2 fluorescent microscope	Zeiss	N/A
LSM780 confocal microscope	Zeiss	N/A