Skip to main content
. 2023 Jan 5;26(2):105939. doi: 10.1016/j.isci.2023.105939
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
HRP-Conjugated GAPDH Monoclonal Antibody Proteintech Cat#HRP-60004; RRID: AB_2737588
Rabbit Peregrin antibody [N1N2], N-term GeneTex Cat#GTX102778; RRID: AB_1949759
mouse anti-OCT-3/4 Santa Cruz Biotechnology Cat#sc-5279; RRID: AB_628051
Rabbit anti-HIST3H3 (H3) Abcam Cat#ab1791; RRID: AB_302613
Rabbit anti-Histone H3 (acetyl K23) Abcam Cat#ab177275; RRID: AB_2927706
Rabbit anti-Histone H3 (tri methyl K4) Abcam Cat#ab8580; RRID: AB_306649
Rabbit anti-NANOG Cell Signaling Technology Cat#3580; RRID: AB_2150399
mouse Monoclonal ANTI-FLAG Sigma Cat#F1804; RRID: AB_262044
mouse anti-SSEA4 Santa Cruz Biotechnology Cat#sc-21704; RRID: AB_628289
mouse anti-Glial Fibrillary Acidic Protein Millipore Cat#MAB360; RRID: AB_11212597
Rabbit anti-CALPONIN Abcam Cat#AB46794; RRID: AB_2291941
Rabbit anti-HNF3β/FOXA2 Millipore Cat#07–633; RRID: AB_390153
Rabbit anti-Histone H3 (trimethyl K4) Abcam Cat#ab8580; RRID: AB_306649
Goat anti-Mouse IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat#A-11004; RRID: AB_2534072
Goat anti-Rabbit IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat#A-11011; RRID: AB_143157
Goat anti-Mouse IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat#A-11001; RRID: AB_2534069
Chemicals, peptides, and recombinant proteins
Matrigel Corning Cat#354277
DMEM/F12 basic Gibco Cat#C11330500BT
mTeSR1 STEMCELL Technology Cat#85850
Accutase Sigma Cat#A6964
PBS GENOM Cat#GNM20012-2
EDTA Genstar Cat#VA17876-500g
Penicillin-Streptomycin (100×) Hyclone Cat#SV30010
Y27632 Selleck Cat#S6390
DMSO Sigma Cat#D1435
Thiazovivin Selleck Cat#S1459
DAPI Sigma Cat#D9542
NcTarget Nuwacell Cat#RP01020
Puromycin Gibco Cat#A1113803
TRI Reagent Molecular Research Center Cat#TR118
Critical commercial assays
FastPure Gel DNA Extraction Mini Kit Vazyme Cat#DC301
pEASY-Uni Seamless Cloning and Assembly Kit TransGen Biotech Cat#CU101
E.Z.N.A. Endo-Free Plasmid DNA Midi Kit OMEGA Cat#D6915
DNA Ligation Kit Ver.2.1 TaKaRa Cat#6022
Equalbit dsDNA HS Assay Kit Vazyme Cat#EQ111
AMAXA Basic Nucleofector Kit for Prim. Mammalian Epithelial cells Lonza Cat#VPI-1005
mRNA-seq V3 Library Prep Kit for Illumina Vazyme Cat#NR611
RNA Adapters set3 - set6 for Illumina Vazyme Cat#N809
EdU Flow Cytometry Assay Kits Invitrogen Cat#C10425
Universal DNA Library Prep Kit for Illumina Vazyme Cat#ND607
TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Cat#TD501
Deposited data
RNA-Seq, ATAC-seq, and ChIP-seq data This paper GEO: GSE213695
RNA-Seq, ATAC-seq, and ChIP-seq data This paper HRA001928
Experimental models: Cell lines
Human embryonic stem cell line H1 (WA01) WiCell RRID: CVCL_9771
Oligonucleotides
KO-BRPF1-sgRNA:
ATGGTGGAGGTGGACTTGCA		 This paper N/A
KO-BRPF1-LA forward primer:
GAGCATGCCTAGATTGTCGCG		 This paper N/A
KO-BRPF1-LA reverse primer:
CTTTTTCTTGTGCTTGCGGAGTG		 This paper N/A
KO-BRPF1-RA forward primer:
GGAGAACACTGAGACACCAGCTGC		 This paper N/A
KO-BRPF1-RA reverse primer:
CATCAGAATGCCTTTTTTGCCTTG		 This paper N/A
KO-BRPF1 forward primer:
CCACAACTTGCGGGCGACTA		 This paper N/A
KO-BRPF1 reverse primer:
GGTGGGGCATCAGGGGTGT		 This paper N/A
KI-BRPF1-sgRNA:
TGCGGTGCTGCAGAGCCCTG		 This paper N/A
KI-BRPF1-LA forward primer:
CTGGATGCTCTGGACCTCGTGT		 This paper N/A
KI-BRPF1-LA reverse primer:
ATCACTATCGCTGGTCTCACTGCTC		 This paper N/A
KI-BRPF1-RA forward primer:
TACTGCTCAACACAGCCCAACCTATA		 This paper N/A
KI-BRPF1-RA reverse primer:
GCAGCGGATTGACCCTTGTGT		 This paper N/A
KI-BRPF1 forward primer:
CTTGTTCTCCCTGAGATGATTTATTTGAT		 This paper N/A
KI-BRPF1 reverse primer:
TTACAGTATTTACAACAGCAGGGGAGG		 This paper N/A
OE-BRPF1-WT forward primer:
ATGGGGGTGGACTTTGATGTGAAGA		 This paper N/A
OE-BRPF1-WT reverse primer:
TCAATCACTATCGCTGGTCTCACTG		 This paper N/A
OE-BRPF1-N- forward primer:
ATCTGGCTGGATATCATGAATGAGC		 This paper N/A
OE-BRPF1-N- reverse primer:
TCAATCACTATCGCTGGTCTCACTG		 This paper N/A
OE-BRPF1-PWWP- forward primer:
ATGGGGGTGGACTTTGATGTGAAGA		 This paper N/A
OE-BRPF1-PWWP- reverse primer:
TCGCTGATGGGCAAGCTTCC		 This paper N/A
OE-BRPF1-PZP- −1 forward primer:
ATGGGGGTGGACTTTGATGTGAAGA		 This paper N/A
OE-BRPF1-PZP- −1 reverse primer:
GTAGTCCTCCTCGTCCATGTCATACTCT		 This paper N/A
OE-BRPF1-PZP- −2 forward primer:
AGAGTATGACATGGACGAGGAGGACT
ACTGGACACTGAAGCGGCAGTC		 This paper N/A
OE-BRPF1-PZP- −2 reverse primer:
TCAATCACTATCGCTGGTCTCACTG		 This paper N/A
FUW-BRPF1 forward primer:
ATGGGGGTGGACTTTGATGTGAA		 This paper N/A
FUW-BRPF1 reverse primer:
ATCACTATCGCTGGTCTCACTGCTCT		 This paper N/A
GAPDH forward primer:
GGAGCGAGATCCCTCCAAAAT		 This paper N/A
GAPDH reverse primer:
GGCTGTTGTCATACTTCTCATGG		 This paper N/A
OCT4 forward primer:
CCTCACTTCACTGCACTGTA		 This paper N/A
OCT4 reverse primer:
CAGGTTTTCTTTCCCTAGCT		 This paper N/A
SOX2 forward primer:
CCCAGCAGACTTCACATGT		 This paper N/A
SOX2 reverse primer:
CCTCCCATTTCCCTCGTTTT		 This paper N/A
NANOG forward primer:
TGAACCTCAGCTACAAACAG		 This paper N/A
NANOG reverse primer:
TGGTGGTAGGAAGAGTAAAG		 This paper N/A
PAX6 forward primer:
ATGTGTGAGTAAAATTCTGGGCA		 This paper N/A
PAX6 reverse primer:
GCTTACAACTTCTGGAGTCGCTA		 This paper N/A
SOX1 forward primer:
AATTTTATTTTCGGCGTTGC		 This paper N/A
SOX1 reverse primer:
TGGGCTCTGTCTCTTAAATTTGT		 This paper N/A
T forward primer:
TATGAGCCTCGAATCCACATAGT		 This paper N/A
T reverse primer:
CCTCGTTCTGATAAGCAGTCAC		 This paper N/A
RUNX1 forward primer:
CTGCCCATCGCTTTCAAGGT		 This paper N/A
RUNX1 reverse primer:
GCCGAGTAGTTTTCATCATTGCC		 This paper N/A
FOXA2 forward primer:
ACTACCCCGGCTACGGTTC		 This paper N/A
FOXA2 reverse primer:
AGGCCCGTTTTGTTCGTGA		 This paper N/A
GATA6 forward primer:
CTCAGTTCCTACGCTTCGCAT		 This paper N/A
GATA6 reverse primer:
GTCGAGGTCAGTGAACAGCA		 This paper N/A
SOX17 forward primer:
CGCACGGAATTTGAACAGTA		 This paper N/A
SOX17 reverse primer:
GGATCAGGGACCTGTCACAC		 This paper N/A
BRPF1 forward primer:
CCCCTGAGAATGGCAGCAACA		 This paper N/A
BRPF1 reverse primer:
TGATATCCAGCCAGATGTAGTCCTCCT		 This paper N/A
BRPF1 (WT) forward primer:
GACACAGGCAACATCTTCAGCGA		 This paper N/A
BRPF1 (WT) reverse primer:
GCGGTAAGCCTCCAAGTTCTGC		 This paper N/A
B_N− forward primer:
GCTACTCCCAAGTCAGGCAAACATA		 This paper N/A
B_N− reverse primer:
ATGTCATACTCTACTTCCTCGTCCAGC		 This paper N/A
B_PWWP− forward primer:
GTGGAAACCAACCAGTGAAGAAGAGT		 This paper N/A
B_PWWP− reverse primer:
GGTATCCTCACTGCTGTCCTCTGG		 This paper N/A
B_PZP− forward primer:
ACGCCTCCAGGTTCAGCACG		 This paper N/A
B_PZP− reverse primer:
GGTCAGGCGGTTGGTGATTTTACT		 This paper N/A
Software and algorithms
Integrative Genomics Viewer (IGV) Robinson et al., 201160 http://software.broadinstitute.org/software/igv/
R version 4.1.0 R Core Team, 202271 https://www.r-project.org/
Samtools Li et al., 200972 https://samtools.sourceforge.net/
DeepTools Ramirez et al., 201473 https://deeptools.readthedocs.io/en/develop/
Other
Culture plates (6 well) Greiner Bio-one Cat#657160
Culture plates (12 well) Greiner Bio-one Cat#665180
Culture plates (24 well) Greiner Bio-one Cat#662160
Counting chambers Marienfeld Cat#0650030