REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse polyclonal anti-Pou5f3 protein antibody	This paper	N/A
Rabbit polyclonal anti-Pou5f3 protein antibody	This paper	N/A
Mouse polyclonal anti-PABPC1L protein antibody	This paper	N/A
Mouse monoclonal anti-Oct3/4 protein antibody (clone 10)	Santa Cruz Biotechnology	Cat#sc-5279; RRID: AB_628051
Rabbit polyclonal anti-RPL11 protein antibody	Abcam	Cat#ab79352; RRID: AB_2042832
Mouse monoclonal anti-Puromycin antibody (3RH11)	Kerafast	Cat#EQ0001; RRID: AB_2620162
Anti-DIG-alkaline phosphatase antibody	Roche	Cat#11093274910
Anti-DIG-horseradish peroxidase antibody	Roche	Cat#11207733910
Anti-DNP-Alexa 488 antibody	Molecular probes	Cat#A11097; RRID: AB_2314332
Anti-Fluorescein-horseradish peroxidase antibody	Roche	Cat#11426346910
Goat Anti-mouse IgG Alexa 488 antibody	Molecular probes	Cat#A11017 RRID: AB_143160
Goat Anti-mouse IgG Alexa 546 antibody	Molecular probes	Cat#A11003; RRID: AB_141370
Goat Anti-rabbit IgG Alexa 546 antibody	Molecular probes	Cat#A11010; RRID: AB_2534077
Chemicals, peptides, and recombinant proteins
Trizol reagent	Invitrogen	Cat#15596-018
Tyramide-dinitrophenyl	PerkinElmer	Cat#NEL746A
Tyramide-Fluorescein	PerkinElmer	Cat#NEL741
Tyramide-Cy3	PerkinElmer	Cat#NEL744
Hoechst 33258, Pentahydrate [bis-Benzimide]	Setareh Biotech	Cat#7075
Proteinase K	Sigma	Cat#P2308
Blocking reagent	Roche	Cat#10447200
VECTASHIELD Mounting Medium containing DAPI	Vector Laboratories, Inc	Cat#H1200
T4 RNA ligase	New England Biolabs	Cat#M0204S
Puromycin	Invitrogen	Cat#ant-pr-1
1,6-Hexanediol	Sigma	Cat#240117
1,2,6-Hexanetriol	Sigma	Cat#T66206
RNasin Plus Rnase Inhibitor	Promega	Cat#N2611
Newborn calf serum	Sigma	Cat#N4762
Critical commercial assays
Tyramide signal amplification (TSA) Plus DNP system	PerkinElmer	Cat#NEL747A
Duolink In situ PLA Probe Anti-Mouse PLUS	Sigma	Cat#DUO92001
Duolink In situ PLA Probe Anti-Rabbit MINUS	Sigma	Cat#DUO92005
Duolink In situ PLA Detection Reagents FarRed	Sigma	Cat#DUO92013
Oligonucleotides
See Table S1	See Table S1	See Table S1
Software and algorithms
Image J	NIH	imagej.net
AIVIA	Leica	aivia-software.com